From d0dc65f0ff374151f315e3ed971137d994626d3d Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Nicolas=20FERNANDEZ=20NU=C3=91EZ?=
<nicolas.fernandez@ird.fr>
Date: Thu, 3 Apr 2025 17:13:15 +0200
Subject: [PATCH] v.2025.04_beta
---
Run_GeVarLi.sh | 46 +-
config/config.yaml | 286 ++++++++-----
resources/primers/bedpe/.gitkeep | 1 -
resources/primers/fasta/.gitkeep | 1 -
resources/primers_schemes/bed/LICENSE | 395 ++++++++++++++++++
.../bed/MPXV/V1/MPXV.primer.bed | 326 +++++++++++++++
.../bed/Nipah/V1/NiV_6_Malaysia.primer.bed | 120 ++++++
resources/primers_schemes/bed/README.md | 74 ++++
.../bed/ZaireEbola/V1/ZaireEbola.primer.bed | 46 ++
.../bed/ZaireEbola/V2/ZaireEbola.primer.bed | 94 +++++
.../bed/ZaireEbola/V3/ZaireEbola.primer.bed | 124 ++++++
.../bed/nCoV-2019/V1/nCoV-2019.primer.bed | 196 +++++++++
.../bed/nCoV-2019/V2/nCoV-2019.primer.bed | 196 +++++++++
.../bed/nCoV-2019/V3/nCoV-2019.primer.bed | 218 ++++++++++
.../bed/nCoV-2019/V4.1/SARS-CoV-2.primer.bed | 209 +++++++++
.../bed/nCoV-2019/V4/SARS-CoV-2.primer.bed | 198 +++++++++
.../nCoV-2019/V5.3.2/SARS-CoV-2.primer.bed | 192 +++++++++
.../bed => primers_schemes/bedpe}/.gitkeep | 0
...s_Zaire_AF-272001-1_artic-primers-V2.bedpe | 0
...s_Zaire_KR-063671-1_artic-primers-V1.bedpe | 0
...s_Zaire_KR-063671-1_artic-primers-V3.bedpe | 0
...alaysia_AJ-564622-1_artic-primers-V1.bedpe | 0
...2_Wuhan_MN-908947-3_artic-primers-V1.bedpe | 0
...2_Wuhan_MN-908947-3_artic-primers-V2.bedpe | 0
...2_Wuhan_MN-908947-3_artic-primers-V3.bedpe | 0
...Wuhan_MN-908947-3_artic-primers-V4-1.bedpe | 0
...2_Wuhan_MN-908947-3_artic-primers-V4.bedpe | 0
workflow/Snakefile | 139 +++---
workflow/envs/workflow-core.yaml | 5 +-
workflow/envs/yq_v.3.4.3.yaml | 7 -
workflow/rules/consensus_calling.smk | 73 ++--
workflow/rules/coverage_stats.smk | 9 +-
workflow/rules/duplicates_removing.smk | 10 +-
workflow/rules/genomes_indexing.smk | 8 +-
workflow/rules/gisaid_submission.smk | 7 +-
workflow/rules/lineages_calling.smk | 7 +-
workflow/rules/lowcov_masking.smk | 7 +-
workflow/rules/primers_clipping.smk | 71 ++--
workflow/rules/quality_controls.smk | 2 +-
workflow/rules/reads_cleanning.smk | 38 +-
workflow/rules/reads_mapping.smk | 12 +-
workflow/rules/results_merging.smk | 45 +-
...ymlinks_renamming.smk => samples_prep.smk} | 39 +-
workflow/rules/variants_calling.smk | 25 +-
workflow/rules/workflow_reporting.smk | 148 ++-----
workflow/schemas/config.schema.yaml | 342 +++++++--------
.../__pycache__/__init__.cpython-312.pyc | Bin 154 -> 0 bytes
.../__pycache__/functions.cpython-312.pyc | Bin 6456 -> 0 bytes
workflow/scripts/functions.py | 362 ++++++++++++++--
workflow/scripts/settings.py | 214 ----------
workflow/scripts/settings.sh | 196 ---------
51 files changed, 3354 insertions(+), 1134 deletions(-)
delete mode 100644 resources/primers/bedpe/.gitkeep
delete mode 100644 resources/primers/fasta/.gitkeep
create mode 100644 resources/primers_schemes/bed/LICENSE
create mode 100644 resources/primers_schemes/bed/MPXV/V1/MPXV.primer.bed
create mode 100644 resources/primers_schemes/bed/Nipah/V1/NiV_6_Malaysia.primer.bed
create mode 100644 resources/primers_schemes/bed/README.md
create mode 100644 resources/primers_schemes/bed/ZaireEbola/V1/ZaireEbola.primer.bed
create mode 100644 resources/primers_schemes/bed/ZaireEbola/V2/ZaireEbola.primer.bed
create mode 100644 resources/primers_schemes/bed/ZaireEbola/V3/ZaireEbola.primer.bed
create mode 100644 resources/primers_schemes/bed/nCoV-2019/V1/nCoV-2019.primer.bed
create mode 100644 resources/primers_schemes/bed/nCoV-2019/V2/nCoV-2019.primer.bed
create mode 100644 resources/primers_schemes/bed/nCoV-2019/V3/nCoV-2019.primer.bed
create mode 100644 resources/primers_schemes/bed/nCoV-2019/V4.1/SARS-CoV-2.primer.bed
create mode 100644 resources/primers_schemes/bed/nCoV-2019/V4/SARS-CoV-2.primer.bed
create mode 100644 resources/primers_schemes/bed/nCoV-2019/V5.3.2/SARS-CoV-2.primer.bed
rename resources/{primers/bed => primers_schemes/bedpe}/.gitkeep (100%)
rename resources/{primers => primers_schemes}/bedpe/Ebola-virus_Zaire_AF-272001-1_artic-primers-V2.bedpe (100%)
rename resources/{primers => primers_schemes}/bedpe/Ebola-virus_Zaire_KR-063671-1_artic-primers-V1.bedpe (100%)
rename resources/{primers => primers_schemes}/bedpe/Ebola-virus_Zaire_KR-063671-1_artic-primers-V3.bedpe (100%)
rename resources/{primers => primers_schemes}/bedpe/Nipah-virus_Malaysia_AJ-564622-1_artic-primers-V1.bedpe (100%)
rename resources/{primers => primers_schemes}/bedpe/SARS-CoV-2_Wuhan_MN-908947-3_artic-primers-V1.bedpe (100%)
rename resources/{primers => primers_schemes}/bedpe/SARS-CoV-2_Wuhan_MN-908947-3_artic-primers-V2.bedpe (100%)
rename resources/{primers => primers_schemes}/bedpe/SARS-CoV-2_Wuhan_MN-908947-3_artic-primers-V3.bedpe (100%)
rename resources/{primers => primers_schemes}/bedpe/SARS-CoV-2_Wuhan_MN-908947-3_artic-primers-V4-1.bedpe (100%)
rename resources/{primers => primers_schemes}/bedpe/SARS-CoV-2_Wuhan_MN-908947-3_artic-primers-V4.bedpe (100%)
delete mode 100644 workflow/envs/yq_v.3.4.3.yaml
rename workflow/rules/{symlinks_renamming.smk => samples_prep.smk} (68%)
delete mode 100644 workflow/scripts/__pycache__/__init__.cpython-312.pyc
delete mode 100644 workflow/scripts/__pycache__/functions.cpython-312.pyc
delete mode 100644 workflow/scripts/settings.py
delete mode 100644 workflow/scripts/settings.sh
diff --git a/Run_GeVarLi.sh b/Run_GeVarLi.sh
index b0fc8bf..5bcf2c4 100755
--- a/Run_GeVarLi.sh
+++ b/Run_GeVarLi.sh
@@ -10,12 +10,12 @@
### ###
###I###R###D######U###2###3###3#######T###R###A###N###S###V###I###H###M###I####
# Name ___________________ Run_GeVarLi.sh
-# Version ________________ v.2025.03
+# Version ________________ v.2025.04
# Author _________________ Nicolas Fernandez
# Affiliation ____________ IRD_U233_TransVIHMI
# Aim ____________________ Bash script running GeVarLi snakefile
# Date ___________________ 2021.10.12
-# Latest modifications ___ 2025.03.12
+# Latest modifications ___ 2025.04.04
# Use ____________________ '. Run_GeVarLi.sh'
###############################################################################
@@ -106,28 +106,28 @@ then # If 'exist'
ENV_YAML="${workdir}/workflow/envs/workflow-core.yaml"
CURRENT_ENV=$(conda env export --no-builds --name workflow-core | grep -v '^prefix:')
EXPECTED_ENV=$(grep -v '^prefix:' "$ENV_YAML")
- if false #diff <(echo "$CURRENT_ENV") <(echo "$EXPECTED_ENV") > /dev/null
- then # If 'up-to-date'
- echo -e "\n ${ylo}Workflow-Core${nc} environment is already up-to-date."
- else # If 'not' up-to-date
- if [[ $network == "Offline" ]]
- then # If 'offline'
- echo -e "\n Cannot update ${ylo}Workflow-Core${nc} environment.
- ${green}Network${nc}: ${red}${network}${nc}."
- else # If 'online'
- echo -e "\n Updating ${ylo}Workflow-Core${nc} environment. \n"
- run_with_spinner \
- conda env update \
- --prune \
- --name workflow-core \
- --file $ENV_YAML
- fi
- fi
+ #if false #diff <(echo "$CURRENT_ENV") <(echo "$EXPECTED_ENV") > /dev/null
+ #hen # If 'up-to-date'
+ # echo -e "\n ${ylo}Workflow-Core${nc} environment is already up-to-date."
+ #else # If 'not' up-to-date
+ # if [[ $network == "Offline" ]]
+ # then # If 'offline'
+ # echo -e "\n Cannot update ${ylo}Workflow-Core${nc} environment.
+ # ${green}Network${nc}: ${red}${network}${nc}."
+ # else # If 'online'
+ # echo -e "\n Updating ${ylo}Workflow-Core${nc} environment. \n"
+ # run_with_spinner \
+ # conda env update \
+ # --prune \
+ # --name workflow-core \
+ # --file $ENV_YAML
+ # fi
+ #fi
else # If 'not' exist
echo -e "\n ${ylo}Workflow-Core${nc} conda environment not found."
if [[ $network == "Online" ]]
then # If 'online'
- echo -e "\n ${ylo}Workflow-Core${nc} conda environment will be create, with:
+ echo -e "\n ${ylo}Workflow-Core${nc} conda environment will be created, with:
> ${red}Snakemake${nc}
> ${red}Snakedeploy${nc}
> ${red}Snakemake Slurm plugin${nc} \n"
@@ -176,12 +176,14 @@ echo -e "\n ${green} > Snakemake: list conda environments${nc} \n"
snakemake \
--directory ${workdir}/ \
--snakefile ${workdir}/workflow/Snakefile \
+ --rerun-incomplete \
--list-conda-envs
echo -e "\n ${green} > Snakemake: create conda environments${nc} \n"
snakemake \
--directory ${workdir}/ \
--snakefile ${workdir}/workflow/Snakefile \
+ --rerun-incomplete \
--conda-create-envs-only \
--use-conda
@@ -189,6 +191,7 @@ echo -e "\n ${green} > Snakemake: dry run${nc} \n"
snakemake \
--directory ${workdir}/ \
--snakefile ${workdir}/workflow/Snakefile \
+ --rerun-incomplete \
--use-conda \
--dry-run \
--quiet host rules
@@ -197,8 +200,6 @@ echo -e "\n ${green} > Snakemake: run${nc} \n"
snakemake \
--directory ${workdir}/ \
--snakefile ${workdir}/workflow/Snakefile \
- --cores ${max_threads} \
- --resources mem_gb=${max_memory} \
--rerun-incomplete \
--keep-going \
--use-conda \
@@ -213,3 +214,4 @@ echo -e "\n Deactivate ${ylo}Workflow-Core${nc} conda environment."
conda deactivate
###############################################################################
+###############################################################################
diff --git a/config/config.yaml b/config/config.yaml
index 77c3741..22305ad 100755
--- a/config/config.yaml
+++ b/config/config.yaml
@@ -10,13 +10,14 @@
### ###
###I###R###D######U###2###3###3#######T###R###A###N###S###V###I###H###M###I####
# Name ___________________ config.yaml
-# Version ________________ v.2025.01
+# Version ________________ v.2025.04
# Author _________________ Nicolas Fernandez
# Affiliation ____________ IRD_U233_TransVIHMI
# Aim ____________________ Configuration yaml file for gevarli.smk snakefile
# Date ___________________ 2021.10.12
-# Latest modifications ___ 2025.03.12
+# Latest modifications ___ 2025.04.04
# Use ____________________ Edit default settings
+###############################################################################
###############################################################################
################################## GENERAL ####################################
@@ -27,84 +28,76 @@ fastq_dir: 'resources/reads/' # Path to reads fastq.gz files (default: 'resource
modules: # GeVarLi analysis modules, set 'true' or 'false' [BOOL]
qualities: true # Perform reads quality controls (FastQC, Fastq-Screen) (default: true)
keeptrim: false # Keep trimmed reads files (Cutadapt / Sickle-trim) (default: false)
- clipping: false # Perform reads clipping (Bamclipper) (default: false)
+ clipping: true # Perform reads clipping (iVar) (default: false)
covstats: true # Perform coverage statistics (Fagstat, Covstats) (default: true)
consensus: true # Perform reads mapping to reference (BWA, Minimap2, Bowtie2) (default: true)
lineages: true # Perform clade and lineage assignations (Nexclade, Pangolin) (default: true)
gisaid: false # Perform gisaid submission template (GisAid : TODO) (default: false)
-consensus:
- reference: 'SARS-CoV-2_Wuhan_MN908947.3' # Your reference, in fasta format (default: 'SARS-CoV-2_Wuhan_MN-908947-3') [STR]
- # Available options (not exhaustive):
- ##- 'SARS-CoV-2_Wuhan_MN908947.3' # SARS-CoV-2 (with Nextclade and Pangolin)(default)
- ###
- ##- 'Monkeypox-virus_Zaire_AF380138.1' # Monkeypox [MPXV] (with Nextclade and Pangolin)
- ##- 'Monkeypox-virus_UK_MT903345.1' # Monkeypox [MPXV] (with Nextclade and Pangolin)
- ##- 'Swinepox-virus_India_MW036632.1' # Swinepox [SPXV] (with Nextclade)
- ###
- ##- 'Ebola-virus_Zaire_AF272001.1' # Ebola [EBOV]
- ##- 'Ebola-virus_Sudan_MH121162.1' # Ebola [EBOV]
- ##- 'Marburg-virus_NC001608.3' # Marburg [MarV]
- ###
- ##- 'Measles-virus_Ichinose-B95a_NC001498.1' # Measles [MeV]
- ##- 'Measles-virus_B3_Khartoum-Sudan_MG912590.1' # Measles [MeV]
- ##- 'Measles-virus_B3_Kole-Uganda_ON642796.1' # Measles [MeV]
- ##- 'Measles-virus_B3_Bura-Kenya_MZ615446.1_partial' # Measles [MeV]
- ##- 'Measles-virus_C2_Netherland-Bilthoven_MG912589.1' # Measles [MeV]
- ##- 'Measles-virus_H1_Netherland-Amsterdam_MG912594.1' # Measles [MeV]
- ###
- ##- 'Lassa-virus_NC004297.1_Seg-L' # Lassa Josiah L
- ##- 'Lassa-virus_NC004297.1_Seg-S' # Lassa Josiah S
- ##- 'Lassa-virus_Guinea_Faranah_MG812684.1_Seg-L' # Lassa Guinea L
- ##- 'Lassa-virus_Guinea_Faranah_MG812685.1_Seg-S' # Lassa Guinea S
- ##- 'Lassa-virus_Benin_Ben-16131_MT193231.1_Seg-L' # Lassa Benin L
- ##- 'Lassa-virus_Benin_Ben-16131_MT193282.1_Seg-S' # Lassa Benin S
- ###
- ##- 'Chikungunya-virus_HM045817.1' # Chikungunya [CHIKV]
- ##- 'Dengue-virus-1_NC001477.1' # Dengue 1
- ##- 'Dengue-virus-2_NC001474.2' # Dengue 2
- ##- 'Dengue-virus-3_NC001475.2' # Dengue 3
- ##- 'Dengue-virus-4_NC002640.1' # Dengue 4
- ##- 'West-Nile-virus_M12294.2' # West Nile [WNV]
- ##- 'Zika-virus_French-Polynesia_KX369547.1' # Zika [ZV]
- ###
- ##- 'Nipah-virus_Malaysia_AJ564622.1' # Nipah
- ###
- ##- 'Human-herpesvirus-5_NC006273.2' # Herpes [HCMV]
- ##- 'Human-herpesvirus-3_NC001348.1' # Varicella [VZV]
- ##- 'Human-adenovirus-A_NC001460.1' # Adeno
- ##- 'Human-enterovirus-68_AY426531.1' # Entero
- ###
- ##- 'HIV-1_HXB2_K03455.1' # HIV-1 [HIV]
-
- min_cov: '30' # Minimum coverage, mask lower regions with "N" (default: '30') [INT]
- # Available options (not exhaustive):
- ##- '100' # 100 x : for greater coverage
- ##- '30' # 30 X : for AFROSCREEN SARS-CoV-2 consortium, with Illumina amplicons sequencing (default)
- ##- '10' # 10 X : for some applications...
- ##- '3' # 3 X : only for exploration!
- ##- '1' # 1 X : not recommanded
- min_freq: '0.2' # Minimum allele frequency allowed (default: "0.2") [FLOAT] *** LoFreq ***
- iupac: '--iupac-code' # Output variants in the form of IUPAC ambiguity codes (default: "activate")
- # Available options, set only one:
- ##- '--iupac-code' # Activate (default)
- ##- '' # Deactivate
+tools:
mapper: 'bwa' # Select your favorite mapper (default: 'bwa')
# Available options:
##- 'bwa' # Better, faster (default)
##- 'bowtie2' # Slower, "sensitivity" requiried (see below "Bowtie2" options)
##- 'minimap2' # Versatile
- caller: 'ivar'
+ caller: 'ivar' # Select your favorite variant caller (default: 'ivar')
+ # Available options:
+ ##- 'ivar' # iVar: a toolkit for analysis of viral NGS data (default)
assigner: 'nextclade' # Select your favorite clades / lineages assigner (default: 'nextclade')
# Available options:
##- 'nextclade' # Clade assignment, mutation calling, phylogenetic placement and quality checks (default)
##- 'pangolin' # PANGO: Phylogenetic Assignment of Named Global Outbreak Lineages
+reference: 'SARS-CoV-2_Wuhan_MN908947.3' # Your reference, in fasta format (default: 'SARS-CoV-2_Wuhan_MN-908947-3') [STR]
+# Available options (not exhaustive):
+ ##- 'SARS-CoV-2_Wuhan_MN908947.3' # SARS-CoV-2 (with Nextclade and Pangolin)(default)
+ ###
+ ##- 'Monkeypox-virus_Zaire_AF380138.1' # Monkeypox [MPXV] (with Nextclade and Pangolin)
+ ##- 'Monkeypox-virus_UK_MT903345.1' # Monkeypox [MPXV] (with Nextclade and Pangolin)
+ ##- 'Swinepox-virus_India_MW036632.1' # Swinepox [SPXV] (with Nextclade)
+ ###
+ ##- 'Ebola-virus_Zaire_AF272001.1' # Ebola [EBOV]
+ ##- 'Ebola-virus_Sudan_MH121162.1' # Ebola [EBOV]
+ ##- 'Marburg-virus_NC001608.3' # Marburg [MarV]
+ ###
+ ##- 'Measles-virus_Ichinose-B95a_NC001498.1' # Measles [MeV]
+ ##- 'Measles-virus_B3_Khartoum-Sudan_MG912590.1' # Measles [MeV]
+ ##- 'Measles-virus_B3_Kole-Uganda_ON642796.1' # Measles [MeV]
+ ##- 'Measles-virus_B3_Bura-Kenya_MZ615446.1_partial' # Measles [MeV]
+ ##- 'Measles-virus_C2_Netherland-Bilthoven_MG912589.1' # Measles [MeV]
+ ##- 'Measles-virus_H1_Netherland-Amsterdam_MG912594.1' # Measles [MeV]
+ ###
+ ##- 'Lassa-virus_NC004297.1_Seg-L' # Lassa Josiah L
+ ##- 'Lassa-virus_NC004297.1_Seg-S' # Lassa Josiah S
+ ##- 'Lassa-virus_Guinea_Faranah_MG812684.1_Seg-L' # Lassa Guinea L
+ ##- 'Lassa-virus_Guinea_Faranah_MG812685.1_Seg-S' # Lassa Guinea S
+ ##- 'Lassa-virus_Benin_Ben-16131_MT193231.1_Seg-L' # Lassa Benin L
+ ##- 'Lassa-virus_Benin_Ben-16131_MT193282.1_Seg-S' # Lassa Benin S
+ ###
+ ##- 'Chikungunya-virus_HM045817.1' # Chikungunya [CHIKV]
+ ##- 'Dengue-virus-1_NC001477.1' # Dengue 1
+ ##- 'Dengue-virus-2_NC001474.2' # Dengue 2
+ ##- 'Dengue-virus-3_NC001475.2' # Dengue 3
+ ##- 'Dengue-virus-4_NC002640.1' # Dengue 4
+ ##- 'West-Nile-virus_M12294.2' # West Nile [WNV]
+ ##- 'Zika-virus_French-Polynesia_KX369547.1' # Zika [ZV]
+ ###
+ ##- 'Nipah-virus_Malaysia_AJ564622.1' # Nipah
+ ###
+ ##- 'Human-herpesvirus-5_NC006273.2' # Herpes [HCMV]
+ ##- 'Human-herpesvirus-3_NC001348.1' # Varicella [VZV]
+ ##- 'Human-adenovirus-A_NC001460.1' # Adeno
+ ##- 'Human-enterovirus-68_AY426531.1' # Entero
+ ###
+ ##- 'HIV-1_HXB2_K03455.1' # HIV-1 [HIV]
+ ###
+ ##- 'your_custom_reference' # Add your custom reference
+
###############################################################################
-################################### GISAID ####################################
+################################ SUBMISSIONS ##################################
###############################################################################
-gisaid: ## TODO ##
+gisaid: ##TODO##
username: 'username'
threshold: '30'
name: 'hCoV-19'
@@ -119,52 +112,110 @@ gisaid: ## TODO ##
nextclade:
path: 'resources/nextclade/' # Path to nextclade datasets (default: "resources/nextclade/")
dataset: 'sars-cov-2' # Nextclade dataset
+ # Available options (not exhaustive), set only one:
+ ##- 'sars-cov-2' # SARS-CoV-2 (default)
+ ##- 'MPXV' # MPox - all clades
+ ##- 'hMPXV' # human MPox
+ ##- 'hMPXV_B1' # human MPox - only lineage B1*
+
+###############################################################################
+################################# CONSENSUS ###################################
+###############################################################################
+
+consensus:
+ min_depth: '30' # Minimum coverage, mask lower regions with "N" (default: '10', recomanded: '30') [INT]
# Available options (not exhaustive):
- #- 'sars-cov-2' # SARS-CoV-2 (default)
- #- 'MPXV' # MPox - all clades
- #- 'hMPXV' # human MPox
- #- 'hMPXV_B1' # human MPox - only lineage B1*
+ ##- '100' # 100 X : for greater coverage
+ ##- '60' # 30 X : for better coverage
+ ##- '30' # 30 X : for AFROSCREEN SARS-CoV-2 consortium, with Illumina amplicons sequencing (recomanded)
+ ##- '10' # 10 X : for some applications (default)
+ ##- '3' # 3 X : only for exploration...
+ ##- '1' # 1 X : not recommanded!
+
+ max_depth: '0' # Max per-file depth; avoids excessive memory usage (default: '8000', recomanded "0") [INT]
+ # Passing zero for this option sets it to the highest possible value, effectively removing the depth limit.
+
+ min_freq: '0.2' # Minimum allele frequency allowed (default: "0.2") [FLOAT]
+ min_insert: '0' # Minimum insertion frequency threshold (0 to 1) to call consensus [FLOAT] (Default: 0.8)
+
+ map_qual: '--no-BAQ' # Disable BAQ, per-Base Alignment Quality (default: '--no-BAQ')
+ # Available options, set only one:
+ ##- '--no-BAQ' # no, don't merge mapping quality: disable (default, recommanded with Samtools)
+ ##- '' # yes, merge mapping quality: enable (not recommanded with Samtools)
+ min_bq: '0' # -Q: Skip bases with baseQ/BAQ smaller than (default: '13', recomanded: '0') [INT]
+ min_qual: '0' # -q: Minimum quality score threshold to count base (Default: '20', recomanded: '0') [INT]
###############################################################################
################################## VARIANTS ###################################
###############################################################################
-ivar:
- #min_depth: '0' # Minimum read depth to call variants (Default: '0') [INT] *** iVar ***
- #min_freq: '0.03' # Minimum frequency threshold to call variants (Default: '0.03') [FLOAT] *** iVar ***
- #min_insert: '0.8' # Minimum insertion frequency threshold to call variants (Default: '0.8') [FLOAT] *** iVar ***
- max_depth: '1000000' # Max per-file depth; avoids excessive memory usage (default: '8000', recomanded "1000000") [INT]
- min_bq: '0' # -Q: Skip bases with baseQ/BAQ smaller than (default: '13', recomanded: '0') [INT]
- min_qual: '0' # -q: Minimum quality score threshold to count base (Default: '20', recomanded: '0') [INT]
- map_qual: '--no-BAQ' # Disable BAQ, per-Base Alignment Quality (default: '--no-BAQ' (disable))
- # Available options:
- ##- '--no-BAQ' # no, don't merge mapping quality: disable (default)
+variant:
+ min_depth: '30' # Minimum coverage, mask lower regions with "N" (default: '10', recomanded: '30') [INT]
+ # Available options (not exhaustive):
+ ##- '100' # 100x : for greater coverage
+ ##- '60' # 30x : for better coverage
+ ##- '30' # 30x : for AFROSCREEN SARS-CoV-2 consortium, with Illumina amplicons sequencing (recomanded)
+ ##- '10' # 10x : for some applications (default)
+ ##- '3' # 3x : only for exploration...
+ ##- '1' # 1x : not recommanded!
+
+ max_depth: '0' # Max per-file depth; avoids excessive memory usage (default: '8000', recomanded "0") [INT]
+ # Passing zero for this option sets it to the highest possible value, effectively removing the depth limit.
+
+ min_freq: '0.2' # Minimum allele frequency allowed (default: "0.2") [FLOAT]
+ min_insert: '0' # Minimum insertion frequency threshold (0 to 1) to call consensus [FLOAT] (Default: 0.8)
+
+ map_qual: '--no-BAQ' # Disable BAQ, per-Base Alignment Quality (default: '--no-BAQ')
+ # Available options, set only one:
+ ##- '--no-BAQ' # no, don't merge mapping quality: disable (default, recommanded with Samtools)
##- '' # yes, merge mapping quality: enable (not recommanded with Samtools)
+ min_bq: '0' # -Q: Skip bases with baseQ/BAQ smaller than (default: '13', recomanded: '0') [INT]
+ min_qual: '0' # -q: Minimum quality score threshold to count base (Default: '20', recomanded: '0') [INT]
###############################################################################
-############################## PRIMER CLEAPING ###############################
+############################# PRIMERS CLEAPING ###############################
###############################################################################
-bamclipper:
- path: 'resources/primers/bedpe/' # Path to primers bedpe files (default 'resources/primer/bedpe') [PATH]
- primers: '' # Your primer set, in BEDPE format (no default: you need to know which kit / ref you used)
- # Reference sequence names and coordinates of BAM and BED are assumed to be derived from identical reference sequences
- # Available options (not exhaustive), set only one:
- ##- 'SARS-CoV-2_Wuhan_MN-908947-3_artic-primers-V4-1' # SARS-CoV-2 Artic V4.1 (update to the V4, see Artic README)
- ##- 'SARS-CoV-2_Wuhan_MN-908947-3_artic-primers-V4' # SARS-CoV-2 Artic V4 (not based on V3, see Artic README)
- ##- 'SARS-CoV-2_Wuhan_MN-908947-3_artic-primers-V3' # SARS-CoV-2 Artic V3
- ##- 'SARS-CoV-2_Wuhan_MN-908947-3_artic-primers-V2' # SARS-CoV-2 Artic V2
- ##- 'SARS-CoV-2_Wuhan_MN-908947-3_artic-primers-V1' # SARS-CoV-2 Artic V1
- ##- 'Ebola-virus_Zaire_KR-063671-1_artic-primers-V3' # EBOV Artic V3
- ##- 'Ebola-virus_Zaire_AF-272001-1_artic-primers-V2' # EBOV Artic V2 (based on AF272001.1)
- ##- 'Ebola-virus_Zaire_KR-063671-1_artic-primers-V1' # EBOV Artic V1
- ##- 'Nipah-virus_Malaysia_AJ-564622-1_artic-primers-V1' # NIV Artic V1
- ##- 'Monkeypox-virus_UK_MT-903345-1_custom-VGCARE-primers-V1' # MPXV VGCARE V1
- ##- 'Add_your_favorite_amplicon_kit' # Custom
- upstream: '5' # (default: '5') [INT]
- downstream: '5' # (default: '5') [INT]
+primers:
+ offset: '0' # Offset for primer trimming (default: '0') [INT]
+ min_length: '35' # Minimum length of read to retain after trimming (Default: 50% average length of the first 1000 reads) [INT]
+ min_qual: '20' # Minimum quality threshold for sliding window to pass (Default: '20') [INT]
+ slide: '4' # Width of sliding window (Default: '4') [INT]
+ bed:
+ path: 'resources/primers_schemes/bed/' # Path to primers bed files (default 'resources/primer/bed') [PATH]
+ scheme: 'nCoV-2019/V4.1/SARS-CoV-2.primer.bed' # Your primer set, in BED format (no default: you need to know which kit and reference you used!)
+ # Reference sequence names and coordinates of BAM and BED are assumed to be derived from identical reference sequences.
+ # Available options (not exhaustive), set only one:
+ ##- 'nCoV-2019/V5.3.2/SARS-CoV-2.primer.bed' # SARS-CoV-2 Artic V5.3.2 (latest)
+ ##- 'nCoV-2019/V4.1/SARS-CoV-2.primer.bed' # SARS-CoV-2 Artic V4.1 (update to the V4, see Artic README)
+ ##- 'nCoV-2019/V4/SARS-CoV-2.primer.bed' # SARS-CoV-2 Artic V4 (not based on V3, see Artic README)
+ ##- 'nCoV-2019/V3/SARS-CoV-2.primer.bed' # SARS-CoV-2 Artic V3
+ ##- 'nCoV-2019/V2/SARS-CoV-2.primer.bed' # SARS-CoV-2 Artic V2
+ ##- 'nCoV-2019/V1/SARS-CoV-2.primer.bed' # SARS-CoV-2 Artic V1
+ ##- 'ZaireEbola/V3/ZaireEbola.primer.bed' # EBOV Artic V3
+ ##- 'ZaireEbola/V2/ZaireEbola.primer.bed' # EBOV Artic V2 (based on AF272001.1)
+ ##- 'ZaireEbola/V1/ZaireEbola.primer.bed' # EBOV Artic V1
+ ##- 'Nipah/V1/NiV_6_Malaysia.primer.bed' # NIV Artic V1
+ ##- 'MPXV/V1/MPXV.primer.bed' # MPXV V1 (dx.doi.org/10.17504/protocols.io.5qpvob1nbl4o/v4)
+ ##- 'your_custom_amplicon_kit.bed' # Add your custom amplicon kit
+ bedpe:
+ path: 'resources/primers_schemes/bedpe/' # Path to primers bedpe files (default 'resources/primer/bedpe') [PATH]
+ scheme: #'insert_here' # Your primer set, in BEDPE format (no default: you need to know which kit and reference you used!)
+ # Reference sequence names and coordinates of BAM and BED are assumed to be derived from identical reference sequences.
