From 6c2b7b7a3a3361001f7d8a1abd857a5000eba682 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Nicolas=20FERNANDEZ=20NU=C3=91EZ?=
<nicolas.fernandez@ird.fr>
Date: Mon, 17 Apr 2023 16:10:20 +0200
Subject: [PATCH] 2023-04 release
---
README.md | 83 +++++++++++++++++++--------------------
Start_GeVarLi.sh | 4 +-
configuration/config.yaml | 6 +--
3 files changed, 46 insertions(+), 47 deletions(-)
diff --git a/README.md b/README.md
index 70a96b6..172b2bf 100644
--- a/README.md
+++ b/README.md
@@ -1,7 +1,7 @@
# GeVarLi: GEnome assembly, VARiant calling and LIneage assignation #
- | Catalina (10.15.7) | Big Sure (11.6.3) | Monterey (12.6.0) | Ventura (13.2.1)/E6055C?icon=apple&label&list=|&scale=0.9>)
+ | Catalina (10.15.7) | Big Sure (11.6.3) | Monterey (12.6.0) | Ventura (13.3.1)/E6055C?icon=apple&label&list=|&scale=0.9>)
 | Focal Fossa (20.04) | Jammy Jellyfish (22.04)/772953?icon=https://www.svgrepo.com/show/25424/ubuntu-logo.svg&label&list=|&scale=0.9>)
 | Focal Fossa (20.04) | Jammy Jellyfish (22.04)/00BCF2?icon=windows&label&list=|&scale=0.9>)
@@ -12,9 +12,9 @@
-
-
-
+
+
+
## ~ ABOUT