+ # Available options (not exhaustive), set only one:
+ ##- 'SARS-CoV-2_Wuhan_MN-908947-3_artic-primers-V4-1.bedpe' # SARS-CoV-2 Artic V4.1 (update to the V4, see Artic README)
+ ##- 'SARS-CoV-2_Wuhan_MN-908947-3_artic-primers-V4.bedpe' # SARS-CoV-2 Artic V4 (not based on V3, see Artic README)
+ ##- 'SARS-CoV-2_Wuhan_MN-908947-3_artic-primers-V3.bedpe' # SARS-CoV-2 Artic V3
+ ##- 'SARS-CoV-2_Wuhan_MN-908947-3_artic-primers-V2.bedpe' # SARS-CoV-2 Artic V2
+ ##- 'SARS-CoV-2_Wuhan_MN-908947-3_artic-primers-V1.bedpe' # SARS-CoV-2 Artic V1
+ ##- 'Ebola-virus_Zaire_KR-063671-1_artic-primers-V3.bedpe' # EBOV Artic V3
+ ##- 'Ebola-virus_Zaire_AF-272001-1_artic-primers-V2.bedpe' # EBOV Artic V2 (based on AF272001.1)
+ ##- 'Ebola-virus_Zaire_KR-063671-1_artic-primers-V1.bedpe' # EBOV Artic V1
+ ##- 'Nipah-virus_Malaysia_AJ-564622-1_artic-primers-V1.bedpe' # NIV Artic V1
+ ##- 'Monkeypox-virus_UK_MT-903345-1_VGCARE-primers-V1.bedpe' # MPXV VGCARE V1 (based on MT903345.1)
+ ##- 'your_custom_amplicon_kit.bedpe' # Add your custom amplicon kit
###############################################################################
################################### MAPPING ###################################
@@ -172,14 +223,14 @@ bamclipper:
bwa:
algorithm: '' # Algorithm for constructing BWA index (default: auto --> '')
- # Available options:
+ # Available options, set only one:
##- '' # Auto-select (default)
##- '-a is' # Moderately fast, but does not work with database larger than 2GB
##- '-a bwtsw' # This method works with the whole human genome
bowtie2:
algorithm: '' # Algorithm for constructing BT2 index (default: '' (small))
- # Available options:
+ # Available options, set only one:
##- '' # (default)
##- '--large-index' # Force generated index to be "large"
# even if reference has fewer than 4 billion nucleotides
@@ -196,11 +247,12 @@ minimap2:
minimizer_size: '11' # -w: minimizer window size (default: "11") [INT]
split_size: '8G' # -I: split index for every {NUM} input bases (default: "8G") [INT]
homopolymer: '' # -H: use homopolymer-compressed k-mer (default: '' (no))
- # Available options:
+ # Available options, set only one:
##- '' # no (default)
##- '-H' # yes (preferrable for PacBio)
+
preset: 'sr' # -x: Minimap2 presets, always applied before other options (default: 'sr')
- # Available preset options:
+ # Available preset options, set only one:
##- 'sr' # genomic short-read mapping, like Illumina (default)
##- 'map-ont' # Nanopore vs reference mapping
##- 'ava-ont' # Nanopore read overlap
@@ -230,19 +282,21 @@ sickle_trim:
cutadapt:
clipping: '0' # Cut 'n' first nucleotides of each reads (default: 0)
length: '50' # Discard reads shorter than 'length' after trim (default: "50")
- kits: # Sequence of an adapter ligated to the 3' end of the first read (default: Illumina)
- truseq: 'AGATCGGAAGAGC' # Illumina "TruSeq" or "ScriptSeq" based libraries kits
- nextera: 'CTGTCTCTTATACACATC' # Illumina "Nextera" or "TruSight" based libraries kits
- small: 'TGGAATTCTCGGGTGCCAAGG' # Illumina "Small" based libraries kits
+ adapters: # Sequence of an adapter ligated to the 3' end of the first read (default: Illumina kits)
+ # Available options (not exhaustive):
+ - 'AGATCGGAAGAGC' # Illumina "TruSeq" or "ScriptSeq" based libraries kits (default)
+ - 'CTGTCTCTTATACACATC' # Illumina "Nextera" or "TruSight" based libraries kits (default)
+ - 'TGGAATTCTCGGGTGCCAAGG' # Illumina "Small" based libraries kits (default)
+ #- 'your_custom_adapter' # Add your custom adapter
###############################################################################
############################### QUALITY CONTROL ###############################
###############################################################################
-multiqc: ## TODO ##
+multiqc: ##TODO##
path: 'config/multiqc/' # Path to the multiqc configuration file
config: 'default.yaml' # Multiqc configuration file (default: default.yaml)
- # Available options (not exhaustive):
+ # Available options (not exhaustive), set only one:
##- 'default.yaml' # default
##- '' #
tag: '' # Use only modules which tagged with this keyword
@@ -250,11 +304,15 @@ multiqc: ## TODO ##
fastq_screen:
config: 'config/fastq-screen.conf' # Path to the fastq-screen configuration file
subset: '10000' # Don't use whole sequences, but a subset reads (default: "10000") [INT] (0=all)
+
reference: # FastqScreen config file genomes to index [LIST]
+ # Available options (not exhaustive):
+
### MOLECULAR BIOLOGY SEQUENCES
- 'QC_Phi-X174_Coliphage_NC001422.1'
- 'QC_Kanamycin-Resistance-Gene'
- 'QC_UniVec_wo_phiX-kanamycin-NGSseq'
+
### MAIN TRANSVIHMI VIRUSES (small genomes, provided)
- 'SARS-CoV-2_Wuhan_MN908947.3' # without poly-A tail
- 'Monkeypox-virus_Zaire_AF380138.1'
@@ -276,12 +334,14 @@ fastq_screen:
- 'Lassa-virus_Josiah_NC004297.1_Seg-L'
- 'Lassa-virus_Josiah_NC004296.1_Seg-S'
- 'HIV-1_HXB2_K03455.1'
+
### MAIN TRANSVIHMI PUTATIVE HOSTS (large genomes, not provided)
#- 'HOST_Gorilla-gorilla_g4'
#- 'HOST_Pan-troglodytes_t3'
#- 'HOST_Pteropus-vampyrus_v1'
#- 'HOST_Mus-musculus_m39'
#- 'HOST_Homo-sapiens_h38_NC000001.11'
+
### GENERIC LAB MODEL ORGANISMS (putative contaminations)
- 'QC_Echerichia-coli_CP060121.1'
#- 'QC_Saccharomyces-cerevisiae'
@@ -293,12 +353,11 @@ fastq_screen:
#- 'QC_Xenopus-laevis'
#- 'QC_Gallus-gallus'
-
###############################################################################
############################### RENAME SAMPLES ################################
###############################################################################
-rename:
+rename: ##TODO##
barcode_id: true
line_id: true
end_id: true
@@ -311,7 +370,7 @@ resources:
cpus: '8' # Set maximum cpus usage (for multithreading, default: "8") [INT]
ram: '16' # Set maximum memory usage (in Gb, default: "16") [INT]
tmp_dir: '$TMPDIR' # Temporary directory.
- # Available options (not exhaustive):
+ # Available options (not exhaustive), set only one:
## -'$TMPDIR' # System variable $TMPDIR (default)
## -'.' # Local (i.e. GeVarLi directory)
## -'/scratch' # HPC (set it to match your HPC usage)
@@ -336,23 +395,24 @@ envs: # Conda environement yaml files:
sickle_trim: '../envs/sickle-trim_v.1.33.yaml' # Sickle-trim ver. 1.33
tsv2vcf: '../envs/tsv2vcf_v.2025.01.yaml' # tsv2vcf ver. 2025.01 (biopython=1.85 numpy=2.2.2 scipy=1.15.1)
workflow: '../envs/workflow-core.yaml' # workflow ver. 2025.01 (snakemake=8.27.1 graphviz=12.0.0)
- yq: '../envs/yq_v.3.4.3.yaml' # yq ver. 3.4.3
report: # Snakemake reports formats
+
stat:
- extention: # [LIST]
+ extention:
- 'txt'
- 'tsv'
- 'json'
+
graph:
- type: # [LIST]
+ type:
- 'dag'
- 'rulegraph'
- 'filegraph'
- extention: # [LIST]
+ extention:
- 'png'
- 'svg'
- 'pdf'
###############################################################################
-###############################################################################
+###############################################################################
\ No newline at end of file
diff --git a/resources/primers/bedpe/.gitkeep b/resources/primers/bedpe/.gitkeep
deleted file mode 100644
index f13c79c..0000000
--- a/resources/primers/bedpe/.gitkeep
+++ /dev/null
@@ -1 +0,0 @@
-Git: keep this non empty file!
\ No newline at end of file
diff --git a/resources/primers/fasta/.gitkeep b/resources/primers/fasta/.gitkeep
deleted file mode 100644
index f13c79c..0000000
--- a/resources/primers/fasta/.gitkeep
+++ /dev/null
@@ -1 +0,0 @@
-Git: keep this non empty file!
\ No newline at end of file
diff --git a/resources/primers_schemes/bed/LICENSE b/resources/primers_schemes/bed/LICENSE
new file mode 100644
index 0000000..52bd145
--- /dev/null
+++ b/resources/primers_schemes/bed/LICENSE
@@ -0,0 +1,395 @@
+Attribution 4.0 International
+
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+
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+ TO YOU ON ANY LEGAL THEORY (INCLUDING, WITHOUT LIMITATION,
+ NEGLIGENCE) OR OTHERWISE FOR ANY DIRECT, SPECIAL, INDIRECT,
+ INCIDENTAL, CONSEQUENTIAL, PUNITIVE, EXEMPLARY, OR OTHER LOSSES,
+ COSTS, EXPENSES, OR DAMAGES ARISING OUT OF THIS PUBLIC LICENSE OR
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+ ADVISED OF THE POSSIBILITY OF SUCH LOSSES, COSTS, EXPENSES, OR
+ DAMAGES. WHERE A LIMITATION OF LIABILITY IS NOT ALLOWED IN FULL OR
+ IN PART, THIS LIMITATION MAY NOT APPLY TO YOU.
+
+ c. The disclaimer of warranties and limitation of liability provided
+ above shall be interpreted in a manner that, to the extent
+ possible, most closely approximates an absolute disclaimer and
+ waiver of all liability.
+
+
+Section 6 -- Term and Termination.
+
+ a. This Public License applies for the term of the Copyright and
+ Similar Rights licensed here. However, if You fail to comply with
+ this Public License, then Your rights under this Public License
+ terminate automatically.
+
+ b. Where Your right to use the Licensed Material has terminated under
+ Section 6(a), it reinstates:
+
+ 1. automatically as of the date the violation is cured, provided
+ it is cured within 30 days of Your discovery of the
+ violation; or
+
+ 2. upon express reinstatement by the Licensor.
+
+ For the avoidance of doubt, this Section 6(b) does not affect any
+ right the Licensor may have to seek remedies for Your violations
+ of this Public License.
+
+ c. For the avoidance of doubt, the Licensor may also offer the
+ Licensed Material under separate terms or conditions or stop
+ distributing the Licensed Material at any time; however, doing so
+ will not terminate this Public License.
+
+ d. Sections 1, 5, 6, 7, and 8 survive termination of this Public
+ License.
+
+
+Section 7 -- Other Terms and Conditions.
+
+ a. The Licensor shall not be bound by any additional or different
+ terms or conditions communicated by You unless expressly agreed.
+
+ b. Any arrangements, understandings, or agreements regarding the
+ Licensed Material not stated herein are separate from and
+ independent of the terms and conditions of this Public License.
+
+
+Section 8 -- Interpretation.
+
+ a. For the avoidance of doubt, this Public License does not, and
+ shall not be interpreted to, reduce, limit, restrict, or impose
+ conditions on any use of the Licensed Material that could lawfully
+ be made without permission under this Public License.
+
+ b. To the extent possible, if any provision of this Public License is
+ deemed unenforceable, it shall be automatically reformed to the
+ minimum extent necessary to make it enforceable. If the provision
+ cannot be reformed, it shall be severed from this Public License
+ without affecting the enforceability of the remaining terms and
+ conditions.
+
+ c. No term or condition of this Public License will be waived and no
+ failure to comply consented to unless expressly agreed to by the
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+
+ d. Nothing in this Public License constitutes or may be interpreted
+ as a limitation upon, or waiver of, any privileges and immunities
+ that apply to the Licensor or You, including from the legal
+ processes of any jurisdiction or authority.
+
+
+=======================================================================
+
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+will be considered the “Licensor.†The text of the Creative Commons
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\ No newline at end of file
diff --git a/resources/primers_schemes/bed/MPXV/V1/MPXV.primer.bed b/resources/primers_schemes/bed/MPXV/V1/MPXV.primer.bed
new file mode 100644
index 0000000..5f60caa
--- /dev/null
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diff --git a/resources/primers_schemes/bed/Nipah/V1/NiV_6_Malaysia.primer.bed b/resources/primers_schemes/bed/Nipah/V1/NiV_6_Malaysia.primer.bed
new file mode 100644
index 0000000..7a283b4
--- /dev/null
+++ b/resources/primers_schemes/bed/Nipah/V1/NiV_6_Malaysia.primer.bed
@@ -0,0 +1,120 @@
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diff --git a/resources/primers_schemes/bed/README.md b/resources/primers_schemes/bed/README.md
new file mode 100644
index 0000000..9ceacbc
--- /dev/null
+++ b/resources/primers_schemes/bed/README.md
@@ -0,0 +1,74 @@
+# primer-schemes
+
+Primer schemes for real-time genome epidemiology
+
+[](https://travis-ci.org/artic-network/primer-schemes)
+[](https://zenodo.org/badge/latestdoi/96756353)
+
+## About
+
+The primer schemes in this repository were built using [Primal Scheme](https://primalscheme.com/) and are available for the following viruses:
+
+- Ebola
+- Nipah
+- SARS-CoV-2 (nCoV-2019)
+
+Within each virus directory, there are versioned sub-directories which each contain a versioned scheme for that virus.
+
+The following files are available per scheme version:
+
+| file extension | about |
+| ------------------ | -------------------------------------------------------------------------------------- |
+| `.primer.bed` | The coordinates of each primer in the scheme |
+| `.insert.bed` | The coordinates of the expected amplicons that the scheme produces (excluding primers) |
+| `.reference.fasta` | The sequence of the reference genome used for the scheme |
+| `.tsv` | Details on each primer in the scheme (name, sequence, length, GC, TM) |
+
+For more information visit the [ARTIC network website](https://artic.network/).
+
+## Notes
+
+- There may be some additional files in the scheme directories - these are either deprecated and left for backward compatibility (e.g. `scheme.bed`), or are created by Primal Scheme [check here](https://github.com/aresti/primalscheme) for more info.
+- The schemes are in BED format, which is a 0-based, half-open format. This means that reference sequence position counting starts at 0 and the chromEnd is not included in the primer sequence.
+- All the schemes within this repository can be downloaded using [artic-tools](https://github.com/will-rowe/artic-tools) (e.g. `artic-tools get_scheme ebola --schemeVersion 2`)
+- The SARS-CoV-2 directory is an alias to the original nCoV-2019 directory, left for backwards compatibility
+
+## Updated scheme file format
+
+> updated: 25.08.2020
+
+### changes
+
+With the major version bump to [Primal Scheme](https://github.com/aresti/primalscheme), primer schemes are now output to `*.primer.bed` files.
+
+These new files aren't much different to the old `*.scheme.bed` files and the same information is contained within, but they now conform to the [BED standard](https://genome.ucsc.edu/FAQ/FAQformat.html#format1).
+
+The new format has the following columns:
+
+| column | name | type | description |
+| ------ | ---------- | ------------ | --------------------------------------------------------- |
+| 1 | chrom | string | primer reference sequence |
+| 2 | chromStart | int | starting position of the primer in the reference sequence |
+| 3 | chomEnd | int | ending position of the primer in the reference sequence |
+| 4 | name | string | primer name |
+| 5 | primerPool | int | primer pool<sup>\*</sup> |
+| 6 | strand | string (+/-) | primer direction |
+
+<sup>\*</sup> column 5 in the BED spec is an int for score, whereas here we are using it to denote primerPool.
+
+### commands
+
+The `liftover.py` script was used to create a `*.primer.bed` file for each `*.scheme.bed` file, within each scheme directory in this repository.
+
+The `validate_scheme` command from [artic-tools](https://github.com/will-rowe/artic-tools) was used to validate each `*.primer.bed` and also to create the `*.insert.bed` file which is produced by recent versions of [Primal Scheme](https://github.com/aresti/primalscheme).
+
+The following commands where used:
+
+```bash
+for i in */V*/*.scheme.bed;
+do
+basename=${i%%.scheme.bed}
+scripts/liftover.py -i $i -o ${basename}.primer.bed;
+artic-tools validate_scheme ${basename}.primer.bed --outputInserts ${basename}.insert.bed
+done;
+```
diff --git a/resources/primers_schemes/bed/ZaireEbola/V1/ZaireEbola.primer.bed b/resources/primers_schemes/bed/ZaireEbola/V1/ZaireEbola.primer.bed
new file mode 100644
index 0000000..44709f8
--- /dev/null
+++ b/resources/primers_schemes/bed/ZaireEbola/V1/ZaireEbola.primer.bed
@@ -0,0 +1,46 @@
+KR063671.1 32 59 Ebov_1_LEFT 1 +
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diff --git a/resources/primers_schemes/bed/ZaireEbola/V2/ZaireEbola.primer.bed b/resources/primers_schemes/bed/ZaireEbola/V2/ZaireEbola.primer.bed
new file mode 100644
index 0000000..213ef90
--- /dev/null
+++ b/resources/primers_schemes/bed/ZaireEbola/V2/ZaireEbola.primer.bed
@@ -0,0 +1,94 @@
+EBOV|AF272001|Mayinga|Yambuku_DRC|1976 38 64 Ebola-Zaire_1_LEFT 1 +
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+EBOV|AF272001|Mayinga|Yambuku_DRC|1976 434 459 Ebola-Zaire_2_LEFT 2 +
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+EBOV|AF272001|Mayinga|Yambuku_DRC|1976 859 881 Ebola-Zaire_3_LEFT 1 +
+EBOV|AF272001|Mayinga|Yambuku_DRC|1976 1327 1349 Ebola-Zaire_3_RIGHT 1 -
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+EBOV|AF272001|Mayinga|Yambuku_DRC|1976 2143 2165 Ebola-Zaire_5_RIGHT 1 -
+EBOV|AF272001|Mayinga|Yambuku_DRC|1976 2065 2087 Ebola-Zaire_6_LEFT 2 +
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+EBOV|AF272001|Mayinga|Yambuku_DRC|1976 2508 2531 Ebola-Zaire_7_LEFT 1 +
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+EBOV|AF272001|Mayinga|Yambuku_DRC|1976 3291 3313 Ebola-Zaire_9_LEFT 1 +
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diff --git a/resources/primers_schemes/bed/ZaireEbola/V3/ZaireEbola.primer.bed b/resources/primers_schemes/bed/ZaireEbola/V3/ZaireEbola.primer.bed
new file mode 100644
index 0000000..83ef9ad
--- /dev/null
+++ b/resources/primers_schemes/bed/ZaireEbola/V3/ZaireEbola.primer.bed
@@ -0,0 +1,124 @@
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diff --git a/resources/primers_schemes/bed/nCoV-2019/V1/nCoV-2019.primer.bed b/resources/primers_schemes/bed/nCoV-2019/V1/nCoV-2019.primer.bed
new file mode 100644
index 0000000..2a05af6
--- /dev/null
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new file mode 100644
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diff --git a/resources/primers_schemes/bed/nCoV-2019/V3/nCoV-2019.primer.bed b/resources/primers_schemes/bed/nCoV-2019/V3/nCoV-2019.primer.bed
new file mode 100644
index 0000000..76691de
--- /dev/null
+++ b/resources/primers_schemes/bed/nCoV-2019/V3/nCoV-2019.primer.bed
@@ -0,0 +1,218 @@
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diff --git a/resources/primers_schemes/bed/nCoV-2019/V4.1/SARS-CoV-2.primer.bed b/resources/primers_schemes/bed/nCoV-2019/V4.1/SARS-CoV-2.primer.bed
new file mode 100644
index 0000000..5b8e1d4
--- /dev/null
+++ b/resources/primers_schemes/bed/nCoV-2019/V4.1/SARS-CoV-2.primer.bed
@@ -0,0 +1,209 @@
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+MN908947.3 408 431 SARS-CoV-2_1_RIGHT 1 - CTTCTACTAAGCCACAAGTGCCA
+MN908947.3 644 666 SARS-CoV-2_3_LEFT 1 + GTAATAAAGGAGCTGGTGGCCA
+MN908947.3 705 727 SARS-CoV-2_2_RIGHT 2 - ATAAGGATCAGTGCCAAGCTCG
+MN908947.3 944 966 SARS-CoV-2_4_LEFT 2 + GTGTATACTGCTGCCGTGAACA
+MN908947.3 1017 1044 SARS-CoV-2_3_RIGHT 1 - GCCAATTTAATTTCAAAAGGTGTCTGC
+MN908947.3 1245 1266 SARS-CoV-2_5_LEFT 1 + TGAAACTTCATGGCAGACGGG
+MN908947.3 1337 1362 SARS-CoV-2_4_RIGHT 2 - ACAACAGCATTTTGGGGTAAGTAAC
+MN908947.3 1540 1562 SARS-CoV-2_6_LEFT 2 + CGTGCTAGCGCTAACATAGGTT
+MN908947.3 1623 1650 SARS-CoV-2_5_RIGHT 1 - TTGATGTTGACTTTCTCTTTTTGGAGT
+MN908947.3 1851 1875 SARS-CoV-2_7_LEFT 1 + ACTGAGTCCTCTTTATGCATTTGC
+MN908947.3 1925 1948 SARS-CoV-2_6_RIGHT 2 - AACACGCACAGAATTTTGAGCAG
+MN908947.3 2154 2180 SARS-CoV-2_8_LEFT 2 + GCTTGAAGAGAAGTTTAAGGAAGGTG
+MN908947.3 2228 2250 SARS-CoV-2_7_RIGHT 1 - CCACCGACAATTTCACAAGCAC
+MN908947.3 2483 2508 SARS-CoV-2_9_LEFT 1 + TCTTCTTAGAGGGAGAAACACTTCC
+MN908947.3 2544 2571 SARS-CoV-2_8_RIGHT 2 - GGTTGTTCTAATGGTTGTAAATCACCA
+MN908947.3 2780 2813 SARS-CoV-2_10_LEFT_alt1 2 + TGAATATCACTTTTGAACTTGATGAAAGGATTG
+MN908947.3 2826 2850 SARS-CoV-2_10_LEFT 2 + TGAGAAGTGCTCTGCCTATACAGT
+MN908947.3 2861 2885 SARS-CoV-2_9_RIGHT 1 - CACAGGCGAACTCATTTACTTCTG
+MN908947.3 3078 3102 SARS-CoV-2_11_LEFT 1 + AGAAGAGTTTGAGCCATCAACTCA
+MN908947.3 3156 3177 SARS-CoV-2_10_RIGHT_alt1 2 - GGTTGAAGAGCAGCAGAAGTG
+MN908947.3 3183 3210 SARS-CoV-2_10_RIGHT 2 - TCATCTAACCAATCTTCTTCTTGCTCT
+MN908947.3 3390 3412 SARS-CoV-2_12_LEFT 2 + TGCAGACATTGTGGAAGAAGCT
+MN908947.3 3470 3492 SARS-CoV-2_11_RIGHT 1 - TTTAAGGCTCCTGCAACACCTC
+MN908947.3 3683 3705 SARS-CoV-2_13_LEFT 1 + AGCACGAAGTTCTACTTGCACC
+MN908947.3 3769 3794 SARS-CoV-2_12_RIGHT 2 - CAGCTAAGTAGACATTTGTGCGAAC
+MN908947.3 3992 4018 SARS-CoV-2_14_LEFT 2 + TGGAAGAAACTAAGTTCCTCACAGAA
+MN908947.3 4067 4093 SARS-CoV-2_13_RIGHT 1 - GATGTCAATGTCACTAACAAGAGTGG
+MN908947.3 4312 4339 SARS-CoV-2_15_LEFT 1 + AAAAGTGCCTTTTACATTCTACCATCT
+MN908947.3 4387 4409 SARS-CoV-2_14_RIGHT 2 - CATGTGCAAGCATTTCTCGCAA
+MN908947.3 4620 4648 SARS-CoV-2_16_LEFT 2 + TGTAACACATGGCTTAAATTTGGAAGAA
+MN908947.3 4685 4710 SARS-CoV-2_15_RIGHT 1 - GCATCAGGTGAAGAAACAGAAACTG
+MN908947.3 4923 4953 SARS-CoV-2_17_LEFT 1 + TGACAATCTTAAGACACTTCTTTCTTTGAG
+MN908947.3 4995 5017 SARS-CoV-2_16_RIGHT 2 - CACAACTTGCGTGTGGAGGTTA
+MN908947.3 5230 5259 SARS-CoV-2_18_LEFT 2 + TGGAAATACCCACAAGTTAATGGTTTAAC
+MN908947.3 5302 5331 SARS-CoV-2_17_RIGHT 1 - TTCAACTCTATTTGTTGGAGTGTTAACAA
+MN908947.3 5561 5584 SARS-CoV-2_19_LEFT 1 + AAGCTGTTATGTACATGGGCACA
+MN908947.3 5620 5643 SARS-CoV-2_18_RIGHT 2 - GCTTGTTTACCACACGTACAAGG
+MN908947.3 5867 5894 SARS-CoV-2_20_LEFT 2 + ACAAAGAAAACAGTTACACAACAACCA
+MN908947.3 5932 5957 SARS-CoV-2_19_RIGHT 1 - TGTCCAACTTAGGGTCAATTTCTGT
+MN908947.3 6184 6210 SARS-CoV-2_21_LEFT 1 + CACTACACACCCTCTTTTAAGAAAGG
+MN908947.3 6247 6272 SARS-CoV-2_20_RIGHT 2 - ACGTGGCTTTATTAGTTGCATTGTT
+MN908947.3 6478 6507 SARS-CoV-2_22_LEFT 2 + GTAGGAGACATTATACTTAAACCAGCAAA
+MN908947.3 6553 6582 SARS-CoV-2_21_RIGHT 1 - GTAAGACTAGAATTGTCTACATAAGCAGC
+MN908947.3 6747 6776 SARS-CoV-2_23_LEFT 1 + AAACCGTGTTTGTACTAATTATATGCCTT
+MN908947.3 6859 6885 SARS-CoV-2_22_RIGHT 2 - CCGACACTCTTAACAGTATTCTTTGC
+MN908947.3 7057 7084 SARS-CoV-2_24_LEFT 2 + GGTTACAGAGAAGGCTATTTGAACTCT
+MN908947.3 7122 7148 SARS-CoV-2_23_RIGHT 1 - AACCACTAAGACAAACACTACAAGGT
+MN908947.3 7127 7156 SARS-CoV-2_23_RIGHT_alt1 1 - AGAATCTAAACCACTAAGACAAACACTAC
+MN908947.3 7381 7403 SARS-CoV-2_25_LEFT 1 + CAAATGGCCCCGATTTCAGCTA
+MN908947.3 7440 7467 SARS-CoV-2_24_RIGHT 2 - ACAACATGCACATAACTTTTCCATACA
+MN908947.3 7672 7695 SARS-CoV-2_26_LEFT 2 + GCGAGAGACTTGTCACTACAGTT
+MN908947.3 7747 7770 SARS-CoV-2_25_RIGHT 1 - TGGATGGAACCATTCTTCACTGT
+MN908947.3 7997 8019 SARS-CoV-2_27_LEFT 1 + CTGATGTTGGTGATAGTGCGGA
+MN908947.3 8063 8092 SARS-CoV-2_26_RIGHT 2 - GAGTTTTTCCATTGGTACGTTAAAAGTTG
+MN908947.3 8304 8326 SARS-CoV-2_28_LEFT 2 + TGAAAACATGACACCCCGTGAC
+MN908947.3 8367 8392 SARS-CoV-2_27_RIGHT_alt1 1 - AATGTTGTGACTTTTTGCTACCTGC
+MN908947.3 8370 8395 SARS-CoV-2_27_RIGHT 1 - AGCAATGTTGTGACTTTTTGCTACC
+MN908947.3 8596 8619 SARS-CoV-2_29_LEFT 1 + CTTGTGTTCCTTTTTGTTGCTGC
+MN908947.3 8691 8714 SARS-CoV-2_28_RIGHT 2 - TGACACCACCATCAATAGCCTTG
+MN908947.3 8919 8944 SARS-CoV-2_30_LEFT 2 + ACCTAGAGTTTTTAGTGCAGTTGGT
+MN908947.3 8990 9013 SARS-CoV-2_29_RIGHT 1 - AGCCAAAACACAAGCTGATGTTG
+MN908947.3 9168 9192 SARS-CoV-2_31_LEFT 1 + CCTTGAAGGTTCTGTTAGAGTGGT
+MN908947.3 9306 9329 SARS-CoV-2_30_RIGHT 2 - CTACACCACAGAAAACTCCTGGT
+MN908947.3 9470 9497 SARS-CoV-2_32_LEFT 2 + GAGCTTTTGGTGAATACAGTCATGTAG
+MN908947.3 9535 9564 SARS-CoV-2_31_RIGHT 1 - AATGAGTAAACTGGTGTTAAACAGAGTAC
+MN908947.3 9782 9805 SARS-CoV-2_33_LEFT 1 + GTACTTTTGAAGAAGCTGCGCTG
+MN908947.3 9842 9866 SARS-CoV-2_32_RIGHT 2 - GAGGTAATAGCACATCACTACGCA
+MN908947.3 10076 10099 SARS-CoV-2_34_LEFT 2 + TCCCATCTGGTAAAGTTGAGGGT
+MN908947.3 10150 10176 SARS-CoV-2_33_RIGHT 1 - TGTCTTGGACAGTAAACTACGTCATC
+MN908947.3 10393 10419 SARS-CoV-2_35_LEFT 1 + GTGTTAGCTTGTTACAATGGTTCACC
+MN908947.3 10465 10491 SARS-CoV-2_34_RIGHT 2 - CCACATGAACCATTAAGGAATGAACC
+MN908947.3 10713 10742 SARS-CoV-2_36_LEFT 2 + CAATCGATTTACCACAACTCTTAATGACT
+MN908947.3 10785 10810 SARS-CoV-2_35_RIGHT 1 - AGGTCCTAGTATGTCAACATGGTCT
+MN908947.3 11000 11023 SARS-CoV-2_37_LEFT 1 + CACACCACTGGTTGTTACTCACA
+MN908947.3 11092 11116 SARS-CoV-2_36_RIGHT 2 - ACCCATAGCAAAAGGTAAAAAGGC
+MN908947.3 11305 11330 SARS-CoV-2_38_LEFT 2 + GACTGTGTTATGTATGCATCAGCTG
+MN908947.3 11388 11414 SARS-CoV-2_37_RIGHT 1 - GTGTCAAGACATTCATAAGTGTCCAC
+MN908947.3 11624 11651 SARS-CoV-2_39_LEFT 1 + GCTATTTTTGTACTTGTTACTTTGGCC
+MN908947.3 11689 11720 SARS-CoV-2_38_RIGHT 2 - CCTGTGTAGAAACTAAGTAATCATAAACACC
+MN908947.3 11937 11963 SARS-CoV-2_40_LEFT 2 + TGTCCAGTTACACAATGACATTCTCT
+MN908947.3 12011 12033 SARS-CoV-2_39_RIGHT 1 - CCCTGCATGGAAAGCAAAACAG
+MN908947.3 12234 12255 SARS-CoV-2_41_LEFT 1 + ATTTGACCGTGATGCAGCCAT
+MN908947.3 12317 12339 SARS-CoV-2_40_RIGHT 2 - ACTTTTGCCCTCTTGTCCTCAG
+MN908947.3 12519 12546 SARS-CoV-2_42_LEFT 2 + TGGTACAACATTTACTTATGCATCAGC
+MN908947.3 12618 12643 SARS-CoV-2_41_RIGHT 1 - AAGAGGCCATGCTAAATTAGGTGAA
+MN908947.3 12831 12856 SARS-CoV-2_43_LEFT 1 + GGATTTGAAATGGGCTAGATTCCCT
+MN908947.3 12895 12920 SARS-CoV-2_42_RIGHT 2 - TGTCTGTAACAAACCTACAAGGTGG
+MN908947.3 13124 13148 SARS-CoV-2_44_LEFT 2 + GGGGACAACCAATCACTAATTGTG
+MN908947.3 13218 13240 SARS-CoV-2_43_RIGHT 1 - CGATGCACCACCAAAGGATTCT
+MN908947.3 13463 13485 SARS-CoV-2_45_LEFT 1 + TAAACGGGTTTGCGGTGTAAGT
+MN908947.3 13506 13528 SARS-CoV-2_44_RIGHT 2 - CATCAGTACTAGTGCCTGTGCC
+MN908947.3 13752 13775 SARS-CoV-2_46_LEFT 2 + AGAATAGACGGTGACATGGTACC
+MN908947.3 13833 13859 SARS-CoV-2_45_RIGHT 1 - TCACAATTACCTTCATCAAAATGCCT
+MN908947.3 14045 14075 SARS-CoV-2_47_LEFT 1 + TGGTGTACTGACATTAGATAATCAAGATCT
+MN908947.3 14120 14144 SARS-CoV-2_46_RIGHT 2 - TCTACAACAGGAACTCCACTACCT
+MN908947.3 14338 14362 SARS-CoV-2_48_LEFT 2 + ACTGTTTGGATGACAGATGCATTC
+MN908947.3 14428 14457 SARS-CoV-2_47_RIGHT 1 - TGGAACACCATCAACAAATATTTTTCTCA
+MN908947.3 14647 14674 SARS-CoV-2_49_LEFT 1 + ACAATGTTGCTTTTCAAACTGTCAAAC
+MN908947.3 14717 14743 SARS-CoV-2_48_RIGHT 2 - CAGAACTTCCTTCCTTAAAGAAACCC
+MN908947.3 14953 14983 SARS-CoV-2_50_LEFT 2 + CATTTAATAAATGGGGTAAGGCTAGACTTT
+MN908947.3 15023 15050 SARS-CoV-2_49_RIGHT 1 - GGGATGACATTACGTTTTGTATATGCG
+MN908947.3 15214 15237 SARS-CoV-2_51_LEFT 1 + GCAAATTCTATGGTGGTTGGCAC
+MN908947.3 15336 15358 SARS-CoV-2_50_RIGHT 2 - GAGCAAGAACAAGTGAGGCCAT
+MN908947.3 15535 15557 SARS-CoV-2_52_LEFT 2 + CTGTCACGGCCAATGTTAATGC
+MN908947.3 15596 15619 SARS-CoV-2_51_RIGHT 1 - GTCTGTGTTGTAAATTGCGGACA
+MN908947.3 15855 15881 SARS-CoV-2_53_LEFT 1 + ACTAAAGGACCTCATGAATTTTGCTC
+MN908947.3 15917 15941 SARS-CoV-2_52_RIGHT 2 - GGATCTGGGTAAGGAAGGTACACA
+MN908947.3 16112 16137 SARS-CoV-2_54_LEFT 2 + ACATGATGAGTTAACAGGACACATG
+MN908947.3 16239 16260 SARS-CoV-2_53_RIGHT 1 - GCAAAGAACACAAGCCCCAAC
+MN908947.3 16386 16408 SARS-CoV-2_55_LEFT 1 + AATGCTCCAGGTTGTGATGTCA
+MN908947.3 16483 16508 SARS-CoV-2_54_RIGHT 2 - CCAAAAACTTGTCCATTAGCACACA
+MN908947.3 16692 16714 SARS-CoV-2_56_LEFT 2 + ACTGTACGTGAAGTGCTGTCTG
+MN908947.3 16767 16796 SARS-CoV-2_55_RIGHT 1 - ACACGATAACCAGTAAAGACATAATTTCG
+MN908947.3 16986 17013 SARS-CoV-2_57_LEFT 1 + GGCTTATACCCAACACTCAATATCTCA
+MN908947.3 17082 17105 SARS-CoV-2_56_RIGHT 2 - TGACTCTTACCAGTACCAGGTGG
+MN908947.3 17323 17345 SARS-CoV-2_58_LEFT 2 + TGCCTGAGACGACAGCAGATAT
+MN908947.3 17381 17405 SARS-CoV-2_57_RIGHT 1 - CTGGCATTGACAACACTCAAATCA
+MN908947.3 17615 17642 SARS-CoV-2_59_LEFT 1 + GCTTAAAGCACATAAAGACAAATCAGC
+MN908947.3 17688 17711 SARS-CoV-2_58_RIGHT 2 - TGTGGCCTGTTAATTGCAGATGA
+MN908947.3 17911 17939 SARS-CoV-2_60_LEFT 2 + ACAGATTTAATGTTGCTATTACCAGAGC
+MN908947.3 17997 18022 SARS-CoV-2_59_RIGHT 1 - TCCTACGTGGAATTTCAAGACTTGT
+MN908947.3 18244 18267 SARS-CoV-2_61_LEFT 1 + ACCCTAACATGTTTATCACCCGC
+MN908947.3 18307 18328 SARS-CoV-2_60_RIGHT 2 - TAGCATGACACCCCTCGACAT
+MN908947.3 18550 18578 SARS-CoV-2_62_LEFT 2 + GTGACACACTTAAAAATCTCTCTGACAG
+MN908947.3 18624 18652 SARS-CoV-2_61_RIGHT 1 - GCTCAGGTCCTATTTTCACAAAATACTT
+MN908947.3 18869 18891 SARS-CoV-2_63_LEFT 1 + TAGGTGTCTAGCTGTCCACGAG
+MN908947.3 18936 18961 SARS-CoV-2_62_RIGHT 2 - CCGCATTAATCTTCAGTTCATCACC
+MN908947.3 19183 19208 SARS-CoV-2_64_LEFT 2 + GCCTATTTTGGAATTGCAATGTCGA
+MN908947.3 19252 19277 SARS-CoV-2_63_RIGHT 1 - CCAGGCAAGTTAAGGTTAGATAGCA
+MN908947.3 19485 19513 SARS-CoV-2_65_LEFT 1 + GTCTGTAGACATCATGCTAATGAGTACA
+MN908947.3 19558 19586 SARS-CoV-2_64_RIGHT 2 - GTATCAAATTGTTTGTAAACCCACAAGC
+MN908947.3 19810 19836 SARS-CoV-2_66_LEFT 2 + AACCAGTACCAGAGGTGAAAATACTC
+MN908947.3 19877 19901 SARS-CoV-2_65_RIGHT 1 - GCTGGAGCATCTCTTTTGTAGTCC
+MN908947.3 20090 20117 SARS-CoV-2_67_LEFT 1 + CAAACAAGCTAGTCTTAATGGAGTCAC
+MN908947.3 20186 20216 SARS-CoV-2_66_RIGHT 2 - TTTCTACTCTGAGTAAAGTAAGTTTCAGGT
+MN908947.3 20377 20405 SARS-CoV-2_68_LEFT 2 + GACTAGCTAAACGTTTTAAGGAATCACC
+MN908947.3 20472 20497 SARS-CoV-2_67_RIGHT 1 - AACACACACACTTAGATGAACCTGT
+MN908947.3 20677 20699 SARS-CoV-2_69_LEFT 1 + CGGGTGTTGCTATGCCTAATCT
+MN908947.3 20766 20792 SARS-CoV-2_68_RIGHT 2 - GCGACATTCATCATTATGCCTTTAGG
+MN908947.3 20988 21013 SARS-CoV-2_70_LEFT 2 + TTGATTGGTGATTGTGCAACTGTAC
+MN908947.3 21050 21080 SARS-CoV-2_69_RIGHT 1 - TTTGTAACATTTTTAGTCTTAGGGTCGTAC
+MN908947.3 21294 21316 SARS-CoV-2_71_LEFT 1 + GGCAAACCACGCGAACAAATAG
+MN908947.3 21358 21387 SARS-CoV-2_70_RIGHT 2 - AGAATAGGAAGACAACTGAATTGGATTTG
+MN908947.3 21532 21561 SARS-CoV-2_72_LEFT 2 + GTGATGTTCTTGTTAACAACTAAACGAAC
+MN908947.3 21675 21700 SARS-CoV-2_71_RIGHT 1 - TGAGGATCTGAAAACTTTGTCAGGG
+MN908947.3 21865 21889 SARS-CoV-2_73_LEFT 1 + AGAGGCTGGATTTTTGGTACTACT
+MN908947.3 21904 21933 SARS-CoV-2_72_RIGHT 2 - GTAGCGTTATTAACAATAAGTAGGGACTG
+MN908947.3 22091 22113 SARS-CoV-2_74_LEFT 2 + TGGACCTTGAAGGAAAACAGGG
+MN908947.3 22247 22274 SARS-CoV-2_73_RIGHT 1 - ACCTAGTGATGTTAATACCTATTGGCA
+MN908947.3 22402 22428 SARS-CoV-2_75_LEFT 1 + GAAAATGGAACCATTACAGATGCTGT
+MN908947.3 22474 22503 SARS-CoV-2_74_RIGHT 2 - TGATAGATTCCTTTTTCTACAGTGAAGGA
+MN908947.3 22648 22677 SARS-CoV-2_76_LEFT 2 + GCTGATTATTCTGTCCTATATAATTCCGC
+MN908947.3 22742 22774 SARS-CoV-2_76_LEFT_alt1 2 + ATGTCTATGCAGATTCATTTGTAATTAGAGGT
+MN908947.3 22785 22805 SARS-CoV-2_75_RIGHT 1 - TTTGCCCTGGAGCGATTTGT
+MN908947.3 22944 22974 SARS-CoV-2_77_LEFT 1 + CAAACCTTTTGAGAGAGATATTTCAACTGA
+MN908947.3 23028 23057 SARS-CoV-2_76_RIGHT 2 - GTTGGAAACCATATGATTGTAAAGGAAAG
+MN908947.3 23120 23141 SARS-CoV-2_76_RIGHT_alt1 2 - GTCCACAAACAGTTGCTGGTG
+MN908947.3 23219 23246 SARS-CoV-2_78_LEFT 2 + CTGAGTCTAACAAAAAGTTTCTGCCTT
+MN908947.3 23327 23351 SARS-CoV-2_77_RIGHT 1 - CACTGACACCACCAAAAGAACATG
+MN908947.3 23553 23575 SARS-CoV-2_79_LEFT 1 + ACCCATTGGTGCAGGTATATGC
+MN908947.3 23611 23635 SARS-CoV-2_78_RIGHT 2 - GGATTGACTAGCTACACTACGTGC
+MN908947.3 23853 23876 SARS-CoV-2_80_LEFT 2 + CCGTGCTTTAACTGGAATAGCTG
+MN908947.3 23914 23944 SARS-CoV-2_79_RIGHT_alt1 1 - AATTGGTGGTGTTTTGTAAATTTGTTTGAC
+MN908947.3 23927 23955 SARS-CoV-2_79_RIGHT 1 - CCAAAATCTTTAATTGGTGGTGTTTTGT
+MN908947.3 24171 24194 SARS-CoV-2_81_LEFT 1 + TGCTCAATACACTTCTGCACTGT
+MN908947.3 24233 24258 SARS-CoV-2_80_RIGHT 2 - GCAAATGGTATTTGTAATGCAGCAC
+MN908947.3 24426 24448 SARS-CoV-2_82_LEFT 2 + TGCACAAGCTTTAAACACGCTT
+MN908947.3 24545 24567 SARS-CoV-2_81_RIGHT 1 - TGAAGTCTGCCTGTGATCAACC
+MN908947.3 24750 24772 SARS-CoV-2_83_LEFT 1 + GCATGTGACTTATGTCCCTGCA
+MN908947.3 24814 24836 SARS-CoV-2_82_RIGHT 2 - CACGAGGAAAGTGTGCTTTTCC
+MN908947.3 25051 25076 SARS-CoV-2_84_LEFT 2 + GTTGATTTAGGTGACATCTCTGGCA
+MN908947.3 25122 25150 SARS-CoV-2_83_RIGHT 1 - AGATTCATTTAAATTCTTGGCAACCTCA
+MN908947.3 25331 25353 SARS-CoV-2_85_LEFT 1 + ATGAAGACGACTCTGAGCCAGT
+MN908947.3 25438 25461 SARS-CoV-2_84_RIGHT 2 - AGCATCCTTGATTTCACCTTGCT
+MN908947.3 25645 25672 SARS-CoV-2_86_LEFT 2 + TGTTGTTTGTAACAGTTTACTCACACC
+MN908947.3 25711 25740 SARS-CoV-2_85_RIGHT 1 - CTGCAAGAAGTAGACTAAAGCATAAAGAT
+MN908947.3 25951 25979 SARS-CoV-2_87_LEFT 1 + GTGGTTATACTGAAAAATGGGAATCTGG
+MN908947.3 26026 26050 SARS-CoV-2_86_RIGHT 2 - TCAATTGAGTTGAGTACAGCTGGT
+MN908947.3 26242 26268 SARS-CoV-2_88_LEFT_alt1 2 + TTATGTACTCATTCGTTTCGGAAGAG
+MN908947.3 26255 26277 SARS-CoV-2_88_LEFT 2 + CGTTTCGGAAGAGACAGGTACG
+MN908947.3 26338 26360 SARS-CoV-2_87_RIGHT 1 - AATCGAAGCGCAGTAAGGATGG
+MN908947.3 26564 26587 SARS-CoV-2_89_LEFT 1 + AAGCTCCTTGAACAATGGAACCT
+MN908947.3 26592 26621 SARS-CoV-2_89_LEFT_alt1 1 + TAGGTTTCCTATTCCTTACATGGATTTGT
+MN908947.3 26635 26661 SARS-CoV-2_88_RIGHT 2 - ACAAAAACCTATTCCTGTTGGCATAG
+MN908947.3 26873 26895 SARS-CoV-2_90_LEFT 2 + ATTCTTCTCAACGTGCCACTCC
+MN908947.3 26956 26979 SARS-CoV-2_89_RIGHT 1 - CAGCAATACGAAGATGTCCACGA
+MN908947.3 26966 26991 SARS-CoV-2_89_RIGHT_alt1 1 - CTAGATGGTGTCCAGCAATACGAAG
+MN908947.3 27152 27177 SARS-CoV-2_91_LEFT 1 + TCCAGTAGCAGTGACAATATTGCTT
+MN908947.3 27218 27251 SARS-CoV-2_90_RIGHT_alt1 2 - ATTAGTAATATCTCTGCTATAGTAACCTGAAAG
+MN908947.3 27256 27283 SARS-CoV-2_90_RIGHT 2 - TCCAAATGGAAACTTTAAAAGTCCTCA
+MN908947.3 27447 27473 SARS-CoV-2_92_LEFT 2 + CACTACCAAGAGTGTGTTAGAGGTAC
+MN908947.3 27534 27560 SARS-CoV-2_91_RIGHT 1 - AGTGCAAATTTGTTATCAGCTAGAGG
+MN908947.3 27700 27726 SARS-CoV-2_93_LEFT 1 + TTGTTGCGGCAATAGTGTTTATAACA
+MN908947.3 27826 27855 SARS-CoV-2_92_RIGHT 2 - GTTCAAGTGAGAACCAAAAGATAATAAGC
+MN908947.3 27996 28021 SARS-CoV-2_94_LEFT 2 + ACCCGTGTCCTATTCACTTCTATTC
+MN908947.3 28082 28104 SARS-CoV-2_93_RIGHT 1 - TGGGTGATTTAGAACCAGCCTC
+MN908947.3 28190 28214 SARS-CoV-2_95_LEFT 1 + GTGCGTTGTTCGTTCTATGAAGAC
+MN908947.3 28394 28416 SARS-CoV-2_94_RIGHT 2 - TTATTGGGTAAACCTTGGGGCC
+MN908947.3 28512 28536 SARS-CoV-2_96_LEFT 2 + AGATGACCAAATTGGCTACTACCG
+MN908947.3 28572 28598 SARS-CoV-2_95_RIGHT 1 - ACCATCTTGGACTGAGATCTTTCATT
+MN908947.3 28827 28849 SARS-CoV-2_97_LEFT 1 + TTCCTCATCACGTAGTCGCAAC
+MN908947.3 28893 28914 SARS-CoV-2_96_RIGHT 2 - CCATTGCCAGCCATTCTAGCA
+MN908947.3 29136 29161 SARS-CoV-2_98_LEFT 2 + CCAGGAACTAATCAGACAAGGAACT
+MN908947.3 29206 29227 SARS-CoV-2_97_RIGHT 1 - CGACATTCCGAAGAACGCTGA
+MN908947.3 29452 29475 SARS-CoV-2_99_LEFT 1 + CTTCTTCCTGCTGCAGATTTGGA
+MN908947.3 29512 29534 SARS-CoV-2_98_RIGHT 2 - TTTAGGCCTGAGTTGAGTCAGC
+MN908947.3 29827 29854 SARS-CoV-2_99_RIGHT 1 - GCTATTAAAATCACATGGGGATAGCAC
diff --git a/resources/primers_schemes/bed/nCoV-2019/V4/SARS-CoV-2.primer.bed b/resources/primers_schemes/bed/nCoV-2019/V4/SARS-CoV-2.primer.bed
new file mode 100644
index 0000000..c2149c0
--- /dev/null
+++ b/resources/primers_schemes/bed/nCoV-2019/V4/SARS-CoV-2.primer.bed
@@ -0,0 +1,198 @@
+MN908947.3 25 50 SARS-CoV-2_1_LEFT 1 + AACAAACCAACCAACTTTCGATCTC
+MN908947.3 408 431 SARS-CoV-2_1_RIGHT 1 - CTTCTACTAAGCCACAAGTGCCA
+MN908947.3 324 344 SARS-CoV-2_2_LEFT 2 + TTTACAGGTTCGCGACGTGC
+MN908947.3 705 727 SARS-CoV-2_2_RIGHT 2 - ATAAGGATCAGTGCCAAGCTCG
+MN908947.3 644 666 SARS-CoV-2_3_LEFT 1 + GTAATAAAGGAGCTGGTGGCCA
+MN908947.3 1017 1044 SARS-CoV-2_3_RIGHT 1 - GCCAATTTAATTTCAAAAGGTGTCTGC
+MN908947.3 944 966 SARS-CoV-2_4_LEFT 2 + GTGTATACTGCTGCCGTGAACA
+MN908947.3 1337 1362 SARS-CoV-2_4_RIGHT 2 - ACAACAGCATTTTGGGGTAAGTAAC
+MN908947.3 1245 1266 SARS-CoV-2_5_LEFT 1 + TGAAACTTCATGGCAGACGGG
+MN908947.3 1623 1650 SARS-CoV-2_5_RIGHT 1 - TTGATGTTGACTTTCTCTTTTTGGAGT
+MN908947.3 1540 1562 SARS-CoV-2_6_LEFT 2 + CGTGCTAGCGCTAACATAGGTT
+MN908947.3 1925 1948 SARS-CoV-2_6_RIGHT 2 - AACACGCACAGAATTTTGAGCAG
+MN908947.3 1851 1875 SARS-CoV-2_7_LEFT 1 + ACTGAGTCCTCTTTATGCATTTGC
+MN908947.3 2228 2250 SARS-CoV-2_7_RIGHT 1 - CCACCGACAATTTCACAAGCAC
+MN908947.3 2154 2180 SARS-CoV-2_8_LEFT 2 + GCTTGAAGAGAAGTTTAAGGAAGGTG
+MN908947.3 2544 2571 SARS-CoV-2_8_RIGHT 2 - GGTTGTTCTAATGGTTGTAAATCACCA
+MN908947.3 2483 2508 SARS-CoV-2_9_LEFT 1 + TCTTCTTAGAGGGAGAAACACTTCC
+MN908947.3 2861 2885 SARS-CoV-2_9_RIGHT 1 - CACAGGCGAACTCATTTACTTCTG
+MN908947.3 2826 2850 SARS-CoV-2_10_LEFT 2 + TGAGAAGTGCTCTGCCTATACAGT
+MN908947.3 3183 3210 SARS-CoV-2_10_RIGHT 2 - TCATCTAACCAATCTTCTTCTTGCTCT
+MN908947.3 3078 3102 SARS-CoV-2_11_LEFT 1 + AGAAGAGTTTGAGCCATCAACTCA
+MN908947.3 3470 3492 SARS-CoV-2_11_RIGHT 1 - TTTAAGGCTCCTGCAACACCTC
+MN908947.3 3390 3412 SARS-CoV-2_12_LEFT 2 + TGCAGACATTGTGGAAGAAGCT
+MN908947.3 3769 3794 SARS-CoV-2_12_RIGHT 2 - CAGCTAAGTAGACATTTGTGCGAAC
+MN908947.3 3683 3705 SARS-CoV-2_13_LEFT 1 + AGCACGAAGTTCTACTTGCACC
+MN908947.3 4067 4093 SARS-CoV-2_13_RIGHT 1 - GATGTCAATGTCACTAACAAGAGTGG
+MN908947.3 3992 4018 SARS-CoV-2_14_LEFT 2 + TGGAAGAAACTAAGTTCCTCACAGAA
+MN908947.3 4387 4409 SARS-CoV-2_14_RIGHT 2 - CATGTGCAAGCATTTCTCGCAA
+MN908947.3 4312 4339 SARS-CoV-2_15_LEFT 1 + AAAAGTGCCTTTTACATTCTACCATCT
+MN908947.3 4685 4710 SARS-CoV-2_15_RIGHT 1 - GCATCAGGTGAAGAAACAGAAACTG
+MN908947.3 4620 4648 SARS-CoV-2_16_LEFT 2 + TGTAACACATGGCTTAAATTTGGAAGAA
+MN908947.3 4995 5017 SARS-CoV-2_16_RIGHT 2 - CACAACTTGCGTGTGGAGGTTA
+MN908947.3 4923 4953 SARS-CoV-2_17_LEFT 1 + TGACAATCTTAAGACACTTCTTTCTTTGAG
+MN908947.3 5302 5331 SARS-CoV-2_17_RIGHT 1 - TTCAACTCTATTTGTTGGAGTGTTAACAA
+MN908947.3 5230 5259 SARS-CoV-2_18_LEFT 2 + TGGAAATACCCACAAGTTAATGGTTTAAC
+MN908947.3 5620 5643 SARS-CoV-2_18_RIGHT 2 - GCTTGTTTACCACACGTACAAGG
+MN908947.3 5561 5584 SARS-CoV-2_19_LEFT 1 + AAGCTGTTATGTACATGGGCACA
+MN908947.3 5932 5957 SARS-CoV-2_19_RIGHT 1 - TGTCCAACTTAGGGTCAATTTCTGT
+MN908947.3 5867 5894 SARS-CoV-2_20_LEFT 2 + ACAAAGAAAACAGTTACACAACAACCA
+MN908947.3 6247 6272 SARS-CoV-2_20_RIGHT 2 - ACGTGGCTTTATTAGTTGCATTGTT
+MN908947.3 6184 6210 SARS-CoV-2_21_LEFT 1 + CACTACACACCCTCTTTTAAGAAAGG
+MN908947.3 6553 6582 SARS-CoV-2_21_RIGHT 1 - GTAAGACTAGAATTGTCTACATAAGCAGC
+MN908947.3 6478 6507 SARS-CoV-2_22_LEFT 2 + GTAGGAGACATTATACTTAAACCAGCAAA
+MN908947.3 6859 6885 SARS-CoV-2_22_RIGHT 2 - CCGACACTCTTAACAGTATTCTTTGC
+MN908947.3 6747 6776 SARS-CoV-2_23_LEFT 1 + AAACCGTGTTTGTACTAATTATATGCCTT
+MN908947.3 7122 7148 SARS-CoV-2_23_RIGHT 1 - AACCACTAAGACAAACACTACAAGGT
+MN908947.3 7057 7084 SARS-CoV-2_24_LEFT 2 + GGTTACAGAGAAGGCTATTTGAACTCT
+MN908947.3 7440 7467 SARS-CoV-2_24_RIGHT 2 - ACAACATGCACATAACTTTTCCATACA
+MN908947.3 7381 7403 SARS-CoV-2_25_LEFT 1 + CAAATGGCCCCGATTTCAGCTA
+MN908947.3 7747 7770 SARS-CoV-2_25_RIGHT 1 - TGGATGGAACCATTCTTCACTGT
+MN908947.3 7672 7695 SARS-CoV-2_26_LEFT 2 + GCGAGAGACTTGTCACTACAGTT
+MN908947.3 8063 8092 SARS-CoV-2_26_RIGHT 2 - GAGTTTTTCCATTGGTACGTTAAAAGTTG
+MN908947.3 7997 8019 SARS-CoV-2_27_LEFT 1 + CTGATGTTGGTGATAGTGCGGA
+MN908947.3 8370 8395 SARS-CoV-2_27_RIGHT 1 - AGCAATGTTGTGACTTTTTGCTACC
+MN908947.3 8304 8326 SARS-CoV-2_28_LEFT 2 + TGAAAACATGACACCCCGTGAC
+MN908947.3 8691 8714 SARS-CoV-2_28_RIGHT 2 - TGACACCACCATCAATAGCCTTG
+MN908947.3 8596 8619 SARS-CoV-2_29_LEFT 1 + CTTGTGTTCCTTTTTGTTGCTGC
+MN908947.3 8990 9013 SARS-CoV-2_29_RIGHT 1 - AGCCAAAACACAAGCTGATGTTG
+MN908947.3 8919 8944 SARS-CoV-2_30_LEFT 2 + ACCTAGAGTTTTTAGTGCAGTTGGT
+MN908947.3 9306 9329 SARS-CoV-2_30_RIGHT 2 - CTACACCACAGAAAACTCCTGGT
+MN908947.3 9168 9192 SARS-CoV-2_31_LEFT 1 + CCTTGAAGGTTCTGTTAGAGTGGT
+MN908947.3 9535 9564 SARS-CoV-2_31_RIGHT 1 - AATGAGTAAACTGGTGTTAAACAGAGTAC
+MN908947.3 9470 9497 SARS-CoV-2_32_LEFT 2 + GAGCTTTTGGTGAATACAGTCATGTAG
+MN908947.3 9842 9866 SARS-CoV-2_32_RIGHT 2 - GAGGTAATAGCACATCACTACGCA
+MN908947.3 9782 9805 SARS-CoV-2_33_LEFT 1 + GTACTTTTGAAGAAGCTGCGCTG
+MN908947.3 10150 10176 SARS-CoV-2_33_RIGHT 1 - TGTCTTGGACAGTAAACTACGTCATC
+MN908947.3 10076 10099 SARS-CoV-2_34_LEFT 2 + TCCCATCTGGTAAAGTTGAGGGT
+MN908947.3 10465 10491 SARS-CoV-2_34_RIGHT 2 - CCACATGAACCATTAAGGAATGAACC
+MN908947.3 10393 10419 SARS-CoV-2_35_LEFT 1 + GTGTTAGCTTGTTACAATGGTTCACC
+MN908947.3 10785 10810 SARS-CoV-2_35_RIGHT 1 - AGGTCCTAGTATGTCAACATGGTCT
+MN908947.3 10713 10742 SARS-CoV-2_36_LEFT 2 + CAATCGATTTACCACAACTCTTAATGACT
+MN908947.3 11092 11116 SARS-CoV-2_36_RIGHT 2 - ACCCATAGCAAAAGGTAAAAAGGC
+MN908947.3 11000 11023 SARS-CoV-2_37_LEFT 1 + CACACCACTGGTTGTTACTCACA
+MN908947.3 11388 11414 SARS-CoV-2_37_RIGHT 1 - GTGTCAAGACATTCATAAGTGTCCAC
+MN908947.3 11305 11330 SARS-CoV-2_38_LEFT 2 + GACTGTGTTATGTATGCATCAGCTG
+MN908947.3 11689 11720 SARS-CoV-2_38_RIGHT 2 - CCTGTGTAGAAACTAAGTAATCATAAACACC
+MN908947.3 11624 11651 SARS-CoV-2_39_LEFT 1 + GCTATTTTTGTACTTGTTACTTTGGCC
+MN908947.3 12011 12033 SARS-CoV-2_39_RIGHT 1 - CCCTGCATGGAAAGCAAAACAG
+MN908947.3 11937 11963 SARS-CoV-2_40_LEFT 2 + TGTCCAGTTACACAATGACATTCTCT
+MN908947.3 12317 12339 SARS-CoV-2_40_RIGHT 2 - ACTTTTGCCCTCTTGTCCTCAG
+MN908947.3 12234 12255 SARS-CoV-2_41_LEFT 1 + ATTTGACCGTGATGCAGCCAT
+MN908947.3 12618 12643 SARS-CoV-2_41_RIGHT 1 - AAGAGGCCATGCTAAATTAGGTGAA
+MN908947.3 12519 12546 SARS-CoV-2_42_LEFT 2 + TGGTACAACATTTACTTATGCATCAGC
+MN908947.3 12895 12920 SARS-CoV-2_42_RIGHT 2 - TGTCTGTAACAAACCTACAAGGTGG
+MN908947.3 12831 12856 SARS-CoV-2_43_LEFT 1 + GGATTTGAAATGGGCTAGATTCCCT
+MN908947.3 13218 13240 SARS-CoV-2_43_RIGHT 1 - CGATGCACCACCAAAGGATTCT
+MN908947.3 13124 13148 SARS-CoV-2_44_LEFT 2 + GGGGACAACCAATCACTAATTGTG
+MN908947.3 13506 13528 SARS-CoV-2_44_RIGHT 2 - CATCAGTACTAGTGCCTGTGCC
+MN908947.3 13463 13485 SARS-CoV-2_45_LEFT 1 + TAAACGGGTTTGCGGTGTAAGT
+MN908947.3 13833 13859 SARS-CoV-2_45_RIGHT 1 - TCACAATTACCTTCATCAAAATGCCT
+MN908947.3 13752 13775 SARS-CoV-2_46_LEFT 2 + AGAATAGACGGTGACATGGTACC
+MN908947.3 14120 14144 SARS-CoV-2_46_RIGHT 2 - TCTACAACAGGAACTCCACTACCT
+MN908947.3 14045 14075 SARS-CoV-2_47_LEFT 1 + TGGTGTACTGACATTAGATAATCAAGATCT
+MN908947.3 14428 14457 SARS-CoV-2_47_RIGHT 1 - TGGAACACCATCAACAAATATTTTTCTCA
+MN908947.3 14338 14362 SARS-CoV-2_48_LEFT 2 + ACTGTTTGGATGACAGATGCATTC
+MN908947.3 14717 14743 SARS-CoV-2_48_RIGHT 2 - CAGAACTTCCTTCCTTAAAGAAACCC
+MN908947.3 14647 14674 SARS-CoV-2_49_LEFT 1 + ACAATGTTGCTTTTCAAACTGTCAAAC
+MN908947.3 15023 15050 SARS-CoV-2_49_RIGHT 1 - GGGATGACATTACGTTTTGTATATGCG
+MN908947.3 14953 14983 SARS-CoV-2_50_LEFT 2 + CATTTAATAAATGGGGTAAGGCTAGACTTT
+MN908947.3 15336 15358 SARS-CoV-2_50_RIGHT 2 - GAGCAAGAACAAGTGAGGCCAT
+MN908947.3 15214 15237 SARS-CoV-2_51_LEFT 1 + GCAAATTCTATGGTGGTTGGCAC
+MN908947.3 15596 15619 SARS-CoV-2_51_RIGHT 1 - GTCTGTGTTGTAAATTGCGGACA
+MN908947.3 15535 15557 SARS-CoV-2_52_LEFT 2 + CTGTCACGGCCAATGTTAATGC
+MN908947.3 15917 15941 SARS-CoV-2_52_RIGHT 2 - GGATCTGGGTAAGGAAGGTACACA
+MN908947.3 15855 15881 SARS-CoV-2_53_LEFT 1 + ACTAAAGGACCTCATGAATTTTGCTC
+MN908947.3 16239 16260 SARS-CoV-2_53_RIGHT 1 - GCAAAGAACACAAGCCCCAAC
+MN908947.3 16112 16137 SARS-CoV-2_54_LEFT 2 + ACATGATGAGTTAACAGGACACATG
+MN908947.3 16483 16508 SARS-CoV-2_54_RIGHT 2 - CCAAAAACTTGTCCATTAGCACACA
+MN908947.3 16386 16408 SARS-CoV-2_55_LEFT 1 + AATGCTCCAGGTTGTGATGTCA
+MN908947.3 16767 16796 SARS-CoV-2_55_RIGHT 1 - ACACGATAACCAGTAAAGACATAATTTCG
+MN908947.3 16692 16714 SARS-CoV-2_56_LEFT 2 + ACTGTACGTGAAGTGCTGTCTG
+MN908947.3 17082 17105 SARS-CoV-2_56_RIGHT 2 - TGACTCTTACCAGTACCAGGTGG
+MN908947.3 16986 17013 SARS-CoV-2_57_LEFT 1 + GGCTTATACCCAACACTCAATATCTCA
+MN908947.3 17381 17405 SARS-CoV-2_57_RIGHT 1 - CTGGCATTGACAACACTCAAATCA
+MN908947.3 17323 17345 SARS-CoV-2_58_LEFT 2 + TGCCTGAGACGACAGCAGATAT
+MN908947.3 17688 17711 SARS-CoV-2_58_RIGHT 2 - TGTGGCCTGTTAATTGCAGATGA
+MN908947.3 17615 17642 SARS-CoV-2_59_LEFT 1 + GCTTAAAGCACATAAAGACAAATCAGC
+MN908947.3 17997 18022 SARS-CoV-2_59_RIGHT 1 - TCCTACGTGGAATTTCAAGACTTGT
+MN908947.3 17911 17939 SARS-CoV-2_60_LEFT 2 + ACAGATTTAATGTTGCTATTACCAGAGC
+MN908947.3 18307 18328 SARS-CoV-2_60_RIGHT 2 - TAGCATGACACCCCTCGACAT
+MN908947.3 18244 18267 SARS-CoV-2_61_LEFT 1 + ACCCTAACATGTTTATCACCCGC
+MN908947.3 18624 18652 SARS-CoV-2_61_RIGHT 1 - GCTCAGGTCCTATTTTCACAAAATACTT
+MN908947.3 18550 18578 SARS-CoV-2_62_LEFT 2 + GTGACACACTTAAAAATCTCTCTGACAG
+MN908947.3 18936 18961 SARS-CoV-2_62_RIGHT 2 - CCGCATTAATCTTCAGTTCATCACC
+MN908947.3 18869 18891 SARS-CoV-2_63_LEFT 1 + TAGGTGTCTAGCTGTCCACGAG
+MN908947.3 19252 19277 SARS-CoV-2_63_RIGHT 1 - CCAGGCAAGTTAAGGTTAGATAGCA
+MN908947.3 19183 19208 SARS-CoV-2_64_LEFT 2 + GCCTATTTTGGAATTGCAATGTCGA
+MN908947.3 19558 19586 SARS-CoV-2_64_RIGHT 2 - GTATCAAATTGTTTGTAAACCCACAAGC
+MN908947.3 19485 19513 SARS-CoV-2_65_LEFT 1 + GTCTGTAGACATCATGCTAATGAGTACA
+MN908947.3 19877 19901 SARS-CoV-2_65_RIGHT 1 - GCTGGAGCATCTCTTTTGTAGTCC
+MN908947.3 19810 19836 SARS-CoV-2_66_LEFT 2 + AACCAGTACCAGAGGTGAAAATACTC
+MN908947.3 20186 20216 SARS-CoV-2_66_RIGHT 2 - TTTCTACTCTGAGTAAAGTAAGTTTCAGGT
+MN908947.3 20090 20117 SARS-CoV-2_67_LEFT 1 + CAAACAAGCTAGTCTTAATGGAGTCAC
+MN908947.3 20472 20497 SARS-CoV-2_67_RIGHT 1 - AACACACACACTTAGATGAACCTGT
+MN908947.3 20377 20405 SARS-CoV-2_68_LEFT 2 + GACTAGCTAAACGTTTTAAGGAATCACC
+MN908947.3 20766 20792 SARS-CoV-2_68_RIGHT 2 - GCGACATTCATCATTATGCCTTTAGG
+MN908947.3 20677 20699 SARS-CoV-2_69_LEFT 1 + CGGGTGTTGCTATGCCTAATCT
+MN908947.3 21050 21080 SARS-CoV-2_69_RIGHT 1 - TTTGTAACATTTTTAGTCTTAGGGTCGTAC
+MN908947.3 20988 21013 SARS-CoV-2_70_LEFT 2 + TTGATTGGTGATTGTGCAACTGTAC
+MN908947.3 21358 21387 SARS-CoV-2_70_RIGHT 2 - AGAATAGGAAGACAACTGAATTGGATTTG
+MN908947.3 21294 21316 SARS-CoV-2_71_LEFT 1 + GGCAAACCACGCGAACAAATAG
+MN908947.3 21675 21700 SARS-CoV-2_71_RIGHT 1 - TGAGGATCTGAAAACTTTGTCAGGG
+MN908947.3 21532 21561 SARS-CoV-2_72_LEFT 2 + GTGATGTTCTTGTTAACAACTAAACGAAC
+MN908947.3 21904 21933 SARS-CoV-2_72_RIGHT 2 - GTAGCGTTATTAACAATAAGTAGGGACTG
+MN908947.3 21865 21889 SARS-CoV-2_73_LEFT 1 + AGAGGCTGGATTTTTGGTACTACT
+MN908947.3 22247 22274 SARS-CoV-2_73_RIGHT 1 - ACCTAGTGATGTTAATACCTATTGGCA
+MN908947.3 22091 22113 SARS-CoV-2_74_LEFT 2 + TGGACCTTGAAGGAAAACAGGG
+MN908947.3 22474 22503 SARS-CoV-2_74_RIGHT 2 - TGATAGATTCCTTTTTCTACAGTGAAGGA
+MN908947.3 22402 22428 SARS-CoV-2_75_LEFT 1 + GAAAATGGAACCATTACAGATGCTGT
+MN908947.3 22785 22805 SARS-CoV-2_75_RIGHT 1 - TTTGCCCTGGAGCGATTTGT
+MN908947.3 22648 22677 SARS-CoV-2_76_LEFT 2 + GCTGATTATTCTGTCCTATATAATTCCGC
+MN908947.3 23028 23057 SARS-CoV-2_76_RIGHT 2 - GTTGGAAACCATATGATTGTAAAGGAAAG
+MN908947.3 22944 22974 SARS-CoV-2_77_LEFT 1 + CAAACCTTTTGAGAGAGATATTTCAACTGA
+MN908947.3 23327 23351 SARS-CoV-2_77_RIGHT 1 - CACTGACACCACCAAAAGAACATG
+MN908947.3 23219 23246 SARS-CoV-2_78_LEFT 2 + CTGAGTCTAACAAAAAGTTTCTGCCTT
+MN908947.3 23611 23635 SARS-CoV-2_78_RIGHT 2 - GGATTGACTAGCTACACTACGTGC
+MN908947.3 23553 23575 SARS-CoV-2_79_LEFT 1 + ACCCATTGGTGCAGGTATATGC
+MN908947.3 23927 23955 SARS-CoV-2_79_RIGHT 1 - CCAAAATCTTTAATTGGTGGTGTTTTGT
+MN908947.3 23853 23876 SARS-CoV-2_80_LEFT 2 + CCGTGCTTTAACTGGAATAGCTG
+MN908947.3 24233 24258 SARS-CoV-2_80_RIGHT 2 - GCAAATGGTATTTGTAATGCAGCAC
+MN908947.3 24171 24194 SARS-CoV-2_81_LEFT 1 + TGCTCAATACACTTCTGCACTGT
+MN908947.3 24545 24567 SARS-CoV-2_81_RIGHT 1 - TGAAGTCTGCCTGTGATCAACC
+MN908947.3 24426 24448 SARS-CoV-2_82_LEFT 2 + TGCACAAGCTTTAAACACGCTT
+MN908947.3 24814 24836 SARS-CoV-2_82_RIGHT 2 - CACGAGGAAAGTGTGCTTTTCC
+MN908947.3 24750 24772 SARS-CoV-2_83_LEFT 1 + GCATGTGACTTATGTCCCTGCA
+MN908947.3 25122 25150 SARS-CoV-2_83_RIGHT 1 - AGATTCATTTAAATTCTTGGCAACCTCA
+MN908947.3 25051 25076 SARS-CoV-2_84_LEFT 2 + GTTGATTTAGGTGACATCTCTGGCA
+MN908947.3 25438 25461 SARS-CoV-2_84_RIGHT 2 - AGCATCCTTGATTTCACCTTGCT
+MN908947.3 25331 25353 SARS-CoV-2_85_LEFT 1 + ATGAAGACGACTCTGAGCCAGT
+MN908947.3 25711 25740 SARS-CoV-2_85_RIGHT 1 - CTGCAAGAAGTAGACTAAAGCATAAAGAT
+MN908947.3 25645 25672 SARS-CoV-2_86_LEFT 2 + TGTTGTTTGTAACAGTTTACTCACACC
+MN908947.3 26026 26050 SARS-CoV-2_86_RIGHT 2 - TCAATTGAGTTGAGTACAGCTGGT
+MN908947.3 25951 25979 SARS-CoV-2_87_LEFT 1 + GTGGTTATACTGAAAAATGGGAATCTGG
+MN908947.3 26338 26360 SARS-CoV-2_87_RIGHT 1 - AATCGAAGCGCAGTAAGGATGG
+MN908947.3 26255 26277 SARS-CoV-2_88_LEFT 2 + CGTTTCGGAAGAGACAGGTACG
+MN908947.3 26635 26661 SARS-CoV-2_88_RIGHT 2 - ACAAAAACCTATTCCTGTTGGCATAG
+MN908947.3 26564 26587 SARS-CoV-2_89_LEFT 1 + AAGCTCCTTGAACAATGGAACCT
+MN908947.3 26956 26979 SARS-CoV-2_89_RIGHT 1 - CAGCAATACGAAGATGTCCACGA
+MN908947.3 26873 26895 SARS-CoV-2_90_LEFT 2 + ATTCTTCTCAACGTGCCACTCC
+MN908947.3 27256 27283 SARS-CoV-2_90_RIGHT 2 - TCCAAATGGAAACTTTAAAAGTCCTCA
+MN908947.3 27152 27177 SARS-CoV-2_91_LEFT 1 + TCCAGTAGCAGTGACAATATTGCTT
+MN908947.3 27534 27560 SARS-CoV-2_91_RIGHT 1 - AGTGCAAATTTGTTATCAGCTAGAGG
+MN908947.3 27447 27473 SARS-CoV-2_92_LEFT 2 + CACTACCAAGAGTGTGTTAGAGGTAC
+MN908947.3 27826 27855 SARS-CoV-2_92_RIGHT 2 - GTTCAAGTGAGAACCAAAAGATAATAAGC
+MN908947.3 27700 27726 SARS-CoV-2_93_LEFT 1 + TTGTTGCGGCAATAGTGTTTATAACA
+MN908947.3 28082 28104 SARS-CoV-2_93_RIGHT 1 - TGGGTGATTTAGAACCAGCCTC
+MN908947.3 27996 28021 SARS-CoV-2_94_LEFT 2 + ACCCGTGTCCTATTCACTTCTATTC
+MN908947.3 28394 28416 SARS-CoV-2_94_RIGHT 2 - TTATTGGGTAAACCTTGGGGCC
+MN908947.3 28190 28214 SARS-CoV-2_95_LEFT 1 + GTGCGTTGTTCGTTCTATGAAGAC
+MN908947.3 28572 28598 SARS-CoV-2_95_RIGHT 1 - ACCATCTTGGACTGAGATCTTTCATT
+MN908947.3 28512 28536 SARS-CoV-2_96_LEFT 2 + AGATGACCAAATTGGCTACTACCG
+MN908947.3 28893 28914 SARS-CoV-2_96_RIGHT 2 - CCATTGCCAGCCATTCTAGCA
+MN908947.3 28827 28849 SARS-CoV-2_97_LEFT 1 + TTCCTCATCACGTAGTCGCAAC
+MN908947.3 29206 29227 SARS-CoV-2_97_RIGHT 1 - CGACATTCCGAAGAACGCTGA
+MN908947.3 29136 29161 SARS-CoV-2_98_LEFT 2 + CCAGGAACTAATCAGACAAGGAACT
+MN908947.3 29512 29534 SARS-CoV-2_98_RIGHT 2 - TTTAGGCCTGAGTTGAGTCAGC
+MN908947.3 29452 29475 SARS-CoV-2_99_LEFT 1 + CTTCTTCCTGCTGCAGATTTGGA
+MN908947.3 29827 29854 SARS-CoV-2_99_RIGHT 1 - GCTATTAAAATCACATGGGGATAGCAC
diff --git a/resources/primers_schemes/bed/nCoV-2019/V5.3.2/SARS-CoV-2.primer.bed b/resources/primers_schemes/bed/nCoV-2019/V5.3.2/SARS-CoV-2.primer.bed
new file mode 100644
index 0000000..b4e9c18
--- /dev/null
+++ b/resources/primers_schemes/bed/nCoV-2019/V5.3.2/SARS-CoV-2.primer.bed
@@ -0,0 +1,192 @@
+MN908947.3 47 78 SARS-CoV-2_400_1_LEFT_1 1 + CTCTTGTAGATCTGTTCTCTAAACGAACTTT
+MN908947.3 419 447 SARS-CoV-2_400_1_RIGHT_1 1 - AAAACGCCTTTTTCAACTTCTACTAAGC
+MN908947.3 344 366 SARS-CoV-2_400_2_LEFT_0 2 + TCGTACGTGGCTTTGGAGACTC
+MN908947.3 707 732 SARS-CoV-2_400_2_RIGHT_0 2 - TCTTCATAAGGATCAGTGCCAAGCT
+MN908947.3 638 661 SARS-CoV-2_400_3_LEFT_1 1 + AGAACGGTAATAAAGGAGCTGGT
+MN908947.3 1018 1047 SARS-CoV-2_400_3_RIGHT_0 1 - TTTGCCAATTTAATTTCAAAAGGTGTCTG
+MN908947.3 970 995 SARS-CoV-2_400_4_LEFT_0 2 + CATGAAATTGCTTGGTACACGGAAC
+MN908947.3 1340 1370 SARS-CoV-2_400_4_RIGHT_0 2 - AAATTTTAACAACAGCATTTTGGGGTAAGT
+MN908947.3 1292 1320 SARS-CoV-2_400_5_LEFT_0 1 + TTTGTGGCACTGAGAATTTGACTAAAGA
+MN908947.3 1660 1692 SARS-CoV-2_400_5_RIGHT_0 1 - ATAATGGCGATCTCTTCATTAAGTTTAAAGTC
+MN908947.3 1574 1596 SARS-CoV-2_400_6_LEFT_1 2 + GTGTTGTTGGAGAAGGTTCCGA
+MN908947.3 1945 1972 SARS-CoV-2_400_6_RIGHT_1 2 - TATTGTTATAGCGGCCTTCTGTAAAAC
+MN908947.3 1882 1905 SARS-CoV-2_400_7_LEFT_2 1 + GCTGCTCGTGTTGTACGATCAAT
+MN908947.3 2259 2284 SARS-CoV-2_400_7_RIGHT_2 1 - CTCCTTAATTTCCTTTGCACAGGTG
+MN908947.3 2229 2252 SARS-CoV-2_400_8_LEFT_0 2 + TGCTTGTGAAATTGTCGGTGGAC
+MN908947.3 2603 2629 SARS-CoV-2_400_8_RIGHT_0 2 - AAGCCCGTTAATACAAACTGGTGTAC
+MN908947.3 2533 2563 SARS-CoV-2_400_9_LEFT_0 1 + GTCTTGAAAACTGGTGATTTACAACCATTA
+MN908947.3 2900 2933 SARS-CoV-2_400_9_RIGHT_0 1 - GTAATTCAGATACTGGTTGCAAAGTTTTTATGA
+MN908947.3 2854 2880 SARS-CoV-2_400_10_LEFT_0 2 + CTCGGTACAGAAGTAAATGAGTTCGC
+MN908947.3 3233 3254 SARS-CoV-2_400_10_RIGHT_0 2 - TGTCCTCACTGCCGTCTTGTT
+MN908947.3 3184 3213 SARS-CoV-2_400_11_LEFT_0 1 + GAGCAAGAAGAAGATTGGTTAGATGATGA
+MN908947.3 3560 3584 SARS-CoV-2_400_11_RIGHT_0 1 - CGCTTAAAACACAACTACCACCCA
+MN908947.3 3510 3540 SARS-CoV-2_400_12_LEFT_0 2 + CATGCAAGTTGAATCTGATGATTACATAGC
+MN908947.3 3883 3913 SARS-CoV-2_400_12_RIGHT_0 2 - AGTTATAAATGGCTTAACTTCCTCTTTAGG
+MN908947.3 3791 3824 SARS-CoV-2_400_13_LEFT_0 1 + CTGTCTTTGATAAAAATCTCTATGACAAACTTG
+MN908947.3 4147 4180 SARS-CoV-2_400_13_RIGHT_0 1 - CTTTTTAGTAGGTATAACCACAGCAGTTAAAAC
+MN908947.3 4079 4108 SARS-CoV-2_400_14_LEFT_0 2 + GTGACATTGACATCACTTTCTTAAAGAAA
+MN908947.3 4457 4488 SARS-CoV-2_400_14_RIGHT_0 2 - CCCTTATATTTACGCTGTATAGTTGAAACTA
+MN908947.3 4403 4425 SARS-CoV-2_400_15_LEFT_0 1 + CACATGCAGAAGAAACACGCAA
+MN908947.3 4776 4803 SARS-CoV-2_400_15_RIGHT_0 1 - TCTTTATAGGAACCAGCAAGTGAGATG
+MN908947.3 4723 4756 SARS-CoV-2_400_16_LEFT_0 2 + AATGGTTATCTTACTTCTTCTTCTAAAACACCT
+MN908947.3 5089 5119 SARS-CoV-2_400_16_RIGHT_0 2 - AAATGTTTTACCTTCATGTGAATTATGAGG
+MN908947.3 5036 5063 SARS-CoV-2_400_17_LEFT_0 1 + GACAACAGTTTGGTCCAACTTATTTGG
+MN908947.3 5398 5429 SARS-CoV-2_400_17_RIGHT_0 1 - CTGTCTTATTACAGTAGGCTAAGATAAGTGC
+MN908947.3 5344 5370 SARS-CoV-2_400_18_LEFT_0 2 + GCTCTACAAGATGCTTATTACAGAGC
+MN908947.3 5716 5744 SARS-CoV-2_400_18_RIGHT_0 2 - ACTCACTAGCACAAGTAAATGTACCATG
+MN908947.3 5671 5696 SARS-CoV-2_400_19_LEFT_0 1 + CCTTTTGTTATGATGTCAGCACCAC
+MN908947.3 6031 6062 SARS-CoV-2_400_19_RIGHT_0 1 - CACATACAAACTTAAAATTATCGAAGCTTGC
+MN908947.3 5891 5923 SARS-CoV-2_400_20_LEFT_0 2 + CCATAAAACCAGTTACTTATAAATTGGATGGT
+MN908947.3 6257 6288 SARS-CoV-2_400_20_RIGHT_0 2 - CAGGTATTTGGTTTATACGTGGCTTTATTAG
+MN908947.3 6204 6237 SARS-CoV-2_400_21_LEFT_0 1 + GAAAGGAGCTAAATTGTTACATAAACCTATTGT
+MN908947.3 6562 6595 SARS-CoV-2_400_21_RIGHT_0 1 - AGGTTTCTTAATAGTAAGACTAGAATTGTCTAC
+MN908947.3 6515 6542 SARS-CoV-2_400_22_LEFT_0 2 + TAAAAATTACAGAAGAGGTTGGCCACA
+MN908947.3 6882 6915 SARS-CoV-2_400_22_RIGHT_0 2 - TAATTAAATGAAGCCTCTAGACAAAATTTACCG
+MN908947.3 6823 6854 SARS-CoV-2_400_23_LEFT_0 1 + AATTCTAGAATTAAAGCATCTATGCCGACTA
+MN908947.3 7199 7229 SARS-CoV-2_400_23_RIGHT_0 1 - CAAAAGCAGTTAAATCCCATTTAAAAGATG
+MN908947.3 7145 7179 SARS-CoV-2_400_24_LEFT_0 2 + GTTTAGATTCTTTAGACACCTATCCTTCTTTAGA
+MN908947.3 7518 7545 SARS-CoV-2_400_24_RIGHT_0 2 - ACAATAGTTGTACATTCGACTCTTGTT
+MN908947.3 7456 7482 SARS-CoV-2_400_25_LEFT_0 1 + GTGCATGTTGTAGACGGTTGTAATTC
+MN908947.3 7819 7850 SARS-CoV-2_400_25_RIGHT_0 1 - CTCTCAGGTTGTCTAAGTTAACAAAATGAGA
+MN908947.3 7768 7797 SARS-CoV-2_400_26_LEFT_0 2 + CATCTTTACTTTGATAAAGCTGGTCAAAA
+MN908947.3 8136 8169 SARS-CoV-2_400_26_RIGHT_0 2 - GAAATAAAAGTAGATAAGACATTGTCTAAGGAC
+MN908947.3 8085 8112 SARS-CoV-2_400_27_LEFT_0 1 + AAAACTCAAAACACTAGTTGCAACTGC
+MN908947.3 8468 8498 SARS-CoV-2_400_27_RIGHT_0 1 - CACATGTCAACTTAAAAGGTAAGTTATTCT
+MN908947.3 8406 8436 SARS-CoV-2_400_28_LEFT_0 2 + CGTTAAAGATTTCATGTCATTGTCTGAACA
+MN908947.3 8781 8806 SARS-CoV-2_400_28_RIGHT_0 2 - ATTAGTATAACTACCACCACGCTGG
+MN908947.3 8732 8761 SARS-CoV-2_400_29_LEFT_0 1 + CAGATACTTGTTTTGCTAACAAACATGCT
+MN908947.3 9107 9129 SARS-CoV-2_400_29_RIGHT_0 1 - ACATAACGTGTGTCAGGGCGTA
+MN908947.3 9023 9052 SARS-CoV-2_400_30_LEFT_0 2 + CAATTTTTAAAGATGCTTCTGGTAAGCCA
+MN908947.3 9397 9423 SARS-CoV-2_400_30_RIGHT_0 2 - ACAATACCACCAGCTACTATAGATGC
+MN908947.3 9299 9324 SARS-CoV-2_400_31_LEFT_1 1 + GATCTTTACCAGGAGTTTTCTGTGG
+MN908947.3 9673 9706 SARS-CoV-2_400_31_RIGHT_0 1 - ACAAATGATATAAGCAATTGTTATCCAGAAAGG
+MN908947.3 9571 9604 SARS-CoV-2_400_32_LEFT_0 2 + GGTGTTTATTCTGTTATTTACTTGTACTTGACA
+MN908947.3 9949 9971 SARS-CoV-2_400_32_RIGHT_0 2 - TTGCGAGATGACAACAAGCAGC
+MN908947.3 9896 9929 SARS-CoV-2_400_33_LEFT_0 1 + ATAATAAGTACAAGTATTTTAGTGGAGCAATGG
+MN908947.3 10266 10295 SARS-CoV-2_400_33_RIGHT_0 1 - AATGTCCAATAACCCTGAGTTGAACATTA
+MN908947.3 10215 10245 SARS-CoV-2_400_34_LEFT_0 2 + TGAAGATTTACTCATTCGTAAGTCTAATCA
+MN908947.3 10587 10615 SARS-CoV-2_400_34_RIGHT_0 2 - GTCAACAAAAGGTCCATAAAAGTTACCT
+MN908947.3 10527 10557 SARS-CoV-2_400_35_LEFT_0 1 + TTTTTGTTACATGCACCATATGGAATTACC
+MN908947.3 10897 10927 SARS-CoV-2_400_35_RIGHT_0 1 - AAATTCATCTTCTAATAAAGCACTACCCAA
+MN908947.3 10832 10865 SARS-CoV-2_400_36_LEFT_0 2 + CCGTTTTAGATATGTGTGCTTCATTAAAAGAAT
+MN908947.3 11201 11232 SARS-CoV-2_400_36_RIGHT_0 2 - GGCATATAGACCATATTAAAATAAGCTACAG
+MN908947.3 11152 11181 SARS-CoV-2_400_37_LEFT_0 1 + AAACATAAGCATGCATTTCTCTGTTTGTT
+MN908947.3 11514 11536 SARS-CoV-2_400_37_RIGHT_0 1 - ACCTCTGGCCAAAAACATGACA
+MN908947.3 11463 11494 SARS-CoV-2_400_38_LEFT_0 2 + GTGGGCTCTTATAATCTCTGTTACTTCTAAC
+MN908947.3 11832 11863 SARS-CoV-2_400_38_RIGHT_0 2 - CTTTACATCTGACATTTTAGACTGTACAGTG
+MN908947.3 11785 11811 SARS-CoV-2_400_39_LEFT_0 1 + AACATTAAATTGTTGGGTGTTGGTGG
+MN908947.3 12161 12185 SARS-CoV-2_400_39_RIGHT_0 1 - CAGAATCACCATTAGCAACAGCCT
+MN908947.3 12112 12137 SARS-CoV-2_400_40_LEFT_0 2 + TCCCTTCCATCATATGCAGCTTTTG
+MN908947.3 12477 12510 SARS-CoV-2_400_40_RIGHT_0 2 - TTTTTATATGTGTTATAGTCTGGTATGACAACC
+MN908947.3 12419 12444 SARS-CoV-2_400_41_LEFT_0 1 + CAAGAGATGGTTGTGTTCCCTTGAA
+MN908947.3 12794 12819 SARS-CoV-2_400_41_RIGHT_0 1 - AACAGTGCAAGTACAAACCTACCTC
+MN908947.3 12752 12774 SARS-CoV-2_400_42_LEFT_0 2 + GCACTGATGACAATGCGTTAGC
+MN908947.3 13121 13146 SARS-CoV-2_400_42_RIGHT_0 2 - CAATTAGTGATTGGTTGTCCCCCAC
+MN908947.3 13075 13099 SARS-CoV-2_400_43_LEFT_0 1 + GCTTTTGCTGTAGATGCTGCTAAA
+MN908947.3 13458 13480 SARS-CoV-2_400_43_RIGHT_0 1 - CACCGCAAACCCGTTTAAAAAC
+MN908947.3 13415 13435 SARS-CoV-2_400_44_LEFT_0 2 + ATCAACTCCGCGAACCCATG
+MN908947.3 13787 13815 SARS-CoV-2_400_44_RIGHT_0 2 - TGCCATTGTGTATTTAGTAAGACGTTGA
+MN908947.3 13738 13767 SARS-CoV-2_400_45_LEFT_0 1 + ACTTCTTTAAGTTTAGAATAGACGGTGAC
+MN908947.3 14120 14144 SARS-CoV-2_400_45_RIGHT_0 1 - TCTACAACAGGAACTCCACTACCT
+MN908947.3 14073 14100 SARS-CoV-2_400_46_LEFT_0 2 + CTCAATGGTAACTGGTATGATTTCGGT
+MN908947.3 14427 14457 SARS-CoV-2_400_46_RIGHT_0 2 - TGGAACACCATCAACAAATATTTTTCTCAC
+MN908947.3 14375 14407 SARS-CoV-2_400_47_LEFT_0 1 + CTTTAATGTTTTATTCTCTACAGTGTTCCCAC
+MN908947.3 14745 14775 SARS-CoV-2_400_47_RIGHT_0 1 - ATCCTGAGCAAAGAAGAAGTGTTTTAATTC
+MN908947.3 14700 14725 SARS-CoV-2_400_48_LEFT_0 2 + GACTTTGCTGTGTCTAAGGGTTTCT
+MN908947.3 15065 15095 SARS-CoV-2_400_48_RIGHT_0 2 - TTCTTTGCACTAATGGCATACTTAAGATTC
+MN908947.3 15016 15045 SARS-CoV-2_400_49_LEFT_0 1 + CACTTTTCGCATATACAAAACGTAATGTC
+MN908947.3 15386 15416 SARS-CoV-2_400_49_RIGHT_0 1 - CACTCATTAGCTAATCTATAGAAACGGTGT
+MN908947.3 15342 15366 SARS-CoV-2_400_50_LEFT_0 2 + TCACTTGTTCTTGCTCGCAAACAT
+MN908947.3 15716 15742 SARS-CoV-2_400_50_RIGHT_0 2 - TATTGAAACACACAACAGCATCGTCA
+MN908947.3 15659 15688 SARS-CoV-2_400_51_LEFT_0 1 + CTTTGTGAATGAGTTTTACGCATATTTGC
+MN908947.3 16028 16059 SARS-CoV-2_400_51_RIGHT_0 1 - AGGATGTTTAGTAAGTGGGTAAGCATCTATA
+MN908947.3 15992 16018 SARS-CoV-2_400_52_LEFT_2 2 + TGGTACACTTATGATTGAACGGTTCG
+MN908947.3 16386 16409 SARS-CoV-2_400_52_RIGHT_2 2 - GTGACATCACAACCTGGAGCATT
+MN908947.3 16285 16311 SARS-CoV-2_400_53_LEFT_0 1 + GTGCTTGCATACGTAGACCATTCTTA
+MN908947.3 16650 16679 SARS-CoV-2_400_53_RIGHT_0 1 - GACAGTTTAAATGTCTCCTCAGTAGCTTT
+MN908947.3 16624 16647 SARS-CoV-2_400_54_LEFT_1 2 + TCAAGCTTTTTGCAGCAGAAACG
+MN908947.3 17004 17033 SARS-CoV-2_400_54_RIGHT_1 2 - ACATTGCTAGAAAACTCATCTGAGATATT
+MN908947.3 16962 16994 SARS-CoV-2_400_55_LEFT_1 1 + CAAGAGCACTATGTTAGAATTACTGGCTTATA
+MN908947.3 17333 17362 SARS-CoV-2_400_55_RIGHT_1 1 - TTTCATCAAAGACAACTATATCTGCTGTC
+MN908947.3 17182 17212 SARS-CoV-2_400_56_LEFT_0 2 + CACTATGTGAGAAGGCATTAAAATATTTGC
+MN908947.3 17560 17582 SARS-CoV-2_400_56_RIGHT_0 2 - ACAATTTCAGCAGGACAACGCC
+MN908947.3 17478 17507 SARS-CoV-2_400_57_LEFT_0 1 + GGCACACTAGAACCAGAATATTTCAATTC
+MN908947.3 17859 17886 SARS-CoV-2_400_57_RIGHT_0 1 - AGTGGTTTGAGTGAATATGACATAGTC
+MN908947.3 17813 17839 SARS-CoV-2_400_58_LEFT_0 2 + GGGACTACCAACTCAAACTGTTGATT
+MN908947.3 18181 18212 SARS-CoV-2_400_58_RIGHT_0 2 - ATCATAGAGATGAGTCTTCTATAGGTCATGT
+MN908947.3 18121 18153 SARS-CoV-2_400_59_LEFT_0 1 + GTGTTGACACTAAATTCAAAACTGAAGGTTTA
+MN908947.3 18504 18527 SARS-CoV-2_400_59_RIGHT_0 1 - CGCACTACATTCCAAGGAAGTCC
+MN908947.3 18460 18484 SARS-CoV-2_400_60_LEFT_0 2 + CGCCTGGAGATCAATTTAAACACC
+MN908947.3 18835 18860 SARS-CoV-2_400_60_RIGHT_0 2 - GCATCACAACTAGCTACATGTGCAT
+MN908947.3 18789 18815 SARS-CoV-2_400_61_LEFT_0 1 + GGTAACCTACAAAGCAACCATGATCT
+MN908947.3 19170 19195 SARS-CoV-2_400_61_RIGHT_0 1 - TCCAAAATAGGCATACACCATCTGT
+MN908947.3 19087 19112 SARS-CoV-2_400_62_LEFT_2 2 + TCTATGATGCACAGCCTTGTAGTGA
+MN908947.3 19469 19495 SARS-CoV-2_400_62_RIGHT_0 2 - GTCTACAGACAGCACCACCTAAATTG
+MN908947.3 19415 19449 SARS-CoV-2_400_63_LEFT_0 1 + AGTGTCAGATATAGATTATGTACCACTAAAGTCT
+MN908947.3 19770 19796 SARS-CoV-2_400_63_RIGHT_0 1 - GCCCAAAGCTCAAATGCTACATTAAC
+MN908947.3 19721 19750 SARS-CoV-2_400_64_LEFT_0 2 + AGTTGATGGTGTTGATGTAGAATTGTTTG
+MN908947.3 20091 20121 SARS-CoV-2_400_64_RIGHT_0 2 - TAATGTGACTCCATTAAGACTAGCTTGTTT
+MN908947.3 20028 20054 SARS-CoV-2_400_65_LEFT_0 1 + GCCCGTAATGGTGTTCTTATTACAGA
+MN908947.3 20408 20441 SARS-CoV-2_400_65_RIGHT_0 1 - GTACTGTCCATAGGAATAAAATCTTCTAATTCA
+MN908947.3 20358 20388 SARS-CoV-2_400_66_LEFT_0 2 + GGTTTACATCTACTGATTGGACTAGCTAAA
+MN908947.3 20729 20758 SARS-CoV-2_400_66_RIGHT_0 2 - CACTATCACCATAATTTTGAAGGTCACAC
+MN908947.3 20650 20676 SARS-CoV-2_400_67_LEFT_1 1 + AATTACAATCTAGTCAAGCGTGGCAA
+MN908947.3 21018 21051 SARS-CoV-2_400_67_RIGHT_1 1 - CATATCACTAATAATGAGATCCCATTTATTAGC
+MN908947.3 20991 21018 SARS-CoV-2_400_68_LEFT_0 2 + ATTGGTGATTGTGCAACTGTACATACA
+MN908947.3 21372 21402 SARS-CoV-2_400_68_RIGHT_0 2 - ACTCATGTCAAATAAAGAATAGGAAGACAA
+MN908947.3 21322 21352 SARS-CoV-2_400_69_LEFT_0 1 + ATGTCATGCATGCAAATTACATATTTTGGA
+MN908947.3 21696 21722 SARS-CoV-2_400_69_RIGHT_0 1 - AGTCCTGAGTTGAATGTAAAACTGAG
+MN908947.3 21579 21607 SARS-CoV-2_400_70_LEFT_0 2 + TTTATTGCCACTAGTCTCTAGTCAGTGT
+MN908947.3 21927 21960 SARS-CoV-2_400_70_RIGHT_0 2 - AATTCACAGACTTTAATAACAACATTAGTAGCG
+MN908947.3 21866 21894 SARS-CoV-2_400_71_LEFT_0 1 + GAGGCTGGATTTTTGGTACTACTTTAGA
+MN908947.3 22238 22266 SARS-CoV-2_400_71_RIGHT_0 1 - ATGTTAATACCTATTGGCAAATCTACCA
+MN908947.3 22156 22189 SARS-CoV-2_400_72_LEFT_0 2 + GGTTATTTTAAAATATATTCTAAGCACACGCCT
+MN908947.3 22517 22547 SARS-CoV-2_400_72_RIGHT_0 2 - ATCTAACAATAGATTCTGTTGGTTGGACTC
+MN908947.3 22466 22494 SARS-CoV-2_400_73_LEFT_0 1 + CGTTGAAATCCTTCACTGTAGAAAAAGG
+MN908947.3 22839 22866 SARS-CoV-2_400_73_RIGHT_0 1 - GCTATAACGCAGCCTGTAAAATCATCT
+MN908947.3 22742 22774 SARS-CoV-2_400_74_LEFT_0 2 + ATGTCTATGCAGATTCATTTGTAATTAGAGGT
+MN908947.3 23119 23140 SARS-CoV-2_400_74_RIGHT_0 2 - TCCACAAACAGTTGCTGGTGC
+MN908947.3 23078 23109 SARS-CoV-2_400_75_LEFT_1 1 + AACCATACAGAGTAGTAGTACTTTCTTTTGA
+MN908947.3 23452 23478 SARS-CoV-2_400_75_RIGHT_1 1 - CCTGTAGAATAAACACGCCAAGTAGG
+MN908947.3 23229 23258 SARS-CoV-2_400_76_LEFT_0 2 + CAAAAAGTTTCTGCCTTTCCAACAATTTG
+MN908947.3 23609 23631 SARS-CoV-2_400_76_RIGHT_0 2 - TGACTAGCTACACTACGTGCCC
+MN908947.3 23563 23589 SARS-CoV-2_400_77_LEFT_0 1 + GCAGGTATATGCGCTAGTTATCAGAC
+MN908947.3 23914 23944 SARS-CoV-2_400_77_RIGHT_0 1 - AATTGGTGGTGTTTTGTAAATTTGTTTGAC
+MN908947.3 23823 23853 SARS-CoV-2_400_78_LEFT_0 2 + GCAATATGGCAGTTTTTGTACACAATTAAA
+MN908947.3 24209 24231 SARS-CoV-2_400_78_RIGHT_0 2 - GCACCAAAGGTCCAACCAGAAG
+MN908947.3 24160 24189 SARS-CoV-2_400_79_LEFT_0 1 + GATGAAATGATTGCTCAATACACTTCTGC
+MN908947.3 24535 24560 SARS-CoV-2_400_79_RIGHT_0 1 - TGCCTGTGATCAACCTATCAATTTG
+MN908947.3 24442 24468 SARS-CoV-2_400_80_LEFT_0 2 + ACGCTTGTTAAACAACTTAGCTCCAA
+MN908947.3 24815 24839 SARS-CoV-2_400_80_RIGHT_0 2 - CTTCACGAGGAAAGTGTGCTTTTC
+MN908947.3 24751 24774 SARS-CoV-2_400_81_LEFT_0 1 + CATGTGACTTATGTCCCTGCACA
+MN908947.3 25120 25151 SARS-CoV-2_400_81_RIGHT_0 1 - GAGATTCATTTAAATTCTTGGCAACCTCATT
+MN908947.3 25053 25082 SARS-CoV-2_400_82_LEFT_0 2 + TGATTTAGGTGACATCTCTGGCATTAATG
+MN908947.3 25423 25452 SARS-CoV-2_400_82_RIGHT_0 2 - GATTTCACCTTGCTTCAAAGTTACAGTTC
+MN908947.3 25372 25402 SARS-CoV-2_400_83_LEFT_0 1 + CATTACACATAAACGAACTTATGGATTTGT
+MN908947.3 25744 25777 SARS-CoV-2_400_83_RIGHT_0 1 - GCCAAAGCCTCATTATTATTCTTACAAAGTTTA
+MN908947.3 25653 25680 SARS-CoV-2_400_84_LEFT_2 2 + GTAACAGTTTACTCACACCTTTTGCTC
+MN908947.3 26048 26072 SARS-CoV-2_400_84_RIGHT_2 2 - TGTTCAACACCARTGTCTGTACTC
+MN908947.3 26011 26039 SARS-CoV-2_400_85_LEFT_0 1 + TCACTTCAGACTATTACCAGCTGTACTC
+MN908947.3 26382 26411 SARS-CoV-2_400_85_RIGHT_0 1 - AAAGAAGGTTTTACAAGACTCACGTTAAC
+MN908947.3 26339 26362 SARS-CoV-2_400_86_LEFT_0 2 + CATCCTTACTGCGCTTCGATTGT
+MN908947.3 26730 26756 SARS-CoV-2_400_86_RIGHT_0 2 - ACCGGTGATCCAATTTATTCTGTAAA
+MN908947.3 26593 26621 SARS-CoV-2_400_87_LEFT_1 1 + AGGTTTCCTATTCCTTACATGGATTTGT
+MN908947.3 26989 27009 SARS-CoV-2_400_87_RIGHT_1 1 - CCTTGATGTCACAGCGTCCT
+MN908947.3 26958 26981 SARS-CoV-2_400_88_LEFT_2 2 + GTGGACATCTTCGTATTGCTGGA
+MN908947.3 27349 27376 SARS-CoV-2_400_88_RIGHT_2 2 - CCATTGGTTGCTCTTCATCTAATTGAG
+MN908947.3 27200 27226 SARS-CoV-2_400_89_LEFT_2 1 + GATGTTTCATCTCGTTGACTTTCAGG
+MN908947.3 27583 27603 SARS-CoV-2_400_89_RIGHT_0 1 - GCCGTCAGGACAAGCAAAAG
+MN908947.3 27530 27558 SARS-CoV-2_400_90_LEFT_0 2 + TCATCCTCTAGCTGATAACAAATTTGCA
+MN908947.3 27927 27950 SARS-CoV-2_400_90_RIGHT_0 2 - TTCTTGGTGAAATGCAGCTACAG
+MN908947.3 27832 27860 SARS-CoV-2_400_91_LEFT_0 1 + TATCTTTTGGTTCTCACTTGAACTGCAA
+MN908947.3 28209 28237 SARS-CoV-2_400_91_RIGHT_0 1 - CGAACGTCATGATACTCTAAAAAGTCTT
+MN908947.3 28135 28166 SARS-CoV-2_400_92_LEFT_0 2 + TTCCTGTTTACCTTTTACAATTAATTGCCAG
+MN908947.3 28513 28539 SARS-CoV-2_400_92_RIGHT_0 2 - CTTCGGTAGTAGCCAATTTGGTCATC
+MN908947.3 28473 28493 SARS-CoV-2_400_93_LEFT_0 1 + TCGAGGACAAGGCGTTCCAA
+MN908947.3 28849 28873 SARS-CoV-2_400_93_RIGHT_0 1 - GCCTGGAGTTGAATTTCTTGAACT
+MN908947.3 28808 28829 SARS-CoV-2_400_94_LEFT_0 2 + GCAGTCAAGCCTCTTCTCGTT
+MN908947.3 29203 29224 SARS-CoV-2_400_94_RIGHT_0 2 - CATTCCGAAGAACGCTGAAGC
+MN908947.3 29159 29183 SARS-CoV-2_400_95_LEFT_0 1 + CTGATTACAAACATTGGCCGCAAA
+MN908947.3 29538 29559 SARS-CoV-2_400_95_RIGHT_0 1 - ATCTGCCTTGTGTGGTCTGCA
+MN908947.3 29462 29486 SARS-CoV-2_400_96_LEFT_1 2 + CTGCAGATTTGGATGATTTCTCCA
+MN908947.3 29840 29873 SARS-CoV-2_400_96_RIGHT_0 2 - TTTGTCATTCTCCTAAGAAGCTATTAAAATCAC
\ No newline at end of file
diff --git a/resources/primers/bed/.gitkeep b/resources/primers_schemes/bedpe/.gitkeep
similarity index 100%
rename from resources/primers/bed/.gitkeep
rename to resources/primers_schemes/bedpe/.gitkeep
diff --git a/resources/primers/bedpe/Ebola-virus_Zaire_AF-272001-1_artic-primers-V2.bedpe b/resources/primers_schemes/bedpe/Ebola-virus_Zaire_AF-272001-1_artic-primers-V2.bedpe
similarity index 100%
rename from resources/primers/bedpe/Ebola-virus_Zaire_AF-272001-1_artic-primers-V2.bedpe
rename to resources/primers_schemes/bedpe/Ebola-virus_Zaire_AF-272001-1_artic-primers-V2.bedpe
diff --git a/resources/primers/bedpe/Ebola-virus_Zaire_KR-063671-1_artic-primers-V1.bedpe b/resources/primers_schemes/bedpe/Ebola-virus_Zaire_KR-063671-1_artic-primers-V1.bedpe
similarity index 100%
rename from resources/primers/bedpe/Ebola-virus_Zaire_KR-063671-1_artic-primers-V1.bedpe
rename to resources/primers_schemes/bedpe/Ebola-virus_Zaire_KR-063671-1_artic-primers-V1.bedpe
diff --git a/resources/primers/bedpe/Ebola-virus_Zaire_KR-063671-1_artic-primers-V3.bedpe b/resources/primers_schemes/bedpe/Ebola-virus_Zaire_KR-063671-1_artic-primers-V3.bedpe
similarity index 100%
rename from resources/primers/bedpe/Ebola-virus_Zaire_KR-063671-1_artic-primers-V3.bedpe
rename to resources/primers_schemes/bedpe/Ebola-virus_Zaire_KR-063671-1_artic-primers-V3.bedpe
diff --git a/resources/primers/bedpe/Nipah-virus_Malaysia_AJ-564622-1_artic-primers-V1.bedpe b/resources/primers_schemes/bedpe/Nipah-virus_Malaysia_AJ-564622-1_artic-primers-V1.bedpe
similarity index 100%
rename from resources/primers/bedpe/Nipah-virus_Malaysia_AJ-564622-1_artic-primers-V1.bedpe
rename to resources/primers_schemes/bedpe/Nipah-virus_Malaysia_AJ-564622-1_artic-primers-V1.bedpe
diff --git a/resources/primers/bedpe/SARS-CoV-2_Wuhan_MN-908947-3_artic-primers-V1.bedpe b/resources/primers_schemes/bedpe/SARS-CoV-2_Wuhan_MN-908947-3_artic-primers-V1.bedpe
similarity index 100%
rename from resources/primers/bedpe/SARS-CoV-2_Wuhan_MN-908947-3_artic-primers-V1.bedpe
rename to resources/primers_schemes/bedpe/SARS-CoV-2_Wuhan_MN-908947-3_artic-primers-V1.bedpe
diff --git a/resources/primers/bedpe/SARS-CoV-2_Wuhan_MN-908947-3_artic-primers-V2.bedpe b/resources/primers_schemes/bedpe/SARS-CoV-2_Wuhan_MN-908947-3_artic-primers-V2.bedpe
similarity index 100%
rename from resources/primers/bedpe/SARS-CoV-2_Wuhan_MN-908947-3_artic-primers-V2.bedpe
rename to resources/primers_schemes/bedpe/SARS-CoV-2_Wuhan_MN-908947-3_artic-primers-V2.bedpe
diff --git a/resources/primers/bedpe/SARS-CoV-2_Wuhan_MN-908947-3_artic-primers-V3.bedpe b/resources/primers_schemes/bedpe/SARS-CoV-2_Wuhan_MN-908947-3_artic-primers-V3.bedpe
similarity index 100%
rename from resources/primers/bedpe/SARS-CoV-2_Wuhan_MN-908947-3_artic-primers-V3.bedpe
rename to resources/primers_schemes/bedpe/SARS-CoV-2_Wuhan_MN-908947-3_artic-primers-V3.bedpe
diff --git a/resources/primers/bedpe/SARS-CoV-2_Wuhan_MN-908947-3_artic-primers-V4-1.bedpe b/resources/primers_schemes/bedpe/SARS-CoV-2_Wuhan_MN-908947-3_artic-primers-V4-1.bedpe
similarity index 100%
rename from resources/primers/bedpe/SARS-CoV-2_Wuhan_MN-908947-3_artic-primers-V4-1.bedpe
rename to resources/primers_schemes/bedpe/SARS-CoV-2_Wuhan_MN-908947-3_artic-primers-V4-1.bedpe
diff --git a/resources/primers/bedpe/SARS-CoV-2_Wuhan_MN-908947-3_artic-primers-V4.bedpe b/resources/primers_schemes/bedpe/SARS-CoV-2_Wuhan_MN-908947-3_artic-primers-V4.bedpe
similarity index 100%
rename from resources/primers/bedpe/SARS-CoV-2_Wuhan_MN-908947-3_artic-primers-V4.bedpe
rename to resources/primers_schemes/bedpe/SARS-CoV-2_Wuhan_MN-908947-3_artic-primers-V4.bedpe
diff --git a/workflow/Snakefile b/workflow/Snakefile
index db6dfd0..aff4e43 100644
--- a/workflow/Snakefile
+++ b/workflow/Snakefile
@@ -8,19 +8,20 @@
### ###
###I###R###D######U###2###3###3#######T###R###A###N###S###V###I###H###M###I####
# Name ___________________ gevarli.smk
-# Version ________________ v.2025.01
+# Version ________________ v.2025.04
# Author _________________ Nicolas Fernandez
# Affiliation ____________ IRD_U233_TransVIHMI
# Aim ____________________ Snakefile running GeVarLi rules
# Date ___________________ 2021.10.12
-# Latest modifications ___ 2025.03.12
-# Use ____________________ snakemake -s Snakefile --use-conda -j
+# Latest modifications ___ 2025.04.04
+# Use ____________________ snakemake -s Snakefile --use-conda
###############################################################################
###############################################################################
### CONFIGURATION ###
#####################
+# Config file
configfile: "config/config.yaml"
###############################################################################
@@ -34,36 +35,40 @@ from snakemake.utils import min_version
from snakemake.utils import validate
from scripts.functions import get_valid_fastq
-from scripts.functions import get_final_outputs
+from scripts.functions import get_settings
from scripts.functions import get_bam_input
from scripts.functions import get_bai_input
+from scripts.functions import get_final_outputs
+from scripts.functions import get_time
# Local
FASTQ_DIR = config["fastq_dir"]
-VALID_FASTQ = get_valid_fastq(FASTQ_DIR)
+VALID_FASTQ, SAMPLE_WARNINGS = get_valid_fastq(FASTQ_DIR)
SAMPLE = list(VALID_FASTQ.keys())
MATE = ["1", "2"]
START_TIME = time.time()
# Exports
import scripts.functions as functions
+functions.FASTQ_DIR = FASTQ_DIR
+functions.SAMPLE_WARNINGS = SAMPLE_WARNINGS
functions.SAMPLE = SAMPLE
functions.MATE = MATE
+functions.START_TIME = START_TIME
functions.MODULES = config["modules"] # Modules
-functions.REFERENCE = config["consensus"]["reference"] # Genome reference sequence, in fasta format
-functions.QC_REF = config["fastq_screen"]["reference"] # FastqScreen config file genomes to index
-functions.MAPPER = config["consensus"]["mapper"] # Mapper ('bwa' 'minimap2' 'bowtie2')
-functions.MIN_COV = config["consensus"]["min_cov"] # Minimum coverage, mask lower regions with 'N'
-functions.CALLER = config["consensus"]["caller"] # Variants caller ('ivar')
-functions.ASSIGNER = config["consensus"]["assigner"] # Tools ('nextclade' 'pangolin')
-
+functions.MAPPER = config["tools"]["mapper"] # Reads mapper ('bwa', 'minimap2' or 'bowtie2')
+functions.CALLER = config["tools"]["caller"] # Variants caller ('ivar' or 'ivar')
+functions.ASSIGNER = config["tools"]["assigner"] # Lineages assigner ('nextclade' or 'pangolin')
+functions.REFERENCE = config["reference"] # Genome reference sequence, in fasta format
+functions.MIN_DEPTH = config["consensus"]["min_depth"] # Minimum depth to call consensus, mark lower regions with 'N'
+functions.QC_REF = config["fastq_screen"]["reference"] # FastqScreen config file genomes to index
functions.STAT_EXT = config["report"]["stat"]["extention"] # Stat reports extentions ('txt' 'tsv' 'json')
# Snakemake version
-min_version("8.27.0")
+min_version("9.1.3")
# Schemas
-validate(config, schema="schemas/config.schema.yaml")
+#validate(config, schema="schemas/config.schema.yaml")
###############################################################################
### WILDCARDS ###
@@ -84,7 +89,6 @@ TMP_DIR = config["resources"]["tmp_dir"] # Temporary directory
### ENVIRONMENTS ###
####################
-YQ = config["envs"]["yq"] # YQ conda environment
FASTQ_SCREEN = config["envs"]["fastq_screen"] # Fastq-Screen conda environment
FASTQC= config["envs"]["fastqc"] # FastQC conda environment
CUTADAPT = config["envs"]["cutadapt"] # Cutadapt conda environment
@@ -96,7 +100,7 @@ SAMTOOLS = config["envs"]["samtools"] # SamTools conda environment
BEDTOOLS = config["envs"]["bedtools"] # BedTools conda environment
BAMCLIPPER = config["envs"]["bamclipper"] # BAMClipper onda environment
GAWK = config["envs"]["gawk"] # Awk (GNU) conda environment
-IVAR = config["envs"]["ivar"] # iVar conda environment
+IVAR = config["envs"] # iVar conda environment
TSV2VCF = config["envs"]["tsv2vcf"] # tsv2vcf conda environment
BCFTOOLS = config["envs"]["bcftools"] # BcfTools conda environment
PANGOLIN = config["envs"]["pangolin"] # Pangolin conda environment
@@ -108,65 +112,55 @@ WORKFLOW = config["envs"]["workflow"] # Workflow conda environment
### PARAMETERS ###
##################
-SUBSET = config["fastq_screen"]["subset"] # Fastq-Screen --subset
+MAPPER = config["tools"]["mapper"] # Mapper ('bwa', 'minimap2' or 'bowtie2')
+CALLER = config["tools"]["caller"] # Variant Caller ('ivar' or 'ivar')
+ASSIGNER = config["tools"]["assigner"] # Lineage assigner ('nextclade' or 'pangolin')
+REFERENCE = config["reference"] # Genome reference sequence, in fasta format
+
+FQC_SUBSET = config["fastq_screen"]["subset"] # Fastq-Screen --subset
FQC_CONFIG = config["fastq_screen"]["config"] # Fastq-Screen --conf
#MQC_PATH = config["multiqc"]["path"] # MultiQC --conf
#MQC_CONF = config["multiqc"]["config"] # MultiQC --conf
#TAG = config["multiqc"]["tag"] # MultiQC --tag
-KMER_SIZE = config["minimap2"]["algorithm"]["k-mer_size"] # MM2 k-mer size
-MINIMIZER_SIZE = config["minimap2"]["algorithm"]["minimizer_size"] # MM2 minimizer window size
-SPLIT_SIZE = config["minimap2"]["algorithm"]["split_size"] # MM2 split index
-#HOMOPOLYMER = config["minimap2"]["algorithm"]["homopolymer"] # MM2 if PacBio
-
-BWA_ALGO = config["bwa"]["algorithm"] # BWA indexing algorithm
-BT2_ALGO = config["bowtie2"]["algorithm"] # BT2 indexing algorithm
-
-#REFERENCE = config["consensus"]["reference"] # Genome reference sequence, in fasta format
-MIN_COV = config["consensus"]["min_cov"] # Minimum coverage, mask lower regions with 'N'
-IUPAC = config["consensus"]["iupac"] # Output variants in the form of IUPAC ambiguity codes
-MAPPER = config["consensus"]["mapper"] # Mapper ('minimap2', 'bwa' or 'bowtie2')
-CALLER = config["consensus"]["caller"] # Variant Caller ('lofreq' or 'ivar')
-ASSIGNER = config["consensus"]["assigner"] # Lineage assigner ('nextclade' or 'pangolin')
-
-CUT_LENGTH = config["cutadapt"]["length"] # Cutadapt --minimum-length
-CUT_TRUSEQ = config["cutadapt"]["kits"]["truseq"] # Cutadapt --adapter Illumina TruSeq
-CUT_NEXTERA = config["cutadapt"]["kits"]["nextera"] # Cutadapt --adapter Illumina Nextera
-CUT_SMALL = config["cutadapt"]["kits"]["small"] # Cutadapt --adapter Illumina Small
CUT_CLIPPING = config["cutadapt"]["clipping"] # Cutadapt --cut
+CUT_LENGTH = config["cutadapt"]["length"] # Cutadapt --minimum-length
+CUT_ADAPTERS = config["cutadapt"]["adapters"] # Cutadapt --adapter
SIC_COMMAND = config["sickle_trim"]["command"] # Sickle-trim command
SIC_ENCODING = config["sickle_trim"]["encoding"] # Sickle-trim --qual-type
SIC_QUALITY = config["sickle_trim"]["quality"] # Sickle-trim --qual-threshold
SIC_LENGTH = config["sickle_trim"]["length"] # Sickle-trim --length-treshold
-MM2_PRESET = config["minimap2"]["preset"] # Minimap2 preset
-#MM2_LENGTH = config["minimap2"]["length"] # Minimap2 length
-#MM2_KMER_SIZE = config["minimap2"]["algorithm"]["k-mer_size"] # Minimap2 k-mer size
-#MM2_MINIMIZER_SIZE = config["minimap2"]["algorithm"]["minimizer_size"] # Minimap2 minimizer window size
-#MM2_SPLIT_SIZE = config["minimap2"]["algorithm"]["split_size"] # Minimap2 split index
-#MM2_HOMOPOLYMER = config["minimap2"]["algorithm"]["homopolymer"] # Minimap2 for PacBio
-
BWA_ALGO = config["bwa"]["algorithm"] # BWA indexing algorithm
+MM2_KMER_SIZE = config["minimap2"]["algorithm"]["k-mer_size"] # MM2 k-mer size
+MM2_MINIMIZER_SIZE = config["minimap2"]["algorithm"]["minimizer_size"] # MM2 minimizer window size
+MM2_SPLIT_SIZE = config["minimap2"]["algorithm"]["split_size"] # MM2 split index
+MM2_PRESET = config["minimap2"]["preset"] # Minimap2 presetv # MM2 preset
+#MM2_LENGTH = config["minimap2"]["length"] # Minimap2 length
+#MM2_HOMOPOLYMER = config["minimap2"]["algorithm"]["homopolymer"] # MM2 homopolymer if PacBio
+
BT2_ALGO = config["bowtie2"]["algorithm"] # Bowtie2 indexing algorithm
BT2_SENSITIVITY = config["bowtie2"]["sensitivity"] # Bowtie2 sensitivity preset
-CLIPPATH = config["bamclipper"]["path"] # Bamclipper path to primers
-PRIMERS = config["bamclipper"]["primers"] # Bamclipper primers bed files
-UPSTREAM = config["bamclipper"]["upstream"] # Bamclipper upstream nucleotides
-DOWNSTREAM = config["bamclipper"]["downstream"] # Bamclipper downstream nucleotides
-
-IVAR_MIN_DEPTH = config["consensus"]["min_cov"] # iVar
-IVAR_MIN_FREQ = config["consensus"]["min_freq"] # iVar minimum allele frequency allowed
-IVAR_MIN_INSERT = config["consensus"]["min_freq"] # iVar minimum insertion frequency allowed
-#IVAR_MIN_DEPTH = config["ivar"]["min_depth"] # iVar
-#IVAR_MIN_FREQ = config["ivar"]["min_freq"] # iVar minimum allele frequency allowed
-#IVAR_MIN_INSERT = config["ivar"]["min_insert"] # iVar minimum insertion frequency allowed
-IVAR_MAX_DEPTH = config["ivar"]["max_depth"] # iVar
-IVAR_MIN_BQ = config["ivar"]["min_bq"] # iVar
-IVAR_MIN_QUAL = config["ivar"]["min_qual"] # iVar
-IVAR_MAP_QUAL = config["ivar"]["map_qual"] # iVar mapping quality
+IVAR_OFFSET = config["primers"]["offset"] # iVar offset
+IVAR_MIN_LENGTH = config["primers"]["min_length"] # iVar minimum length
+IVAR_MIN_QUAL = config["primers"]["min_qual"] # iVar minimum quality
+IVAR_SLIDE = config["primers"]["slide"] # iVar slide windows
+
+PRIMER_BED_PATH = config["primers"]["bed"]["path"] # primer kit bed path
+PRIMER_BED_SCHEME = config["primers"]["bed"]["scheme"] # primer kit bed scheme
+PRIMER_BEDPE_PATH = config["primers"]["bedpe"]["path"] # primer kit bedpe path
+PRIMER_BEDPE_SCHEME = config["primers"]["bedpe"]["scheme"] # primer kit bedpe scheme
+
+MIN_DEPTH = config["consensus"]["min_depth"] # iVar minimum depth
+IVAR_MIN_FREQ = config["consensus"]["min_freq"] # iVar minimum allele frequency
+IVAR_MIN_INSERT = config["consensus"]["min_insert"] # iVar minimum insert frequency
+IVAR_MAX_DEPTH = config["consensus"]["max_depth"] # iVar maximum depth
+IVAR_MIN_BQ = config["consensus"]["min_bq"] # iVar minimum base quality
+IVAR_MIN_QUAL = config["consensus"]["min_qual"] # iVar minimum mapping quality
+IVAR_MAP_QUAL = config["consensus"]["map_qual"] # iVar minimum mapping quality
NEXT_PATH = config["nextclade"]["path"] # Path to nextclade dataset
NEXT_DATASET = config["nextclade"]["dataset"] # Nextclade dataset
@@ -178,7 +172,7 @@ GRAPH_EXT = config["report"]["graph"]["extention"]
### LOAD RULES ###
##################
-include: "rules/symlinks_renamming.smk"
+include: "rules/samples_prep.smk"
include: "rules/quality_controls.smk"
include: "rules/reads_cleanning.smk"
include: "rules/genomes_indexing.smk"
@@ -200,6 +194,31 @@ include: "rules/workflow_reporting.smk"
rule all:
input:
- tarball = "results/Reports_archive.tar.gz"
+ html_report = "results/10_Reports/workflow-report.html"
+
+###############################################################################
+### HOOKS ###
+#############
+
+onstart:
+ print("onstart")
+ get_settings(config, START_TIME)
+
+onsuccess:
+ print("onsuccess")
+ get_time(START_TIME)
+ shell("mkdir -p results/10_Reports/envs/ 2> /dev/null")
+ shell("cp workflow/envs/*.yaml results/10_Reports/envs/ 2> /dev/null")
+ shell("cp config/config.yaml results/10_Reports/config.log 2> /dev/null")
+ shell("tar -zfc results/Reports_archive.tar.gz -C results/ 10_Reports/")
+
+onerror:
+ print("onerror")
+ get_time(START_TIME)
+ shell("mkdir -p results/10_Reports/envs/ 2> /dev/null")
+ shell("cp workflow/envs/*.yaml results/10_Reports/envs/ 2> /dev/null")
+ shell("cp config/config.yaml results/10_Reports/config.log 2> /dev/null")
+ shell("tar -zfc results/Reports_archive.tar.gz -C results/ 10_Reports/")
###############################################################################
+###############################################################################
\ No newline at end of file
diff --git a/workflow/envs/workflow-core.yaml b/workflow/envs/workflow-core.yaml
index f1d7366..ec05646 100644
--- a/workflow/envs/workflow-core.yaml
+++ b/workflow/envs/workflow-core.yaml
@@ -4,10 +4,9 @@ channels:
- bioconda
- nodefaults
dependencies:
- - snakemake=8.27.1
+ - snakemake=9.1.3
- snakedeploy=0.10.3
- snakemake-executor-plugin-slurm
- snakemake-interface-report-plugins
- snakemake-interface-storage-plugins
- - graphviz=12.0.0
- - yq=3.4.3
\ No newline at end of file
+ - graphviz=12.0.0
\ No newline at end of file
diff --git a/workflow/envs/yq_v.3.4.3.yaml b/workflow/envs/yq_v.3.4.3.yaml
deleted file mode 100644
index 03f2662..0000000
--- a/workflow/envs/yq_v.3.4.3.yaml
+++ /dev/null
@@ -1,7 +0,0 @@
-name: yq
-channels:
- - conda-forge
- - bioconda
- - nodefaults
-dependencies:
- - yq=3.4.3
\ No newline at end of file
diff --git a/workflow/rules/consensus_calling.smk b/workflow/rules/consensus_calling.smk
index 4d9d031..d6e9c81 100644
--- a/workflow/rules/consensus_calling.smk
+++ b/workflow/rules/consensus_calling.smk
@@ -8,43 +8,15 @@
### ###
###I###R###D######U###2###3###3#######T###R###A###N###S###V###I###H###M###I####
# Name ___________________ consensus_calling.smk
-# Version ________________ v.2025.01
+# Version ________________ v.2025.04
# Author _________________ Nicolas Fernandez
# Affiliation ____________ IRD_U233_TransVIHMI
# Aim ____________________ Call a consensus genome
# Date ___________________ 2021.10.12
-# Latest modifications ___ 2025.03.12
-# Use ____________________ snakemake -s Snakefile --use-conda -j
+# Latest modifications ___ 2025.04.04
+# Use ____________________ snakemake -s Snakefile --use-conda
###############################################################################
-###############################################################################
-rule sed_rename_headers:
- # Aim: rename all fasta header with sample name
- # Use: sed 's/[OLD]/[NEW]/' [IN] > [OUT]
- message:
- """
- ~ Sed ∞ Rename Fasta Header ~
- Sample: __________ {wildcards.sample}
- Reference: _______ {wildcards.reference}
- Mapper: __________ {wildcards.mapper}
- Min. cov.: _______ {wildcards.min_cov}X
- Caller: __________ {wildcards.caller}
- """
- conda:
- GAWK
- input:
- cons_tmp = "results/05_Consensus/{reference}/{sample}_{mapper}_{min_cov}X_{caller}_consensus.fasta.tmp"
- output:
- consensus = "results/05_Consensus/{reference}/{sample}_{mapper}_{min_cov}X_{caller}_consensus.fasta"
- log:
- "results/10_Reports/tools-log/sed/{reference}/{sample}_{mapper}_{min_cov}X_{caller}_fasta-header.log"
- shell:
- "sed " # Sed, a Stream EDitor used to perform basic text transformations on an input stream
- "'s/^>.*$/>{wildcards.sample}_{wildcards.mapper}_{wildcards.min_cov}X_{wildcards.caller}/' "
- "{input.cons_tmp} " # Input file
- "1> {output.consensus} " # Output file
- "2> {log}" # Log redirection
-
###############################################################################
rule ivar_consensus:
# Aim: call a consensus genome
@@ -52,16 +24,16 @@ rule ivar_consensus:
message:
"""
~ iVar ∞ Call Consensus ~
- Sample: __________ {wildcards.sample}
- Reference: _______ {wildcards.reference}
- Mapper: _________ {wildcards.mapper}
- Min. cov.: _______ {wildcards.min_cov}X
- Caller: __ iVar
+ Sample: _______ {wildcards.sample}
+ Reference: ____ {wildcards.reference}
+ Mapper: _______ {wildcards.mapper}
+ Min. depth: ___ {wildcards.min_depth}x
+ Caller: _______ iVar
"""
conda:
IVAR
params:
- min_depth = IVAR_MIN_DEPTH,
+ min_depth = MIN_DEPTH,
min_freq = IVAR_MIN_FREQ,
min_insert = IVAR_MIN_INSERT,
max_depth = IVAR_MAX_DEPTH,
@@ -70,13 +42,14 @@ rule ivar_consensus:
baq = IVAR_MAP_QUAL
input:
mark_dup = get_bam_input,
- variant_call = "results/04_Variants/{reference}/{sample}_{mapper}_{min_cov}X_ivar_variant-call.tsv"
+ variant_call = "results/04_Variants/{reference}/{sample}_{mapper}_{min_depth}X_ivar_variant-call.tsv"
output:
- prefix = temp("results/05_Consensus/{reference}/{sample}_{mapper}_{min_cov}X_ivar_consensus"),
- cons_tmp = temp("results/05_Consensus/{reference}/{sample}_{mapper}_{min_cov}X_ivar_consensus.fasta.tmp"),
- qual_txt = "results/05_Consensus/{reference}/ivar_consensus-quality/{sample}_{mapper}_{min_cov}X_ivar_consensus.qual.txt",
+ prefix = temp("results/05_Consensus/{reference}/{sample}_{mapper}_{min_depth}X_ivar_consensus"),
+ header = temp("{sample}_{reference}_{mapper}_{min_depth}X_ivar_consensus"),
+ consensus = "results/05_Consensus/{reference}/{sample}_{mapper}_{min_depth}X_ivar_consensus.fasta",
+ qual_txt = "results/05_Consensus/ivar_consensus-quality/{sample}_{reference}_{mapper}_{min_depth}X_ivar_consensus.qual.txt"
log:
- "results/10_Reports/tools-log/ivar/{reference}/{sample}_{mapper}_{min_cov}X_ivar_consensus.log"
+ "results/10_Reports/tools-log/ivar/{reference}/{sample}_{mapper}_{min_depth}x_ivar_consensus.log"
shell:
"samtools mpileup " # Samtools mpileup, tools for alignments in the SAM format with command multi-way pileup
"--verbosity 0 " # Set level of verbosity [INT]
@@ -92,15 +65,17 @@ rule ivar_consensus:
"| " ### PIPE to iVar
"ivar consensus " # iVar, with command 'consensus': Call consensus from aligned BAM file
"-p {output.prefix} " # -p: prefix
+ "-i {output.header} " # -i: Name of fasta header (default: Consensus_<prefix>_threshold_<min_freq>_quality_<min_qual>_<min_insert>)
"-q {params.min_qual} " # -q: Minimum quality score threshold to count base [INT] (Default: 20)
- "-t {params.min_freq} " # -t: Minimum frequency threshold to call variants [FLOAT] (Default: 0.03)
- "-c {params.min_insert} " # -c: Minimum insertion frequency threshold to call consensus [FLOAT] (Default: 0.8)
- "-m {params.min_depth} " # -m: Minimum read depth to call variants [INT] (Default: 0)
+ "-t {params.min_freq} " # -t: Minimum frequency threshold (0 to 1) to call consensus [FLOAT] (Default: 0)
+ "-c {params.min_insert} " # -c: Minimum insertion frequency threshold (0 to 1) to call consensus [FLOAT] (Default: 0.8)
+ "-m {params.min_depth} " # -m: Minimum depth to call consensus [INT] (Default: 10)
"-n N " # -n: Character to print in regions with less than minimum coverage (Default: N)
- #"-i {wildcards.sample} " # -i: Name of fasta header (default: Consensus_<prefix>_threshold_<min_freq>_quality_<min_qual>_<min_insert>
"&> {log} " # Log redirection
- "&& mv {output.prefix}.fa {output.cons_tmp} " # copy consensus.fa (temp) to consensus.fasta.tmp (tmp)
- "&& mv {output.prefix}.qual.txt {output.qual_txt} " # cppty consensus.qual.txt (tmp) to ivar_consensus-quality/ directory
- "&& touch {output.prefix}" # Touch done
+ "&& mv {output.prefix}.fa {output.consensus} " # move consensus.fa (temp) to consensus.fasta
+ "&& mv {output.prefix}.qual.txt {output.qual_txt} " # move consensus.qual.txt (tmp) to ivar_consensus-quality/ directory
+ "&& touch {output.prefix} " # Touch prefix (temp)
+ "&& touch {output.header} " # Touch header (temp)
###############################################################################
+###############################################################################
\ No newline at end of file
diff --git a/workflow/rules/coverage_stats.smk b/workflow/rules/coverage_stats.smk
index bafcbf7..97b7134 100644
--- a/workflow/rules/coverage_stats.smk
+++ b/workflow/rules/coverage_stats.smk
@@ -8,13 +8,13 @@
### ###
###I###R###D######U###2###3###3#######T###R###A###N###S###V###I###H###M###I####
# Name ___________________ coverage_stats.smk
-# Version ________________ v.2025.01
+# Version ________________ v.2025.04
# Author _________________ Nicolas Fernandez
# Affiliation ____________ IRD_U233_TransVIHMI
# Aim ____________________ Compute Genome Coverage Statistics from BED file
# Date ___________________ 2021.10.12
-# Latest modifications ___ 2025.03.12
-# Use ____________________ snakemake -s Snakefile --use-conda -j
+# Latest modifications ___ 2025.04.04
+# Use ____________________ snakemake -s Snakefile --use-conda
###############################################################################
###############################################################################
@@ -33,7 +33,7 @@ rule awk_coverage_statistics:
input:
cutadapt = "results/10_Reports/tools-log/cutadapt/{sample}.log",
sickle = "results/10_Reports/tools-log/sickle-trim/{sample}.log",
- samtools = "results/10_Reports/tools-log/samtools/{reference}/{sample}_{mapper}_mark-dup.log",
+ samtools = "results/10_Reports/tools-log/samtools/{reference}/{sample}_{mapper}_markdup.log",
flagstat = "results/03_Coverage/{reference}/flagstat/{sample}_{mapper}_flagstat.json",
histogram = "results/03_Coverage/{reference}/histogram/{sample}_{mapper}_coverage-histogram.txt",
genome_cov = "results/02_Mapping/{reference}/{sample}_{mapper}_genome-cov.bed"
@@ -234,3 +234,4 @@ rule samtools_flagstat_ext:
"2> {log}" # Log redirection
###############################################################################
+###############################################################################
\ No newline at end of file
diff --git a/workflow/rules/duplicates_removing.smk b/workflow/rules/duplicates_removing.smk
index 53b692c..65f849f 100644
--- a/workflow/rules/duplicates_removing.smk
+++ b/workflow/rules/duplicates_removing.smk
@@ -33,11 +33,11 @@ rule samtools_index_markdup:
resources:
cpus = 6
input:
- mark_dup = "results/02_Mapping/{reference}/{sample}_{mapper}_mark-dup.bam"
+ mark_dup = "results/02_Mapping/{reference}/{sample}_{mapper}_markdup.bam"
output:
- index = "results/02_Mapping/{reference}/{sample}_{mapper}_mark-dup.bam.bai"
+ index = "results/02_Mapping/{reference}/{sample}_{mapper}_markdup.bam.bai"
log:
- "results/10_Reports/tools-log/samtools/{reference}/{sample}_{mapper}_mark-dup-index.log"
+ "results/10_Reports/tools-log/samtools/{reference}/{sample}_{mapper}_markdup-index.log"
shell:
"samtools index " # Samtools index, tools for alignments in the SAM format with command to index alignment
"-@ {resources.cpus} " # --threads: Number of additional threads to use (default: 1)(NB, --threads form dose'nt work)
@@ -64,9 +64,9 @@ rule samtools_markdup:
input:
sorted = "results/02_Mapping/{reference}/{sample}_{mapper}_sorted.bam"
output:
- mark_dup = "results/02_Mapping/{reference}/{sample}_{mapper}_mark-dup.bam"
+ mark_dup = "results/02_Mapping/{reference}/{sample}_{mapper}_markdup.bam"
log:
- "results/10_Reports/tools-log/samtools/{reference}/{sample}_{mapper}_mark-dup.log"
+ "results/10_Reports/tools-log/samtools/{reference}/{sample}_{mapper}_markdup.log"
shell:
"samtools markdup " # Samtools markdup, tools for alignments in the SAM format with command mark duplicates
"--threads {resources.cpus} " # -@: Number of additional threads to use (default: 1)
diff --git a/workflow/rules/genomes_indexing.smk b/workflow/rules/genomes_indexing.smk
index 200c389..1defd03 100644
--- a/workflow/rules/genomes_indexing.smk
+++ b/workflow/rules/genomes_indexing.smk
@@ -87,10 +87,10 @@ rule minimap2_genome_indexing:
conda:
MINIMAP2
params:
- kmer_size = KMER_SIZE,
- minimizer_size = MINIMIZER_SIZE,
- split_size = SPLIT_SIZE
- #homopolymer = HOMOPOLYMER
+ kmer_size = MM2_KMER_SIZE,
+ minimizer_size = MM2_MINIMIZER_SIZE,
+ split_size = MM2_SPLIT_SIZE
+ #homopolymer = MM2_HOMOPOLYMER
input:
fasta = "resources/genomes/{reference}.fasta"
output:
diff --git a/workflow/rules/gisaid_submission.smk b/workflow/rules/gisaid_submission.smk
index c944725..f35ed77 100644
--- a/workflow/rules/gisaid_submission.smk
+++ b/workflow/rules/gisaid_submission.smk
@@ -8,13 +8,13 @@
### ###
###I###R###D######U###2###3###3#######T###R###A###N###S###V###I###H###M###I####
# Name ___________________ gisaid_submission.smk
-# Version ________________ v.2025.01
+# Version ________________ v.2025.04
# Author _________________ Nicolas Fernandez
# Affiliation ____________ IRD_U233_TransVIHMI
# Aim ____________________ Create a Gisaid submission template file
# Date ___________________ 2025.01.31
-# Latest modifications ___ 2025.01.31
-# Use ____________________ snakemake -s Snakefile --use-conda -j
+# Latest modifications ___ 2025.04.04
+# Use ____________________ snakemake -s Snakefile --use-conda
###############################################################################
###############################################################################
@@ -33,3 +33,4 @@ rule gisaid_submission:
""
###############################################################################
+###############################################################################
\ No newline at end of file
diff --git a/workflow/rules/lineages_calling.smk b/workflow/rules/lineages_calling.smk
index 5dbc7c0..ad9cd58 100644
--- a/workflow/rules/lineages_calling.smk
+++ b/workflow/rules/lineages_calling.smk
@@ -8,13 +8,13 @@
### ###
###I###R###D######U###2###3###3#######T###R###A###N###S###V###I###H###M###I####
# Name ___________________ lineages_calling.smk
-# Version ________________ v.2025.01
+# Version ________________ v.2025.04
# Author _________________ Nicolas Fernandez
# Affiliation ____________ IRD_U233_TransVIHMI
# Aim ____________________ Assign lineage to consensus (Nextclade or Pangolin)
# Date ___________________ 2021.10.12
-# Latest modifications ___ 2025.03.12
-# Use ____________________ snakemake -s Snakefile --use-conda -j
+# Latest modifications ___ 2025.04.04
+# Use ____________________ snakemake -s Snakefile --use-conda
###############################################################################
###############################################################################
@@ -92,3 +92,4 @@ rule pangolin_lineage:
"2> /dev/null" # Errors redirection
###############################################################################
+###############################################################################
\ No newline at end of file
diff --git a/workflow/rules/lowcov_masking.smk b/workflow/rules/lowcov_masking.smk
index 9c440b5..4c57a00 100644
--- a/workflow/rules/lowcov_masking.smk
+++ b/workflow/rules/lowcov_masking.smk
@@ -8,13 +8,13 @@
### ###
###I###R###D######U###2###3###3#######T###R###A###N###S###V###I###H###M###I####
# Name ___________________ lowcov_masking.smk
-# Version ________________ v.2025.01
+# Version ________________ v.2025.04
# Author _________________ Nicolas Fernandez
# Affiliation ____________ IRD_U233_TransVIHMI
# Aim ____________________ Mask low coverage regions
# Date ___________________ 2021.10.12
-# Latest modifications ___ 2025.03.12
-# Use ____________________ snakemake -s Snakefile --use-conda -j
+# Latest modifications ___ 2025.04.04
+# Use ____________________ snakemake -s Snakefile --use-conda
###############################################################################
###############################################################################
@@ -99,3 +99,4 @@ rule awk_min_covfilt:
"2> {log} " # Log redirection
###############################################################################
+###############################################################################
\ No newline at end of file
diff --git a/workflow/rules/primers_clipping.smk b/workflow/rules/primers_clipping.smk
index 69853a8..c122863 100644
--- a/workflow/rules/primers_clipping.smk
+++ b/workflow/rules/primers_clipping.smk
@@ -8,53 +8,62 @@
### ###
###I###R###D######U###2###3###3#######T###R###A###N###S###V###I###H###M###I####
# Name ___________________ primers_clipping.smk
-# Version ________________ v.2025.01
+# Version ________________ v.2025.04
# Author _________________ Nicolas Fernandez
# Affiliation ____________ IRD_U233_TransVIHMI
# Aim ____________________ Soft clip amplicons primers
# Date ___________________ 2021.10.12
-# Latest modifications ___ 2025.03.12
-# Use ____________________ snakemake -s Snakefile --use-conda -j
+# Latest modifications ___ 2025.04.04
+# Use ____________________ snakemake -s Snakefile --use-conda
###############################################################################
###############################################################################
-rule bamclipper_amplicon_primers:
+rule ivar_trim:
# Aim: soft-clip amplicon PCR primers from BAM alignments
- # Use: bamclipper.sh -n [THREADS] -b [MARKDUP.bam] -p [PRIMER.bed] -u [UPSTREAM] -d [DOWNSTREAM]
+ # Use: ivar trim -i [INPUT.bam] -b [PRIMER.bed] -p [PREFIX] -e -m 20 -q 20
message:
"""
- ~ BAMClipper ∞ soft-clipping amplicon PCR primers from BAM alignments ~
- Sample: __________ {wildcards.sample}
- Reference: _______ {wildcards.reference}
- Mapper: __________ {wildcards.mapper}
+ ~ iVar ∞ soft-clipping amplicon PCR primers from BAM alignments ~
+ Sample _________ {wildcards.sample}
+ Reference ______ {wildcards.reference}
+ Mapper _________ {wildcards.mapper}
"""
conda:
- BAMCLIPPER
- resources:
- cpus = CPUS
+ IVAR
params:
- path = CLIPPATH,
- primers = PRIMERS,
- upstream = UPSTREAM,
- downstream = DOWNSTREAM
+ path = PRIMER_BED_PATH,
+ bed = PRIMER_BED_SCHEME,
+ #path = PRIMER_BEDPE_PATH,
+ #bedpe = PRIMER_BEDPE_SCHEME,
+ offset = IVAR_OFFSET,
+ min_len = IVAR_MIN_LENGTH,
+ min_qual = IVAR_MIN_QUAL,
+ slide = IVAR_SLIDE
input:
- markdup = "results/02_Mapping/{reference}/{sample}_{mapper}_mark-dup.bam",
- index = "results/02_Mapping/{reference}/{sample}_{mapper}_mark-dup.bam.bai"
+ bam = "results/02_Mapping/{reference}/{sample}_{mapper}_markdup.bam",
+ bai = "results/02_Mapping/{reference}/{sample}_{mapper}_markdup.bam.bai"
output:
- bamclip = "results/02_Mapping/{reference}/{sample}_{mapper}_mark-dup.primerclipped.bam",
- baiclip = "results/02_Mapping/{reference}/{sample}_{mapper}_mark-dup.primerclipped.bam.bai"
+ prefix = temp("results/02_Mapping/{reference}/{sample}_{mapper}_markdup_trimmed"),
+ trimmed_bam = "results/02_Mapping/{reference}/{sample}_{mapper}_markdup_trimmed.bam",
+ trimmed_bai = "results/02_Mapping/{reference}/{sample}_{mapper}_markdup_trimmed.bam.bai"
log:
- "results/10_Reports/tools-log/bamclipper/{reference}/{sample}_{mapper}_primers-clip.log"
+ "results/10_Reports/tools-log/ivar_trim/{reference}/{sample}_{mapper}.log"
shell:
- "bamclipper.sh " # BAMClipper, remove primer sequences from BAM alignments of PCR amplicons by soft-clipping
- "-b {input.markdup} " # Indexed BAM alignment file
- "-p {params.path}{params.primers}.bedpe " # BEDPE of primer pair locations
- "-n {resources.cpus} " # Number of threads (default: 1)
- "-u {params.upstream} " # Number of nuc. upstream for assigning alignments to primers (default: 5)
- "-d {params.downstream} " # Number of nuc. downstream for assigning alignments to primers (default: 5)
- #"-o results/02_Mapping/ " # Path to write output (if BamClipper v.1.1.2) (todo)
- "&> {log} " # Log redirection
- "&& mv {wildcards.sample}_{wildcards.mapper}_mark-dup.primerclipped.bam {output.bamclip} " # because BamClipper v.1 default output system...
- "&& mv {wildcards.sample}_{wildcards.mapper}_mark-dup.primerclipped.bam.bai {output.baiclip}" # because BamClipper v.1 default output system...
+ "ivar trim " # iVar, with command 'trim': soft-clip amplicon PCR primers from BAM alignments
+ "-i {input.bam} " # Input BAM file, with aligned reads, to trim primers and quality
+ "-p {output.prefix} " # Prefix for the output BAM file
+ "-b {params.path}{params.bed} " # BED file with primer sequences and positions
+ # If no BED file is specified, only quality trimming will be done.
+ #"-f {params.path}{params.bedpe} " # Primer pair information file containing left and right primer names for the same amplicon separated by a tab
+ # If provided, reads that do not fall within atleat one amplicon will be ignored prior to primer trimming.
+ "-x {params.offset} " # primer position offset (Default: 0)
+ "-m {params.min_len} " # Minimum length of read to retain after trimming (Default: 50% average length of the first 1000 reads)
+ "-q {params.min_qual} " # Minimum quality threshold for sliding window to pass (Default: 20)
+ "-s {params.slide} " # Width of sliding window (Default: 4)
+ "-e " # Include reads with no primers. By default, reads with no primers are excluded
+ "-k " # Keep reads to allow for reanalysis
+ # Keep reads which would be dropped by alignment length filter or primer requirements, but mark them QCFAIL
+ "&> {log}" # Log redirection
###############################################################################
+###############################################################################
\ No newline at end of file
diff --git a/workflow/rules/quality_controls.smk b/workflow/rules/quality_controls.smk
index 63b4368..21e0288 100644
--- a/workflow/rules/quality_controls.smk
+++ b/workflow/rules/quality_controls.smk
@@ -33,7 +33,7 @@ rule fastqscreen_contamination_check:
cpus = CPUS
params:
config = FQC_CONFIG,
- subset = SUBSET
+ subset = FQC_SUBSET
input:
fastq = "results/symlinks/{sample}_R{mate}.fastq.gz"
output:
diff --git a/workflow/rules/reads_cleanning.smk b/workflow/rules/reads_cleanning.smk
index 62711dc..ee6e1e0 100644
--- a/workflow/rules/reads_cleanning.smk
+++ b/workflow/rules/reads_cleanning.smk
@@ -8,13 +8,13 @@
### ###
###I###R###D######U###2###3###3#######T###R###A###N###S###V###I###H###M###I####
# Name ___________________ reads_cleanning.smk
-# Version ________________ v.2025.01
+# Version ________________ v.2025.04
# Author _________________ Nicolas Fernandez
# Affiliation ____________ IRD_U233_TransVIHMI
# Aim ____________________ Perform Illumina reads quality trimming
# Date ___________________ 2021.10.12
-# Latest modifications ___ 2025.03.12
-# Use ____________________ snakemake -s Snakefile --use-conda -j
+# Latest modifications ___ 2025.04.04
+# Use ____________________ snakemake -s Snakefile --use-conda
###############################################################################
###############################################################################
@@ -34,12 +34,12 @@ rule sickle_trim_quality:
quality = SIC_QUALITY,
length = SIC_LENGTH
input:
- fwd_reads = "results/01_Trimming/cutadapt/{sample}_cutadapt-removed_R1.fastq.gz",
- rev_reads = "results/01_Trimming/cutadapt/{sample}_cutadapt-removed_R2.fastq.gz"
+ fwd_reads = "results/01_Trimming/cutadapt/{sample}_cutadapt_R1.fastq.gz",
+ rev_reads = "results/01_Trimming/cutadapt/{sample}_cutadapt_R2.fastq.gz"
output:
- fwd_reads = temp("results/01_Trimming/sickle/{sample}_cutadapt-sickle-trimmed_R1.fastq.gz"),
- rev_reads = temp("results/01_Trimming/sickle/{sample}_cutadapt-sickle-trimmed_R2.fastq.gz"),
- single = temp("results/01_Trimming/sickle/{sample}_cutadapt-sickle-trimmed_SE.fastq.gz")
+ fwd_reads = temp("results/01_Trimming/sickle/{sample}_cutadapt-sickle-trim_R1.fastq.gz"),
+ rev_reads = temp("results/01_Trimming/sickle/{sample}_cutadapt-sickle-trim_R2.fastq.gz"),
+ single = temp("results/01_Trimming/sickle/{sample}_cutadapt-sickle-trim_SE.fastq.gz")
log:
"results/10_Reports/tools-log/sickle-trim/{sample}.log"
shell:
@@ -54,7 +54,7 @@ rule sickle_trim_quality:
"-o {output.fwd_reads} " # --output-pe1: Output trimmed forward fastq file
"-p {output.rev_reads} " # --output-pe2: Output trimmed reverse fastq file (must use -s option)
"-s {output.single} " # --output-single: Output trimmed singles fastq file
- "&> {log} " # Log redirection
+ "&> {log}" # Log redirection
###############################################################################
rule cutadapt_adapters_removing:
@@ -71,17 +71,15 @@ rule cutadapt_adapters_removing:
resources:
cpus = CPUS
params:
+ cut = CUT_CLIPPING,
length = CUT_LENGTH,
- truseq = CUT_TRUSEQ,
- nextera = CUT_NEXTERA,
- small = CUT_SMALL,
- cut = CUT_CLIPPING
+ adapter_opts = lambda wildcards: " ".join(f"--adapter {a} -A {a}" for a in CUT_ADAPTERS)
input:
fwd_reads = "results/symlinks/{sample}_R1.fastq.gz",
rev_reads = "results/symlinks/{sample}_R2.fastq.gz"
output:
- fwd_reads = temp("results/01_Trimming/cutadapt/{sample}_cutadapt-removed_R1.fastq.gz"),
- rev_reads = temp("results/01_Trimming/cutadapt/{sample}_cutadapt-removed_R2.fastq.gz")
+ fwd_reads = temp("results/01_Trimming/cutadapt/{sample}_cutadapt_R1.fastq.gz"),
+ rev_reads = temp("results/01_Trimming/cutadapt/{sample}_cutadapt_R2.fastq.gz")
log:
"results/10_Reports/tools-log/cutadapt/{sample}.log"
shell:
@@ -91,16 +89,12 @@ rule cutadapt_adapters_removing:
"-U {params.cut} " # -U: Remove 'n' first bases (5') from reverse R2 (hard-clipping, default: 0)
"--trim-n " # --trim-n: Trim N's on ends (3') of reads
"--minimum-length {params.length} " # -m: Discard reads shorter than length
- "--adapter {params.truseq} " # -a: Sequence of an adapter ligated to the 3' end of the first read
- "-A {params.truseq} " # -A: 3' adapter to be removed from second read in a pair
- "--adapter {params.nextera} " # -a: Sequence of an adapter ligated to the 3' end of the first read
- "-A {params.nextera} " # -A: 3' adapter to be removed from second read in a pair
- "--adapter {params.small} " # -a: Sequence of an adapter ligated to the 3' end of the first read
- "-A {params.small} " # -A: 3' adapter to be removed from second read in a pair
+ "{params.adapter_opts} " # -a/-A: Adapters sequences ligated to the 3' end of the first or second read in a pair
"--output {output.fwd_reads} " # -o: Write trimmed reads to FILE
"--paired-output {output.rev_reads} " # -p: Write second read in a pair to FILE
"{input.fwd_reads} " # Input forward reads R1.fastq
"{input.rev_reads} " # Input reverse reads R2.fastq
- "&> {log} " # Log redirection
+ "&> {log}" # Log redirection
###############################################################################
+###############################################################################
\ No newline at end of file
diff --git a/workflow/rules/reads_mapping.smk b/workflow/rules/reads_mapping.smk
index 834e156..c97387c 100644
--- a/workflow/rules/reads_mapping.smk
+++ b/workflow/rules/reads_mapping.smk
@@ -37,8 +37,8 @@ rule minimap2_mapping:
#length = LENGTH
input:
mm2_indexes = "resources/indexes/minimap2/{reference}.mmi",
- fwd_reads = "results/01_Trimming/sickle/{sample}_cutadapt-sickle-trimmed_R1.fastq.gz",
- rev_reads = "results/01_Trimming/sickle/{sample}_cutadapt-sickle-trimmed_R2.fastq.gz"
+ fwd_reads = "results/01_Trimming/sickle/{sample}_cutadapt-sickle-trim_R1.fastq.gz",
+ rev_reads = "results/01_Trimming/sickle/{sample}_cutadapt-sickle-trim_R2.fastq.gz"
output:
mapped = temp("results/02_Mapping/{reference}/{sample}_minimap2-mapped.sam")
log:
@@ -78,8 +78,8 @@ rule bwa_mapping:
cpus = CPUS
input:
bwa_indexes = "resources/indexes/bwa/{reference}",
- fwd_reads = "results/01_Trimming/sickle/{sample}_cutadapt-sickle-trimmed_R1.fastq.gz",
- rev_reads = "results/01_Trimming/sickle/{sample}_cutadapt-sickle-trimmed_R2.fastq.gz"
+ fwd_reads = "results/01_Trimming/sickle/{sample}_cutadapt-sickle-trim_R1.fastq.gz",
+ rev_reads = "results/01_Trimming/sickle/{sample}_cutadapt-sickle-trim_R2.fastq.gz"
output:
mapped = temp("results/02_Mapping/{reference}/{sample}_bwa-mapped.sam")
log:
@@ -113,8 +113,8 @@ rule bowtie2_mapping:
sensitivity = BT2_SENSITIVITY
input:
bt2_indexes = "resources/indexes/bowtie2/{reference}",
- fwd_reads = "results/01_Trimming/sickle/{sample}_cutadapt-sickle-trimmed_R1.fastq.gz",
- rev_reads = "results/01_Trimming/sickle/{sample}_cutadapt-sickle-trimmed_R2.fastq.gz"
+ fwd_reads = "results/01_Trimming/sickle/{sample}_cutadapt-sickle-trim_R1.fastq.gz",
+ rev_reads = "results/01_Trimming/sickle/{sample}_cutadapt-sickle-trim_R2.fastq.gz"
output:
mapped = temp("results/02_Mapping/{reference}/{sample}_bowtie2-mapped.sam")
log:
diff --git a/workflow/rules/results_merging.smk b/workflow/rules/results_merging.smk
index 73f5bfe..6b7e05e 100644
--- a/workflow/rules/results_merging.smk
+++ b/workflow/rules/results_merging.smk
@@ -8,13 +8,13 @@
### ###
###I###R###D######U###2###3###3#######T###R###A###N###S###V###I###H###M###I####
# Name ___________________ results_merging.smk
-# Version ________________ v.2025.01
+# Version ________________ v.2025.04
# Author _________________ Nicolas Fernandez
# Affiliation ____________ IRD_U233_TransVIHMI
# Aim ____________________ Merge results
# Date ___________________ 2025.01.31
-# Latest modifications ___ 2025.03.12
-# Use ____________________ snakemake -s Snakefile --use-conda -j
+# Latest modifications ___ 2025.04.04
+# Use ____________________ snakemake -s Snakefile --use-conda
###############################################################################
###############################################################################
@@ -24,7 +24,7 @@ rule merge_consensus:
~ Merge ∞ Concatenating all samples consensus sequences ~
Reference: _______ {wildcards.reference}
Mapper: __________ {wildcards.mapper}
- Min. cov.: _______ {wildcards.min_cov}X
+ Min. cov.: _______ {wildcards.min_cov}x
Caller: __________ {wildcards.caller}
"""
input:
@@ -39,10 +39,10 @@ rule merge_consensus:
log:
"results/10_Reports/tools-log/merge_consensus/{reference}/{mapper}_{min_cov}X_{caller}_consensus.log"
shell:
- "cat " # Concatenate all consensus sequences
- "{input.consensus} " # Input files
- "> {output.all_consensus} " # Output file
- "2> {log}" # Log redirection
+ "cat " # Concatenate all consensus sequences
+ "{input.consensus} " # Input files
+ "1> {output.all_consensus} " # Output file
+ "2> {log}" # Log redirection
###############################################################################
rule merge_coverage:
@@ -51,7 +51,7 @@ rule merge_coverage:
~ Merge ∞ Concatenating genome coverage statistics ~
Reference: _______ {wildcards.reference}
Mapper: __________ {wildcards.mapper}
- Min. cov.: _______ {wildcards.min_cov}X
+ Min. cov.: _______ {wildcards.min_cov}x
"""
input:
covstats = lambda wildcards: expand("results/03_Coverage/{reference}/{sample}_{mapper}_{min_cov}X_coverage-stats.tsv",
@@ -60,23 +60,23 @@ rule merge_coverage:
mapper = wildcards.mapper,
min_cov = wildcards.min_cov)
output:
- all_covstats = "results/All_{reference}_{mapper}_{min_cov}X_genome_coverages.tsv",
- temp_covstats = temp("results/All_{reference}_{mapper}_{min_cov}X_genome_coverages.temp")
- log:
+ all_covstats = "results/All_{reference}_{mapper}_{min_cov}X_genome_coverages.tsv"
+ log:
"results/10_Reports/tools-log/merge_coverage/{reference}/{mapper}_{min_cov}X_covstats.log"
shell:
- "cat {input.covstats} > {output.temp_covstats} && " # Concatenate all coverage statistics
- "awk 'NR==1 || NR%2==0' {output.temp_covstats} 1> {output.all_covstats} " # Keep only even lines
- "2> {log}" # Log redirection
+ "cat {input.covstats} | " # Concatenate all coverage statistics
+ "awk 'NR==1 || NR%2==0' " # Keep only even lines
+ "1> {output.all_covstats} " # Output file
+ "2> {log}" # Log redirection
###############################################################################
rule merge_clade:
message:
"""
- ~ Merge ∞ Concatenating Pangolin lineage assignments ~
+ ~ Merge ∞ Concatenating lineage assignments ~
Reference: _______ {wildcards.reference}
Mapper: __________ {wildcards.mapper}
- Min. cov.: _______ {wildcards.min_cov}X
+ Min. cov.: _______ {wildcards.min_cov}x
Variant caller: __ {wildcards.caller}
Assigner: ________ {wildcards.assigner}
"""
@@ -89,13 +89,14 @@ rule merge_clade:
caller = wildcards.caller,
assigner = wildcards.assigner)
output:
- all_lineages = "results/All_{reference}_{mapper}_{min_cov}X_{caller}_{assigner}-lineages.tsv",
- temp_lineages = temp("results/All_{reference}_{mapper}_{min_cov}X_{caller}_{assigner}-lineages.temp")
+ all_lineages = "results/All_{reference}_{mapper}_{min_cov}X_{caller}_{assigner}-lineages.tsv"
log:
"results/10_Reports/tools-log/merge_clade/{reference}/{mapper}_{min_cov}X_{caller}_{assigner}-lineages.log"
shell:
- "cat {input.lineages} > {output.temp_lineages} && " # Concatenate all clade assignments
- "awk 'NR==1 || NR%2==0' {output.temp_lineages} 1> {output.all_lineages} " # Keep only even lines
- "2> {log}" # Log redirection
+ "cat {input.lineages} | " # Concatenate all lineage assignments
+ "awk 'NR==1 || NR%2==0' {output.temp_lineages} " # Keep only even lines
+ "1> {output.all_lineages} " # Output file
+ "2> {log}" # Log redirection
###############################################################################
+###############################################################################
\ No newline at end of file
diff --git a/workflow/rules/symlinks_renamming.smk b/workflow/rules/samples_prep.smk
similarity index 68%
rename from workflow/rules/symlinks_renamming.smk
rename to workflow/rules/samples_prep.smk
index f4bfce3..88a5560 100644
--- a/workflow/rules/symlinks_renamming.smk
+++ b/workflow/rules/samples_prep.smk
@@ -7,31 +7,16 @@
### \/ \/ ###
### ###
###I###R###D######U###2###3###3#######T###R###A###N###S###V###I###H###M###I####
-# Name ___________________ symlinks_renamming.smk
-# Version ________________ v.2025.01
+# Name ___________________ sample_prep.smk
+# Version ________________ v.2025.04
# Author _________________ Nicolas Fernandez
# Affiliation ____________ IRD_U233_TransVIHMI
-# Aim ____________________ Create fastq symlinks
+# Aim ____________________ Prepare samples
# Date ___________________ 2025.01.31
-# Latest modifications ___ 2025.03.12
-# Use ____________________ snakemake -s Snakefile --use-conda -j
+# Latest modifications ___ 2025.04.04
+# Use ____________________ snakemake -s Snakefile --use-conda
###############################################################################
-###############################################################################
-rule config:
- # Aim: Load configuration file
- # Use:
- message:
- """
- ~ Configuration ∞ Show analyses settings ~
- """
- input:
- config_file = "config/config.yaml"
- output:
- setting_log = "results/10_Reports/settings.log"
- script:
- "workflow/scripts/settings.py "
-
###############################################################################
rule symlinks:
# Aim: Create fastq files symlinks
@@ -43,18 +28,18 @@ rule symlinks:
Reads: ___________ R{wildcards.mate}
"""
input:
- setting_log = "results/10_Reports/settings.log",
valid_fastq = lambda wildcards: os.path.abspath(VALID_FASTQ[wildcards.sample][wildcards.mate])
output:
symlink = temp("results/symlinks/{sample}_R{mate}.fastq.gz")
log:
"results/10_Reports/tools-log/symlinks/{sample}_R{mate}.log"
shell:
- "mkdir -p $(dirname {output.symlink}) "
- "&& "
- "ln -sf "
- "{input.valid_fastq} "
- "{output.symlink} "
- "&> {log}"
+ "mkdir -p $(dirname {output.symlink}) " # Create output directory
+ "&& " # Create symlink directory
+ "ln -sf " # Create symbolic link
+ "{input.valid_fastq} " # Source file
+ "{output.symlink} " # Link
+ "&> {log}" # Log redirection
###############################################################################
+###############################################################################
\ No newline at end of file
diff --git a/workflow/rules/variants_calling.smk b/workflow/rules/variants_calling.smk
index 29993e9..096b049 100644
--- a/workflow/rules/variants_calling.smk
+++ b/workflow/rules/variants_calling.smk
@@ -8,13 +8,13 @@
### ###
###I###R###D######U###2###3###3#######T###R###A###N###S###V###I###H###M###I####
# Name ___________________ variants_calling.smk
-# Version ________________ v.2025.01
+# Version ________________ v.2025.04
# Author _________________ Nicolas Fernandez
# Affiliation ____________ IRD_U233_TransVIHMI
# Aim ____________________ SNVs and Indels calling
# Date ___________________ 2021.10.12
-# Latest modifications ___ 2025.03.12
-# Use ____________________ snakemake -s Snakefile --use-conda -j
+# Latest modifications ___ 2025.04.04
+# Use ____________________ snakemake -s Snakefile --use-conda
###############################################################################
###############################################################################
@@ -32,6 +32,8 @@ rule convert_tsv2vcf:
"""
conda:
TSV2VCF
+ params:
+ tsv2vcf = "workflow/scripts/ivar_variants_to_vcf.py" # Script (from viralrecon)
input:
tsv = "results/04_Variants/{reference}/{sample}_{mapper}_{min_cov}X_ivar_variant-call.tsv"
output:
@@ -39,11 +41,11 @@ rule convert_tsv2vcf:
log:
"results/10_Reports/tools-log/tsv2vcf/{reference}/{sample}_{mapper}_{min_cov}X_ivar_tsv2vcf.log"
shell:
- "python3 " # Python 3
- "workflow/scripts/ivar_variants_to_vcf.py " # Script (from viralrecon)
- "{input.tsv} " # TSV input
- "{output.vcf} " # VCF output
- "&> {log}" # Log redirection
+ "python3 " # Python 3
+ "{params.tsv2vcf} " # Script (from viralrecon)
+ "{input.tsv} " # TSV input
+ "{output.vcf} " # VCF output
+ "&> {log}" # Log redirection
###############################################################################
rule ivar_variant_calling:
@@ -62,7 +64,7 @@ rule ivar_variant_calling:
conda:
IVAR
params:
- min_depth = IVAR_MIN_DEPTH,
+ min_depth = MIN_DEPTH,
min_freq = IVAR_MIN_FREQ,
min_insert = IVAR_MIN_INSERT,
max_depth = IVAR_MAX_DEPTH,
@@ -90,12 +92,13 @@ rule ivar_variant_calling:
"2>&1 | grep -v '[mpileup] 1 samples in 1 input files' " # Remove this stdout
"| " ### pipe to iVar
"ivar variants " # iVar, with command 'variants': Call variants from aligned BAM file
- "-p {output.variant_call} " # -p: prefix
+ "-p {output.variant_call} " # -p: Prefix for the output tsv variant file
"-q {params.min_qual} " # -q: Minimum quality score threshold to count base (Default: 20) [INT]
- "-t {params.min_freq} " # -t: Minimum frequency threshold to call variants (Default: 0.03) [FLOAT]
+ "-t {params.min_freq} " # -t: Minimum frequency threshold (0 to 1) to call variants (Default: 0.03) [FLOAT]
"-m {params.min_depth} " # -m: Minimum read depth to call variants (Default: 0) [INT]
"-r {input.masked_ref} " # -r: Reference file used for alignment (translate the nuc. sequences and identify intra host single nuc. variants)
#"-g " # -g: A GFF file in the GFF3 format can be supplied to specify coordinates of open reading frames (ORFs)
"&> {log}" # Log redirection
###############################################################################
+###############################################################################
\ No newline at end of file
diff --git a/workflow/rules/workflow_reporting.smk b/workflow/rules/workflow_reporting.smk
index da31bbb..8601e88 100644
--- a/workflow/rules/workflow_reporting.smk
+++ b/workflow/rules/workflow_reporting.smk
@@ -8,40 +8,15 @@
### ###
###I###R###D######U###2###3###3#######T###R###A###N###S###V###I###H###M###I####
# Name ___________________ workflow_reporting.smk
-# Version ________________ v.2025.01
+# Version ________________ v.2025.04
# Author _________________ Nicolas Fernandez
# Affiliation ____________ IRD_U233_TransVIHMI
# Aim ____________________ Generate workflow reports
# Date ___________________ 2025.01.31
-# Latest modifications ___ 2025.03.12
-# Use ____________________ snakemake -s Snakefile --use-conda -j
-###############################################################################
-
-
-
+# Latest modifications ___ 2025.04.04
+# Use ____________________ snakemake -s Snakefile --use-conda
###############################################################################
-###############################################################################
-rule tar_reports:
- # Aim: compresses reports into a tarball
- # Use: tar -zcf 10_Reports_archive.tar.gz 10_Reports/
- message:
- """
- ~ Archive ∞ Compress reports ~
- """
- input:
- html_report = "results/10_Reports/workflow-report.html"
- output:
- tarball = "results/Reports_archive.tar.gz"
- shell:
- "tar " # Tar command
- "-z " # Gzip compression
- "-c " # Create a new archive
- "-f " # Use archive file or device ARCHIVE
- "{output.tarball} " # Output archive
- "-C results/ " # Change to directory 'results/'
- "10_Reports/" # Input directory to compress
-
###############################################################################
rule snakemake_report:
# Aim: generates a workflow report in HTML format
@@ -50,13 +25,12 @@ rule snakemake_report:
"""
~ Report ∞ Generate a workflow report in HTML format ~
"""
- #conda:
- # WORKFLOW
+ conda:
+ WORKFLOW
params:
#style_sheet = STYLE_SHEET
input:
multiqc = "results/10_Reports/multiqc/",
- time = "results/10_Reports/time.log",
summary = "results/10_Reports/files-summary.tsv",
graph = expand("results/10_Reports/graphs/{graph_type}.{ext}",
graph_type = GRAPH_TYPE,
@@ -72,28 +46,6 @@ rule snakemake_report:
" {output.html_report} " # Output report
"2> {log}" # Log redirection
-###############################################################################
-rule snakemake_summary:
- # Aim: generates a workflow summary in txt format
- # Use: snakemake --summary
- message:
- """
- ~ Summary ∞ Generate a files summary in txt format ~
- """
- conda:
- WORKFLOW
- input:
- final_outputs = get_final_outputs()
- output:
- summary = "results/10_Reports/files-summary.tsv"
- log:
- "results/10_Reports/tools-log/files-summary.log"
- shell:
- "snakemake " # Snakemake
- "--summary " # Print a summary of all files created by the workflow
- "1> {output.summary} " # Output files summary
- "2> {log}" # Log redirection
-
###############################################################################
rule snakemake_graph:
# Aim: generates a workflow graph in png, svg or pdf format
@@ -118,6 +70,28 @@ rule snakemake_graph:
"1> {output.graph} " # Output graph
"2> {log}" # Log redirection
+###############################################################################
+rule snakemake_summary:
+ # Aim: generates a workflow summary in txt format
+ # Use: snakemake --summary
+ message:
+ """
+ ~ Summary ∞ Generate a files summary in txt format ~
+ """
+ conda:
+ WORKFLOW
+ input:
+ final_outputs = get_final_outputs()
+ output:
+ summary = "results/10_Reports/files-summary.tsv"
+ log:
+ "results/10_Reports/tools-log/files-summary.log"
+ shell:
+ "snakemake " # Snakemake
+ "--summary " # Print a summary of all files created by the workflow
+ "1> {output.summary} " # Output files summary
+ "2> {log}" # Log redirection
+
###############################################################################
rule multiqc_aggregation:
# Aim: aggregates bioinformatics analyses results into a single report
@@ -154,70 +128,4 @@ rule multiqc_aggregation:
"2> /dev/null" # Suppress error messages
###############################################################################
-rule log_time:
- # Aim: log workflow start and end time
- # Use: date +"%Y-%m-%d %H:%M"
- message:
- """
- ~ Log ∞ Workflow time ~
- """
- input:
- final_outputs = get_final_outputs()
- output:
- time_log = "results/10_Reports/time.log"
- run:
- time_stamp_start = time.strftime("%Y-%m-%d %H:%M", time.localtime(START_TIME))
- time_stamp_end = time.strftime("%Y-%m-%d %H:%M", time.localtime())
- elapsed_time = int(time.time() - START_TIME)
- hours = elapsed_time // 3600
- minutes = (elapsed_time % 3600) // 60
- seconds = elapsed_time % 60
- formatted_time = f"{hours:02d}:{minutes:02d}:{seconds:02d}"
- green = "\033[32m"
- ylo = "\033[33m"
- nc = "\033[0m"
- message_time = f"""
-{green}Start time{nc} _____________ {time_stamp_start}
-{green}End time{nc} _______________ {time_stamp_end}
-{green}Processing time{nc} ________ {ylo}{formatted_time}{nc}
-"""
- print(message_time)
- ansi_escape = re.compile(r'\x1B\[[0-?]*[ -/]*[@-~]')
- message_clean = ansi_escape.sub('', message_time)
- with open(output.time_log, "w") as f:
- f.write(message_clean)
-
-###############################################################################
-rule log_environments:
- # Aim: copy conda environments files to results
- # Use: cp workflow/envs/*.yaml results/10_Reports/envs/
- message:
- """
- ~ Log ∞ Workflow environments ~
- """
- input:
- envs = "workflow/envs"
- output:
- envs_log = directory("results/10_Reports/envs/")
- shell:
- "mkdir -p {output.envs_log} && " # Create directory
- "cp {input.envs}/*.yaml {output.envs_log} " # Copy envs files
- "2> /dev/null" # Suppress error messages
-
-###############################################################################
-rule log_config:
- # Aim: copy settings file to results
- # Use: cp config/config.yaml results/10_Reports/config.log
- message:
- """
- ~ Log ∞ Workflow configuration ~
- """
- input:
- config = "config/config.yaml"
- output:
- config_log = "results/10_Reports/config.log"
- shell:
- "cp {input.config} {output.config_log} " # Copy config file
- "2> /dev/null" # Suppress error messages
-
-###############################################################################
+###############################################################################
\ No newline at end of file
diff --git a/workflow/schemas/config.schema.yaml b/workflow/schemas/config.schema.yaml
index a399a7c..fe384c2 100644
--- a/workflow/schemas/config.schema.yaml
+++ b/workflow/schemas/config.schema.yaml
@@ -1,39 +1,11 @@
$schema: "http://json-schema.org/draft-07/schema#"
-title: "GeVarLi Configuration Schema"
+title: "GeVarLi Config Schema"
type: object
-required:
- - fastq_dir
- - modules
- - consensus
- - gisaid
- - nextclade
- - ivar
- - bamclipper
- - bwa
- - bowtie2
- - minimap2
- - sickle_trim
- - cutadapt
- - multiqc
- - fastq_screen
- - rename
- - resources
- - envs
- - report
properties:
fastq_dir:
type: string
-
modules:
type: object
- required:
- - qualities
- - keeptrim
- - clipping
- - covstats
- - consensus
- - lineages
- - gisaid
properties:
qualities:
type: boolean
@@ -49,42 +21,36 @@ properties:
type: boolean
gisaid:
type: boolean
-
- consensus:
- type: object
required:
- - reference
- - min_cov
- - min_freq
- - iupac
- - mapper
- - caller
- - assigner
+ - qualities
+ - keeptrim
+ - clipping
+ - covstats
+ - consensus
+ - lineages
+ - gisaid
+ tools:
+ type: object
properties:
- reference:
- type: string
- min_cov:
- type: string
- min_freq:
- type: string
- iupac:
- type: string
mapper:
type: string
caller:
type: string
assigner:
type: string
-
- gisaid:
+ required:
+ - mapper
+ - caller
+ - assigner
+ consensus:
type: object
+ properties:
+ reference:
+ type: string
required:
- - username
- - threshold
- - name
- - country
- - identifier
- - year
+ - reference
+ gisaid:
+ type: object
properties:
username:
type: string
@@ -98,42 +64,78 @@ properties:
type: string
year:
type: string
-
+ required:
+ - username
+ - threshold
+ - name
+ - country
+ - identifier
+ - year
nextclade:
type: object
- required:
- - path
- - dataset
properties:
path:
type: string
dataset:
type: string
-
+ required:
+ - path
+ - dataset
ivar:
type: object
- required:
- - max_depth
- - min_bq
- - min_qual
- - map_qual
properties:
- max_depth:
- type: string
- min_bq:
- type: string
- min_qual:
- type: string
- map_qual:
- type: string
-
+ consensus:
+ type: object
+ properties:
+ min_depth:
+ type: string
+ max_depth:
+ type: string
+ min_freq:
+ type: string
+ map_qual:
+ type: string
+ min_bq:
+ type: string
+ min_qual:
+ type: string
+ required:
+ - min_depth
+ - max_depth
+ - min_freq
+ - map_qual
+ - min_bq
+ - min_qual
+ variant:
+ type: object
+ properties:
+ min_depth:
+ type: string
+ max_depth:
+ type: string
+ min_freq:
+ type: string
+ map_qual:
+ type: string
+ min_bq:
+ type: string
+ min_qual:
+ type: string
+ required:
+ - min_depth
+ - max_depth
+ - min_freq
+ - map_qual
+ - min_bq
+ - min_qual
+ primerclipping:
+ type: [ "object", "null" ]
+ required:
+ - consensus
+ - variant
+ - primerclipping
bamclipper:
type: object
- required:
- - path
- - primers
- - upstream
- - downstream
properties:
path:
type: string
@@ -143,43 +145,35 @@ properties:
type: string
downstream:
type: string
-
+ required:
+ - path
+ - primers
+ - upstream
+ - downstream
bwa:
type: object
- required:
- - algorithm
properties:
algorithm:
type: string
-
- bowtie2:
- type: object
required:
- algorithm
- - sensitivity
+ bowtie2:
+ type: object
properties:
algorithm:
type: string
sensitivity:
type: string
-
- minimap2:
- type: object
required:
- - preset
- algorithm
+ - sensitivity
+ minimap2:
+ type: object
properties:
- preset:
- type: string
algorithm:
type: object
- required:
- - "k-mer_size"
- - minimizer_size
- - split_size
- - homopolymer
properties:
- "k-mer_size":
+ k-mer_size:
type: string
minimizer_size:
type: string
@@ -187,14 +181,18 @@ properties:
type: string
homopolymer:
type: string
-
+ required:
+ - k-mer_size
+ - minimizer_size
+ - split_size
+ - homopolymer
+ preset:
+ type: string
+ required:
+ - algorithm
+ - preset
sickle_trim:
type: object
- required:
- - quality
- - length
- - command
- - encoding
properties:
quality:
type: string
@@ -204,13 +202,13 @@ properties:
type: string
encoding:
type: string
-
- cutadapt:
- type: object
required:
- - clipping
+ - quality
- length
- - kits
+ - command
+ - encoding
+ cutadapt:
+ type: object
properties:
clipping:
type: string
@@ -218,10 +216,6 @@ properties:
type: string
kits:
type: object
- required:
- - truseq
- - nextera
- - small
properties:
truseq:
type: string
@@ -229,13 +223,16 @@ properties:
type: string
small:
type: string
-
+ required:
+ - truseq
+ - nextera
+ - small
+ required:
+ - clipping
+ - length
+ - kits
multiqc:
type: object
- required:
- - path
- - config
- - tag
properties:
path:
type: string
@@ -243,13 +240,12 @@ properties:
type: string
tag:
type: string
-
- fastq_screen:
- type: object
required:
+ - path
- config
- - subset
- - reference
+ - tag
+ fastq_screen:
+ type: object
properties:
config:
type: string
@@ -259,13 +255,12 @@ properties:
type: array
items:
type: string
-
+ required:
+ - config
+ - subset
+ - reference
rename:
type: object
- required:
- - barcode_id
- - line_id
- - end_id
properties:
barcode_id:
type: boolean
@@ -273,13 +268,12 @@ properties:
type: boolean
end_id:
type: boolean
-
+ required:
+ - barcode_id
+ - line_id
+ - end_id
resources:
type: object
- required:
- - cpus
- - ram
- - tmp_dir
properties:
cpus:
type: string
@@ -287,28 +281,12 @@ properties:
type: string
tmp_dir:
type: string
-
+ required:
+ - cpus
+ - ram
+ - tmp_dir
envs:
type: object
- required:
- - bamclipper
- - bcftools
- - bedtools
- - bowtie2
- - bwa
- - cutadapt
- - fastq_screen
- - fastqc
- - gawk
- - ivar
- - minimap2
- - multiqc
- - nextclade
- - pangolin
- - samtools
- - sickle_trim
- - tsv2vcf
- - workflow
properties:
bamclipper:
type: string
@@ -346,27 +324,39 @@ properties:
type: string
workflow:
type: string
-
+ required:
+ - bamclipper
+ - bcftools
+ - bedtools
+ - bowtie2
+ - bwa
+ - cutadapt
+ - fastq_screen
+ - fastqc
+ - gawk
+ - ivar
+ - minimap2
+ - multiqc
+ - nextclade
+ - pangolin
+ - samtools
+ - sickle_trim
+ - tsv2vcf
+ - workflow
report:
type: object
- required:
- - stat
- - graph
properties:
stat:
type: object
- required:
- - extention
properties:
extention:
type: array
items:
type: string
- graph:
- type: object
required:
- - type
- extention
+ graph:
+ type: object
properties:
type:
type: array
@@ -375,4 +365,30 @@ properties:
extention:
type: array
items:
- type: string
\ No newline at end of file
+ type: string
+ required:
+ - type
+ - extention
+ required:
+ - stat
+ - graph
+required:
+ - fastq_dir
+ - modules
+ - tools
+ - consensus
+ - gisaid
+ - nextclade
+ - ivar
+ - bamclipper
+ - bwa
+ - bowtie2
+ - minimap2
+ - sickle_trim
+ - cutadapt
+ - multiqc
+ - fastq_screen
+ - rename
+ - resources
+ - envs
+ - report
\ No newline at end of file
diff --git a/workflow/scripts/__pycache__/__init__.cpython-312.pyc b/workflow/scripts/__pycache__/__init__.cpython-312.pyc
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diff --git a/workflow/scripts/functions.py b/workflow/scripts/functions.py
index e55beb1..a3b26ef 100644
--- a/workflow/scripts/functions.py
+++ b/workflow/scripts/functions.py
@@ -8,12 +8,12 @@
### ###
###I###R###D######U###2###3###3#######T###R###A###N###S###V###I###H###M###I####
# Name ___________________ functions.py
-# Version ________________ v.2025.01
+# Version ________________ v.2025.04
# Author _________________ Nicolas Fernandez
# Affiliation ____________ IRD_U233_TransVIHMI
# Aim ____________________ Snakefile functions
# Date ___________________ 2021.10.12
-# Latest modifications ___ 2025.03.12
+# Latest modifications ___ 2025.04.04
# Use ____________________ import scripts.functions as functions
###############################################################################
@@ -21,9 +21,7 @@
### IMPORTS ###
###############
-import os
-import re
-import glob
+import os, re, glob, time, sys, subprocess, platform, yaml
from snakemake.io import expand
from collections import defaultdict
@@ -31,12 +29,19 @@ from collections import defaultdict
### GLOBAL VARIABLES ###
########################
+# Define colors
+blue = "\033[1;34m"
+green = "\033[1;32m"
+red = "\033[1;31m"
+ylo = "\033[1;33m"
+nc = "\033[0m"
###############################################################################
### FUNCTIONS ###
##################
-# get_valid_fastq
+###############################################################################
+# GET_VALID_FASTQ
def get_valid_fastq(fastq_dir):
fastq_files = glob.glob(os.path.join(fastq_dir, "*.fastq.gz"))
sample_dict = defaultdict(dict)
@@ -51,8 +56,7 @@ def get_valid_fastq(fastq_dir):
mate = match.group("mate")
sample_dict[sample][mate] = fastq
else:
- warnings.append(f"[WARNING] File '{basename}' does not match the expected naming pattern. Skipping.")
-
+ warnings.append(f"{red}[WARNING]{nc} File '{basename}' does not match the expected naming pattern. Skipping.")
# Is paired ?
valid_fastq = {}
for sample, mates in sample_dict.items():
@@ -60,27 +64,29 @@ def get_valid_fastq(fastq_dir):
valid_fastq[sample] = mates
else:
missing = "R1" if "1" not in mates else "R2"
- warnings.append(f"[WARNING] Sample '{sample}' is incomplete (missing {missing}). Skipping.")
+ warnings.append(f"{red}[WARNING]{nc} Sample '{sample}' is incomplete (missing {missing}). Skipping.")
+ warnings.append(f"\n{blue}[INFO]{nc} Total valid samples: {len(valid_fastq)}")
- warnings.append(f"\n[INFO] Total valid samples: {len(valid_fastq)}")
+ return valid_fastq, warnings
- return valid_fastq
-
-# get_bam_input
+###############################################################################
+## GET_BAM_INPUT
def get_bam_input(wildcards):
- markdup = "results/02_Mapping/{reference}/{sample}_{mapper}_mark-dup.bam"
+ markdup = "results/02_Mapping/{reference}/{sample}_{mapper}_markdup.bam"
if "cleapping" in MODULES:
- markdup = "results/02_Mapping/{reference}/{sample}_{mapper}_mark-dup.primerclipped.bam"
+ markdup = "results/02_Mapping/{reference}/{sample}_{mapper}_markdup_trimmed.bam"
return markdup
-# get_bai_input
+###############################################################################
+## GET_BAI_INPUT
def get_bai_input(wildcards):
- index = "results/02_Mapping/{reference}/{sample}_{mapper}_mark-dup.bam.bai"
+ index = "results/02_Mapping/{reference}/{sample}_{mapper}_markdup.bam.bai"
if "cleapping" in MODULES:
- index = "results/02_Mapping/{reference}/{sample}_{mapper}_mark-dup.primerclipped.bam.bai"
+ index = "results/02_Mapping/{reference}/{sample}_{mapper}_markdup_trimmed.bam.bai"
return index
-# GET_FINAL_OUTPUTS
+###############################################################################
+## GET_FINAL_OUTPUTS
def get_final_outputs():
final_outputs = []
# quality_controls
@@ -93,11 +99,11 @@ def get_final_outputs():
mate = MATE))
# reads_trimming
if MODULES["keeptrim"]:
- final_outputs.append(expand("results/01_Trimming/sickle/{sample}_cutadapt-sickle-trimmed_R1.fastq.gz",
+ final_outputs.append(expand("results/01_Trimming/sickle/{sample}_cutadapt-sickle-trim_R1.fastq.gz",
sample = SAMPLE))
- final_outputs.append(expand("results/01_Trimming/sickle/{sample}_cutadapt-sickle-trimmed_R2.fastq.gz",
+ final_outputs.append(expand("results/01_Trimming/sickle/{sample}_cutadapt-sickle-trim_R2.fastq.gz",
sample = SAMPLE))
- final_outputs.append(expand("results/01_Trimming/sickle/{sample}_cutadapt-sickle-trimmed_SE.fastq.gz",
+ final_outputs.append(expand("results/01_Trimming/sickle/{sample}_cutadapt-sickle-trim_SE.fastq.gz",
sample = SAMPLE))
# genomes_indexing
final_outputs.append(expand("resources/indexes/fastq-screen/{qc_ref}",
@@ -105,21 +111,21 @@ def get_final_outputs():
# reads_mapping
# primers_clipping
if MODULES["clipping"]:
- final_outputs.append(expand("results/02_Mapping/{reference}/{sample}_{mapper}_mark-dup.primerclipped.bam",
+ final_outputs.append(expand("results/02_Mapping/{reference}/{sample}_{mapper}_markdup_trimmed.bam",
reference = REFERENCE,
sample = SAMPLE,
mapper = MAPPER))
- final_outputs.append(expand("results/02_Mapping/{reference}/{sample}_{mapper}_mark-dup.primerclipped.bam.bai",
+ final_outputs.append(expand("results/02_Mapping/{reference}/{sample}_{mapper}_markdup_trimmed.bam.bai",
reference = REFERENCE,
sample = SAMPLE,
mapper = MAPPER))
# duplicates_removing
# coverage_stats
if MODULES["covstats"]:
- final_outputs.append(expand("results/03_Coverage/{reference}/{sample}_{mapper}_{min_cov}X_coverage-stats.tsv",
+ final_outputs.append(expand("results/03_Coverage/{reference}/{sample}_{mapper}_{min_depth}X_coverage-stats.tsv",
reference = REFERENCE,
sample = SAMPLE,
- min_cov=MIN_COV,
+ min_depth=MIN_DEPTH,
mapper = MAPPER))
final_outputs.append(expand("results/03_Coverage/{reference}/histogram/{sample}_{mapper}_coverage-histogram.txt",
reference = REFERENCE,
@@ -134,49 +140,319 @@ def get_final_outputs():
# variants_calling
# consensus_calling
if MODULES["consensus"]:
- final_outputs.append(expand("results/05_Consensus/{reference}/{sample}_{mapper}_{min_cov}X_{caller}_consensus.fasta",
+ final_outputs.append(expand("results/05_Consensus/{reference}/{sample}_{mapper}_{min_depth}X_{caller}_consensus.fasta",
reference = REFERENCE,
sample = SAMPLE,
mapper = MAPPER,
- min_cov=MIN_COV,
+ min_depth=MIN_DEPTH,
caller=CALLER))
- final_outputs.append(expand("results/04_Variants/{reference}/{sample}_{mapper}_{min_cov}X_{caller}_variant-filt.vcf",
+ final_outputs.append(expand("results/04_Variants/{reference}/{sample}_{mapper}_{min_depth}X_{caller}_variant-filt.vcf",
reference = REFERENCE,
sample = SAMPLE,
mapper = MAPPER,
- min_cov = MIN_COV,
+ min_depth = MIN_DEPTH,
caller = CALLER))
# lineages_calling
if MODULES["lineages"]:
- final_outputs.append(expand("results/06_Lineages/{reference}/{sample}_{mapper}_{min_cov}X_{caller}_{assigner}-report.tsv",
+ final_outputs.append(expand("results/06_Lineages/{reference}/{sample}_{mapper}_{min_depth}X_{caller}_{assigner}-report.tsv",
reference = REFERENCE,
sample = SAMPLE,
mapper = MAPPER,
- min_cov = MIN_COV,
+ min_depth = MIN_DEPTH,
caller = CALLER,
assigner = ASSIGNER))
# results_merging
- final_outputs.append(expand("results/All_{reference}_{mapper}_{min_cov}X_{caller}_consensus_sequences.fasta",
+ final_outputs.append(expand("results/All_{reference}_{mapper}_{min_depth}X_{caller}_consensus_sequences.fasta",
reference = REFERENCE,
mapper = MAPPER,
- min_cov = MIN_COV,
+ min_depth = MIN_DEPTH,
caller = CALLER))
- final_outputs.append(expand("results/All_{reference}_{mapper}_{min_cov}X_genome_coverages.tsv",
+ final_outputs.append(expand("results/All_{reference}_{mapper}_{min_depth}X_genome_coverages.tsv",
reference = REFERENCE,
mapper = MAPPER,
- min_cov = MIN_COV))
- final_outputs.append(expand("results/All_{reference}_{mapper}_{min_cov}X_{caller}_{assigner}-lineages.tsv",
+ min_depth = MIN_DEPTH))
+ final_outputs.append(expand("results/All_{reference}_{mapper}_{min_depth}X_{caller}_{assigner}-lineages.tsv",
reference = REFERENCE,
mapper = MAPPER,
- min_cov = MIN_COV,
+ min_depth = MIN_DEPTH,
caller = CALLER,
assigner = ASSIGNER))
- # logs
- #final_outputs.append("results/10_Reports/setup.log")
- final_outputs.append("results/10_Reports/settings.log")
- final_outputs.append("results/10_Reports/config.log")
- final_outputs.append("results/10_Reports/envs/")
# return final_outpus
return final_outputs
###############################################################################
+# GET_SETTINGS
+def get_settings(config, start_time):
+ # Get working directory
+ workdir = os.getcwd()
+
+ # Get GeVarLi version
+ version_file = os.path.join(workdir, "VERSION.txt")
+ try:
+ with open(version_file, "r") as vf:
+ version = vf.read().strip()
+ except Exception:
+ version = "N/A"
+
+ # Get
+ shell = os.environ.get("SHELL", "N/A")
+
+ # Get system information
+ system_platform = platform.system().lower()
+ if "darwin" in system_platform:
+ os_type = "osx"
+ elif "linux" in system_platform:
+ os_type = "linux"
+ elif "bsd" in system_platform:
+ os_type = "bsd"
+ elif "sunos" in system_platform:
+ os_type = "solaris"
+ elif "windows" in system_platform:
+ os_type = "windows"
+ else:
+ os_type = "unknown (" + system_platform + ")"
+
+ # Get hardware information
+ if os_type == "osx":
+ try:
+ model_name = subprocess.check_output(["sysctl", "-n", "machdep.cpu.brand_string"]).decode().strip()
+ physical_cpu = subprocess.check_output(["sysctl", "-n", "hw.physicalcpu"]).decode().strip()
+ logical_cpu = subprocess.check_output(["sysctl", "-n", "hw.logicalcpu"]).decode().strip()
+ mem_size = subprocess.check_output(["sysctl", "-n", "hw.memsize"]).decode().strip() # en octets
+ ram_gb = int(mem_size) // (1024 ** 3)
+ except Exception:
+ model_name = physical_cpu = logical_cpu = ram_gb = "N/A"
+ elif os_type in ["linux", "bsd", "solaris"]:
+ try:
+ lscpu_out = subprocess.check_output(["lscpu"]).decode()
+ model_name = ""
+ physical_cpu = ""
+ threads_cpu = ""
+ for line in lscpu_out.splitlines():
+ if "Model name:" in line:
+ model_name = line.split(":", 1)[1].strip()
+ if line.startswith("CPU(s):"):
+ physical_cpu = line.split(":", 1)[1].strip()
+ if "Thread(s) per core:" in line:
+ threads_cpu = line.split(":", 1)[1].strip()
+ if physical_cpu and threads_cpu:
+ logical_cpu = int(physical_cpu) * int(threads_cpu)
+ else:
+ logical_cpu = "N/A"
+ except Exception:
+ model_name = physical_cpu = logical_cpu = "N/A"
+ try:
+ with open("/proc/meminfo", "r") as meminfo:
+ for line in meminfo:
+ if line.startswith("MemTotal:"):
+ mem_kb = int(re.findall(r'\d+', line)[0])
+ ram_gb = mem_kb // (1024 ** 2)
+ break
+ except Exception:
+ ram_gb = "N/A"
+ else:
+ print(f"\nPlease, use a UNIX-like operating system (linux, osx, WSL).")
+ sys.exit(0)
+
+ # Get network status
+ def is_online():
+ for host in ["google.com", "cloudflare.com"]:
+ try:
+ subprocess.check_call(
+ ["ping", "-c", "1", "-W", "5", host],
+ stdout=subprocess.DEVNULL,
+ stderr=subprocess.DEVNULL,
+ )
+ return True
+ except subprocess.CalledProcessError:
+ continue
+ return False
+
+ network = "Online" if is_online() else "Offline"
+
+ # Get Conda / Snakemake version
+ def get_version(cmd, fallback="N/A"):
+ try:
+ return subprocess.check_output(cmd).decode().strip()
+ except Exception:
+ return fallback
+
+ conda_version = get_version(["conda", "--version"])
+ mamba_version = get_version(["mamba", "--version"]).splitlines()[0]
+ snakemake_version = get_version(["snakemake", "--version"])
+
+ # Get resources
+ resources = config.get("resources", {})
+ max_threads = resources.get("cpus", "N/A")
+ max_memory = resources.get("ram", "N/A")
+ tmp_dir = resources.get("tmp_dir", "N/A")
+
+ # Get modules
+ modules = config.get("modules", {})
+ qualities = modules.get("qualities", "N/A")
+ keeptrim = modules.get("keeptrim", "N/A")
+ clipping = modules.get("clipping", "N/A")
+ covstats = modules.get("covstats", "N/A")
+ consensus = modules.get("consensus", "N/A")
+ lineages = modules.get("lineages", "N/A")
+ gisaid = modules.get("gisaid", "N/A")
+
+ # Get tools
+
+ tools = config.get("tools", {})
+ mapper = tools.get("mapper", "N/A")
+ caller = tools.get("caller", "N/A")
+ assigner = tools.get("assigner", "N/A")
+
+ # Get consensus parameters
+ reference = config.get("consensus", {}).get("reference", "N/A")
+
+ ivar_consensus = config.get("ivar", {}).get("consensus", {})
+ min_depth = ivar_consensus.get("min_depth", "N/A")
+ max_depth = ivar_consensus.get("max_depth", "N/A")
+ min_freq = ivar_consensus.get("min_freq", "N/A")
+ min_insert = ivar_consensus.get("min_insert", "N/A")
+
+ # Get other parameters
+ nextclade_dataset = config.get("nextclade", {}).get("dataset", "N/A")
+ fastqscreen_subset = config.get("fastq_screen", {}).get("subset", "N/A")
+ cutadapt_clipping = config.get("cutadapt", {}).get("clipping", "N/A")
+
+ # Get time stamp
+ time_stamp_start = time.strftime("%Y-%m-%d %H:%M", time.localtime(start_time))
+
+ # Définir les listes de samples et warnings formatées
+ samples_list = "\n".join(SAMPLE) if SAMPLE else "No samples"
+ warnings_list = "\n".join(SAMPLE_WARNINGS) if SAMPLE_WARNINGS else "No warnings"
+
+ # Create message
+ message_settings = f"""
+ {blue}------------------------------------------------------------------------{nc}
+ {blue}#####{nc} {red}About{nc} {blue}#####{nc}
+ {blue}-----------------{nc}
+
+ {green}Name{nc} _________________________ GeVarLi
+ {green}Version{nc} ______________________ {ylo}{version}{nc}
+ {green}Author{nc} _______________________ Nicolas Fernandez
+ {green}Affiliation{nc} __________________ IRD_U233_TransVIHMI
+ {green}Aim{nc} __________________________ {red}Ge{nc}nome assembling, {red}Var{nc}iant calling and {red}Li{nc}neage assignation
+ {green}Date{nc} _________________________ 2021.10.12
+ {green}Latest modifications{nc} _________ 2025.03.26
+ {green}Use{nc} __________________________ '{ylo}snakemake --use-conda{nc}'
+
+
+ {blue}------------------------------------------------------------------------{nc}
+ {blue}#####{nc} {red}Operating System{nc} {blue}#####{nc}
+ {blue}----------------------------{nc}
+
+ {green}Operating system{nc} _____________ {red}{os_type}{nc}
+ {green}Shell{nc} ________________________ '{ylo}{shell}{nc}'
+
+
+ {blue}------------------------------------------------------------------------{nc}
+ {blue}#####{nc} {red}Hardware{nc} {blue}#####{nc}
+ {blue}--------------------{nc}
+
+ {ylo}Brand(R){nc} | {ylo}Type(R){nc} | {ylo}Model{nc} | {ylo}@ Speed GHz{nc}
+ {green}Chip Model Name{nc} ______________ {model_name}
+ {green}Physical CPUs{nc} ________________ {red}{physical_cpu}{nc}
+ {green}Logical CPUs{nc} _________________ {red}{logical_cpu}{nc} threads
+ {green}System Memory{nc} ________________ {red}{ram_gb}{nc} Gb of RAM
+
+
+ {blue}------------------------------------------------------------------------{nc}
+ {blue}#####{nc} {red}Configuration{nc} {blue}#####{nc}
+ {blue}-------------------------{nc}
+
+ {green}Starting time{nc} ________________ {time_stamp_start}
+
+ {green}Conda version{nc} ________________ {ylo}{conda_version}{nc}
+ {green}Mamba version{nc} ________________ {ylo}{mamba_version}{nc}
+ {green}Snakemake version{nc} ____________ {ylo}{snakemake_version}{nc}
+
+ {green}Max threads{nc} __________________ {red}{max_threads}{nc} of {ylo}{logical_cpu}{nc} threads available
+ {green}Max memory{nc} ___________________ {red}{max_memory}{nc} Gb of {ylo}{ram_gb}{nc} Gb available
+ {green}Temp directory{nc} _______________ '{ylo}{tmp_dir}{nc}'
+
+ {green}Network{nc} ______________________ {red}{network}{nc}
+
+ {green}Working directory{nc} ____________ '{ylo}{workdir}{nc}'
+ {green}Fastq directory{nc} ______________ '{ylo}{FASTQ_DIR}{nc}'
+
+ {green} > Warnings:{nc}
+
+{warnings_list}
+
+ {green} > Samples list:{nc}
+
+{samples_list}
+
+ {blue}Modules:{nc}
+ {green} > Quality Control{nc} ___________ {ylo}{qualities}{nc}
+ {green} > Keep Trim{nc} _________________ {ylo}{keeptrim}{nc}
+ {green} > Soft Clipping{nc} _____________ {ylo}{clipping}{nc}
+ {green} > Cov Stats{nc} _________________ {ylo}{covstats}{nc}
+ {green} > Consensus{nc} _________________ {ylo}{consensus}{nc}
+ {green} > Lineages{nc} __________________ {ylo}{lineages}{nc}
+ {green} > Gisaid{nc} ____________________ {ylo}{gisaid}{nc}
+
+ {blue}Tools:{nc}
+ {green} > Mapper{nc} ____________________ {ylo}{mapper}{nc}
+ {green} > Caller{nc} ____________________ {ylo}{caller}{nc}
+ {green} > Assigner{nc} __________________ {ylo}{assigner}{nc}
+
+ {blue}Params:{nc}
+ {green} > Reference genome{nc} __________ {ylo}{reference}{nc}
+ {green} > Min depth{nc} _________________ {red}{min_depth}{nc}x
+ {green} > Max depth{nc} _________________ {red}{max_depth}{nc}x
+ {green} > Min allele frequency{nc} ______ {red}{min_freq}{nc}
+ {green} > Min insertion frequency{nc} ___ {red}{min_insert}{nc}
+
+ {green} > Nextclade dataset{nc} _________ {ylo}{nextclade_dataset}{nc}
+ {green} > Fastq-Screen subset{nc} _______ {red}{fastqscreen_subset}{nc} reads/sample
+ {green} > Hard clipping{nc} _____________ {red}{cutadapt_clipping}{nc}nt (with cutadapt)
+ """
+
+ # Clean message
+ ansi_escape = re.compile(r'\x1B\[[0-9;]*[mK]')
+ message_clean = ansi_escape.sub('', message_settings)
+
+ # Create log file
+ results_dir = os.path.join(workdir, "results", "10_Reports")
+ os.makedirs(results_dir, exist_ok=True)
+
+ # Write log file
+ log_file = os.path.join(results_dir, "settings.log")
+ with open(log_file, "w") as logf:
+ logf.write(message_clean)
+
+ # Print message
+ print(message_settings)
+
+###############################################################################
+# GET_TIME
+def get_time(start_time):
+ time_stamp_start = time.strftime("%Y-%m-%d %H:%M", time.localtime(start_time))
+ time_stamp_end = time.strftime("%Y-%m-%d %H:%M", time.localtime())
+ elapsed_time = int(time.time() - start_time)
+ hours = elapsed_time // 3600
+ minutes = (elapsed_time % 3600) // 60
+ seconds = elapsed_time % 60
+ formatted_time = f"{hours:02d}:{minutes:02d}:{seconds:02d}"
+ green = "\033[32m"
+ ylo = "\033[33m"
+ nc = "\033[0m"
+ message_time = f"""
+{green}Start time{nc} _____________ {time_stamp_start}
+{green}End time{nc} _______________ {time_stamp_end}
+ {green}Processing time{nc} ________ {ylo}{formatted_time}{nc}
+ {green} > Hard clipping{nc} _____________ {red}{cutadapt_clipping} nt{nc} (with cutadapt)
+"""
+ print(message_time)
+ ansi_escape = re.compile(r'\x1B\[[0-?]*[ -/]*[@-~]')
+ message_clean = ansi_escape.sub('', message_time)
+ with open("results/10_Reports/time.log", "w") as f:
+ f.write(message_clean)
+
+###############################################################################
+###############################################################################
\ No newline at end of file
diff --git a/workflow/scripts/settings.py b/workflow/scripts/settings.py
deleted file mode 100644
index 5d9a94b..0000000
--- a/workflow/scripts/settings.py
+++ /dev/null
@@ -1,214 +0,0 @@
-#!/usr/bin/env python3
-
-import os
-import sys
-import subprocess
-import platform
-import re
-import glob
-import time
-import yaml
-
-# Get working directory
-workdir = os.path.abspath(os.path.join(os.path.dirname(__file__), "../../"))
-
-# Get version
-version_file = os.path.join(workdir, "VERSION.txt")
-try:
- with open(version_file, "r") as vf:
- version = vf.read().strip()
-except Exception:
- version = "N/A"
-
-# Define colors
-blue = "\033[1;34m"
-green = "\033[1;32m"
-red = "\033[1;31m"
-ylo = "\033[1;33m"
-nc = "\033[0m"
-
-# Get system information
-system_platform = platform.system().lower()
-if "darwin" in system_platform:
- os_type = "osx"
-elif "linux" in system_platform:
- os_type = "linux"
-elif "bsd" in system_platform:
- os_type = "bsd"
-elif "sunos" in system_platform:
- os_type = "solaris"
-elif "windows" in system_platform:
- os_type = "windows"
-else:
- os_type = "unknown (" + system_platform + ")"
-
-# Get hardware information
-if os_type == "osx":
- try:
- model_name = subprocess.check_output(["sysctl", "-n", "machdep.cpu.brand_string"]).decode().strip()
- physical_cpu = subprocess.check_output(["sysctl", "-n", "hw.physicalcpu"]).decode().strip()
- logical_cpu = subprocess.check_output(["sysctl", "-n", "hw.logicalcpu"]).decode().strip()
- mem_size = subprocess.check_output(["sysctl", "-n", "hw.memsize"]).decode().strip() # en octets
- ram_gb = int(mem_size) // (1024 ** 3)
- except Exception:
- model_name = physical_cpu = logical_cpu = ram_gb = "N/A"
-elif os_type in ["linux", "bsd", "solaris"]:
- try:
- lscpu_out = subprocess.check_output(["lscpu"]).decode()
- model_name = ""
- physical_cpu = ""
- threads_cpu = ""
- for line in lscpu_out.splitlines():
- if "Model name:" in line:
- model_name = line.split(":", 1)[1].strip()
- if line.startswith("CPU(s):"):
- physical_cpu = line.split(":", 1)[1].strip()
- if "Thread(s) per core:" in line:
- threads_cpu = line.split(":", 1)[1].strip()
- if physical_cpu and threads_cpu:
- logical_cpu = int(physical_cpu) * int(threads_cpu)
- else:
- logical_cpu = "N/A"
- except Exception:
- model_name = physical_cpu = logical_cpu = "N/A"
- try:
- with open("/proc/meminfo", "r") as meminfo:
- for line in meminfo:
- if line.startswith("MemTotal:"):
- mem_kb = int(re.findall(r'\d+', line)[0])
- ram_gb = mem_kb // (1024 ** 2)
- break
- except Exception:
- ram_gb = "N/A"
-else:
- print(f"\nPlease, use a UNIX-like operating system (linux, osx, WSL).")
- sys.exit(0)
-
-# Get network status
-def is_online():
- for host in ["google.com", "cloudflare.com"]:
- try:
- subprocess.check_call(
- ["ping", "-c", "1", "-W", "5", host],
- stdout=subprocess.DEVNULL,
- stderr=subprocess.DEVNULL,
- )
- return True
- except subprocess.CalledProcessError:
- continue
- return False
-
-network = "Online" if is_online() else "Offline"
-
-# Get version
-def get_version(cmd, fallback="N/A"):
- try:
- return subprocess.check_output(cmd).decode().strip()
- except Exception:
- return fallback
-
-conda_version = get_version(["conda", "--version"])
-mamba_version = get_version(["mamba", "--version"]).splitlines()[0]
-snakemake_version = get_version(["snakemake", "--version"])
-
-# Get configuration
-config_file = os.path.join(workdir, "config", "config.yaml")
-with open(config_file, "r") as cf:
- config_data = yaml.safe_load(cf)
-
-# Get fastq directory
-fastq_dir = config_data.get("fastq_dir", "")
-fastq_files = len(glob.glob(os.path.join(fastq_dir, "*.fastq.gz")))
-fastq_R1 = len(glob.glob(os.path.join(fastq_dir, "*R1*.fastq.gz")))
-fastq_R2 = len(glob.glob(os.path.join(fastq_dir, "*R2*.fastq.gz")))
-
-# Get resources
-resources = config_data.get("resources", {})
-max_threads = resources.get("cpus", "N/A")
-max_memory = resources.get("ram", "N/A")
-
-# Get modules
-modules = config_data.get("modules", {})
-qualities = modules.get("qualities", "N/A")
-keeptrim = modules.get("keeptrim", "N/A")
-cleapping = modules.get("cleapping", "N/A")
-covstats = modules.get("covstats", "N/A")
-consensus = modules.get("consensus", "N/A")
-lineages = modules.get("lineages", "N/A")
-gisaid = modules.get("gisaid", "N/A")
-
-# Get consensus parameters
-consensus_params = config_data.get("consensus", {})
-reference_conf = consensus_params.get("reference", "N/A")
-mapper = consensus_params.get("mapper", "N/A")
-min_cov = consensus_params.get("min_cov", "N/A")
-min_freq = consensus_params.get("min_freq", "N/A")
-assigner = consensus_params.get("assigner", "N/A")
-
-# Get other parameters
-nextclade_dataset = config_data.get("nextclade", {}).get("dataset", "N/A")
-fastqscreen_subset = config_data.get("fastq_screen", {}).get("subset", "N/A")
-cutadapt_clipping = config_data.get("cutadapt", {}).get("clipping", "N/A")
-
-# Get time stamp
-time_stamp_start = time.strftime("%Y-%m-%d %H:%M", time.localtime())
-
-# Create message
-message_settings = f"""{blue}------------------------------------------------------------------------{nc}
-{blue}#####{nc} {red}Configuration{nc} {blue}#####{nc}
-{blue}-------------------------{nc}
-
-{green}Starting time{nc} ______________ {time_stamp_start}
-
-{green}Conda version{nc} ______________ {ylo}{conda_version}{nc}
-{green}Mamba version{nc} ______________ {ylo}{mamba_version}{nc}
-{green}Snakemake version{nc} __________ {ylo}{snakemake_version}{nc}
-
-{green}Max threads{nc} ________________ {red}{max_threads}{nc} of {ylo}{logical_cpu}{nc} threads available
-{green}Max memory{nc} _________________ {red}{max_memory}{nc} of {ylo}{ram_gb}{nc} Gb available
-{green}Jobs memory{nc} ________________ {red}N/A{nc} Gb per job
-
-{green}Network{nc} ____________________ {red}{network}{nc}
-
-{green}Working directory{nc} _________ '{ylo}{workdir}{nc}'
-
-{green}Fastq directory{nc} ___________ '{ylo}{fastq_dir}{nc}'
-{green} > Fastq processed{nc} ________ {red}{fastq_files}{nc} fastq files
-{green} > Forward reads{nc} __________ {red}{fastq_R1}{nc} R1
-{green} > Reverse reads{nc} __________ {red}{fastq_R2}{nc} R2
-
-{blue}Modules:{nc}
-{green} > Quality Control{nc} ________ {red}{qualities}{nc}
-{green} > Keep Trim{nc} ______________ {red}{keeptrim}{nc}
-{green} > Soft Clipping{nc} __________ {red}{cleapping}{nc}
-{green} > Cov Stats{nc} ______________ {red}{covstats}{nc}
-{green} > Consensus{nc} ______________ {red}{consensus}{nc}
-{green} > Lineages{nc} _______________ {red}{lineages}{nc}
-{green} > Gisaid{nc} _________________ {red}{gisaid}{nc}
-
-{blue}Params:{nc}
-{green} > Reference genome{nc} _______ {ylo}{reference_conf}{nc}
-{green} > Mapper{nc} ________________ {ylo}{mapper}{nc}
-{green} > Min coverage{nc} ___________ {red}{min_cov}{nc} X
-{green} > Min allele frequency{nc} ___ {red}{min_freq}{nc}
-{green} > Assigner{nc} ______________ {red}{assigner}{nc}
-{green} - Nextclade dataset{nc} _____ {red}{nextclade_dataset}{nc}
-{green} > Fastq-Screen subset{nc} ____ {red}{fastqscreen_subset}{nc}
-{green} > Cutadapt clipping{nc} ______ {red}{cutadapt_clipping} nt{nc}
-"""
-
-# Print message
-print(message_settings)
-
-# Clean message
-ansi_escape = re.compile(r'\x1B\[[0-9;]*[mK]')
-message_clean = ansi_escape.sub('', message_settings)
-
-# Create log file
-results_dir = os.path.join(workdir, "results", "10_Reports")
-os.makedirs(results_dir, exist_ok=True)
-
-# Write log file
-log_file = os.path.join(results_dir, "settings.log")
-with open(log_file, "w") as logf:
- logf.write(message_clean)
\ No newline at end of file
diff --git a/workflow/scripts/settings.sh b/workflow/scripts/settings.sh
deleted file mode 100644
index 55863c8..0000000
--- a/workflow/scripts/settings.sh
+++ /dev/null
@@ -1,196 +0,0 @@
-#!/bin/bash
-
-###I###R###D######U###2###3###3#######T###R###A###N###S###V###I###H###M###I####
-### ###
-### /\ ______ ___ ____ _ _ __ ____ __ ____ ______ /\ ###
-### || \ \ \ \ / __( ___( \/ )__\ ( _ ( ) (_ _) / / / / || ###
-### || > > > > ( (_-.)__) \ /(__)\ ) /)(__ _)(_ < < < < || ###
-### || /_/_/_/ \___(____) \(__)(__(_)\_(____(____) \_\_\_\ || ###
-### \/ \/ ###
-### ###
-###I###R###D######U###2###3###3#######T###R###A###N###S###V###I###H###M###I####
-# Name ___________________ Run_GeVarLi.sh
-# Version ________________ v.2025.03
-# Author _________________ Nicolas Fernandez
-# Affiliation ____________ IRD_U233_TransVIHMI
-# Aim ____________________ Bash script running GeVarLi snakefile
-# Date ___________________ 2021.10.12
-# Latest modifications ___ 2025.03.12
-# Use ____________________ '. Run_GeVarLi.sh'
-###############################################################################
-
-###############################################################################
-### ABOUT ###
-#############
-
-workdir=$(cd "$(dirname "${BASH_SOURCE[0]}" )"/../../ && pwd) # Get working directory
-version=$(<${workdir}/VERSION.txt) # Get version
-
-blue="\033[1;34m" # blue
-green="\033[1;32m" # green
-red="\033[1;31m" # red
-ylo="\033[1;33m" # yellow
-nc="\033[0m" # no color
-
-###############################################################################
-### OPERATING SYSTEM ###
-########################
-
-shell=$SHELL # Get shell
-
-# Get operating system
-case "$OSTYPE" in
- darwin*) os="osx" ;;
- linux*) os="linux" ;;
- bsd*) os="bsd" ;;
- solaris*) os="solaris" ;;
- msys*) os="windows" ;;
- cygwin*) os="windows" ;;
- *) os="unknown (${OSTYPE})" ;;
-esac
-
-###############################################################################
-### HARDWARE ###
-################
-
-if [[ ${os} == "osx" ]]
-then
- model_name=$(sysctl -n machdep.cpu.brand_string) # Get chip model name
- physical_cpu=$(sysctl -n hw.physicalcpu) # Get physical cpu
- logical_cpu=$(sysctl -n hw.logicalcpu) # Get logical cpu
- mem_size=$(sysctl -n hw.memsize) # Get memory size (bit)
- ram_gb=$(expr ${mem_size} \/ $((1024**3))) # mem_size / 1024**3 = Gb
-elif [[ ${os} == "linux" || ${os} == "bsd" || ${os} == "solaris" ]]
-then
- model_name=$(lscpu | grep -o -E "Model name: +.+" | sed -E "s/Model name: +//") # Get chip model name
- physical_cpu=$(lscpu | grep -o -E "^CPU\(s\): +[0-9]+" | sed -E "s/CPU\(s\): +//") # Get physical cpu
- threads_cpu=$(lscpu | grep -o -E "^Thread\(s\) per core: +[0-9]+" | sed -E "s/Thread\(s\) per core: +//") # Get thread(s) per core
- logical_cpu=$(expr ${physical_cpu} \* ${threads_cpu}) # Calcul logical cpu
- mem_size=$(grep -o -E "MemTotal: +[0-9]+" /proc/meminfo | sed -E "s/MemTotal: +//") # Get memory size (Kb)
- ram_gb=$(expr ${mem_size} \/ $((1024**2))) # mem_size / 1024**2 = Gb
-else
- echo -e "\n Please, use an '${ylo}UNIX${nc}' operating system, like:
- > '${green}linux${nc}'
- > '${green}osx${nc}'
- > '${green}WSL${nc}' \n"
- return 0
-fi
-
-###############################################################################
-### NETWORK ###
-###############
-
-if ping -c 1 -W 5 google.com > /dev/null 2>&1 || \
- ping -c 1 -W 5 cloudflare.com > /dev/null 2>&1
-then
- network="Online"
-else
- network="Offline"
-fi
-
-###############################################################################
-### CONDA ###
-#############
-
-message_conda="
-$(conda --version)
-Path: $(which conda)
-$(conda config --show channels)
-"
-
-###############################################################################
-### CONFIGURATION ###
-#####################
-
-conda_version=$(conda --version | sed 's/conda //') # Conda version
-mamba_version=$(mamba --version | head -n 1 | sed 's/mamba //') # Mamba version
-snakemake_version=$(snakemake --version) # Snakemake version
-
-fastq_dir=$(yq -Mr '.fastq_dir' ${config_file}) # Get path to fastq files directory
-fastq_files=$(/bin/ls -l ${fastq_dir}/*.fastq.gz 2> /dev/null | wc -l | sed 's/ //') # Get fastq.gz files count
-fastq_R1=$(/bin/ls -l ${fastq_dir}/*R1*.fastq.gz 2> /dev/null | wc -l | sed 's/ //') # Get R1 fastq files count
-fastq_R2=$(/bin/ls -l ${fastq_dir}/*R2*.fastq.gz 2> /dev/null | wc -l | sed 's/ //') # Get R2 fastq files count
-
-max_threads=$(yq -Mr '.resources.cpus' ${config_file}) # Get user config: max threads
-max_memory=$(yq -Mr '.resources.ram' ${config_file}) # Get user config: max memory (Gb)
-
-qualities=$(yq -Mr '.modules.qualities' ${config_file}) # Reads QC
-keeptrim=$(yq -Mr '.modules.keeptrim' ${config_file}) # Keep trimmed reads
-cleapping=$(yq -Mr '.modules.cleapping' ${config_file}) # Reads cleapping
-covstats=$(yq -Mr '.modules.covstats' ${config_file}) # Mapping coverage stats
-consensus=$(yq -Mr '.modules.consensus' ${config_file}) # Consensus
-lineages=$(yq -Mr '.modules.lineages' ${config_file}) # Lineages assignation
-gisaid=$(yq -Mr '.modules.gisaid' ${config_file}) # Gisaid submission file
-
-# Get user config: genome reference
-reference=$(yq -Mc '.consensus.reference' ${config_file} | sed 's/\[\"//' | sed 's/\"\]//' | sed 's/\"\,\"/ ; /g')
-# Get user config: mapper
-mapper=$(yq -Mc '.consensus.mapper' ${config_file} | sed 's/\[\"//' | sed 's/\"\]//' | sed 's/\"\,\"/ ; /g')
-# Get user config: minimum coverage
-min_cov=$(yq -Mc '.consensus.min_cov' ${config_file} | sed 's/\[\"//' | sed 's/\"\]//' | sed 's/\"\,\"/ ; /g')
-# Get user config: minimum allele frequency
-min_freq=$(yq -Mr '.consensus.min_freq' ${config_file})
-# Get user config: assigner tool
-assigner=$(yq -Mc '.consensus.assigner' ${config_file} | sed 's/\[\"//' | sed 's/\"\]//' | sed 's/\"\,\"/ ; /g')
-# Get user config: hard clipping option
-hard_clipping=$(yq -Mr '.cutadapt.clipping' ${config_file})
-# Get user config: dataset for nextclade
-nextclade_dataset=$(yq -Mc '.nextclade.dataset' ${config_file} | sed 's/\[\"//' | sed 's/\"\]//')
-# Get user config: fastq_screen subsetption
-fastqscreen_subset=$(yq -Mr '.fastq_screen.subset' ${config_file})
-# Get user config: cutadapt clipping
-cutadapt_clipping=$(yq -Mr '.cutadapt.clipping' ${config_file})
-
-
-message_settings="""
-${blue}------------------------------------------------------------------------${nc}
-${blue}#####${nc} ${red}Configuration${nc} ${blue}#####${nc}
-${blue}-------------------------${nc}
-
-${green}Starting time${nc} ______________ ${time_stamp_start}
-
-${green}Conda version${nc} ______________ ${ylo}${conda_version}${nc}
-${green}Mamba version${nc} ______________ ${ylo}${mamba_version}${nc}
-${green}Snakemake version${nc} __________ ${ylo}${snakemake_version}${nc}
-
-${green}Max threads${nc} ________________ ${red}${max_threads}${nc} of ${ylo}${logical_cpu}${nc} threads available
-${green}Max memory${nc} _________________ ${red}${max_memory}${nc} of ${ylo}${ram_gb}${nc} Gb available
-${green}Jobs memory${nc} ________________ ${red}${memory_per_job}${nc} Gb per job
-
-${green}Network${nc} ____________________ ${red}${network}${nc}
-
-${green}Working directory${nc} _________ '${ylo}${workdir}/${nc}'
-
-${green}Fastq directory${nc} ___________ '${ylo}${fastq_dir}${nc}'
-${green} > Fastq processed${nc} ________ ${red}${fastq_files}${nc} fastq files
-${green} > Forward reads${nc} __________ ${red}${fastq_R1}${nc} R1
-${green} > Reverse reads${nc} __________ ${red}${fastq_R2}${nc} R2
-
-${blue}Modules:${nc}
-${green} > Quality Control${nc} ________ ${red}${qualities}${nc}
-${green} > Keep Trim${nc} ______________ ${red}${keeptrim}${nc}
-${green} > Soft Clipping${nc} __________ ${red}${cleapping}${nc}
-${green} > Cov Stats${nc} ______________ ${red}${covstats}${nc}
-${green} > Consensus${nc} ______________ ${red}${consensus}${nc}
-${green} > Lineages${nc} _______________ ${red}${lineages}${nc}
-${green} > Gisaid${nc} _________________ ${red}${gisaid}${nc}
-
-${blue}Params:${nc}
-${green} > Reference genome${nc} _______ ${ylo}${reference}${nc}
-${green} > Mapper${nc} ________________ ${ylo}${mapper}${nc}
-${green} > Min coverage${nc} ___________ ${red}${min_cov}${nc} X
-${green} > Min allele frequency${nc} ___ ${red}${min_freq}${nc}
-${green} > Assigner${nc} _ ${red}${assigner}${nc}
-${green} - Nextclade dataset${nc} _____ ${red}${nextclade_dataset}${nc}
-${green} > Fastq-Screen subset${nc} ____ ${red}${fastqscreen_subset}${nc}
-${green} > Cutadapt clipping${nc} ______ ${red}${cutadapt_clipping} nt${nc}
-"""
-
-# Print settings message
-echo -e "${message}"
-
-# Log settings message
-mkdir -p ${workdir}/results/10_Reports/ 2> /dev/null
-echo -e "${message}" \
- | sed "s/\x1B\[[0-9;]*[mK]//g" \
- > ${workdir}/results/10_Reports/settings.log
\ No newline at end of file
--
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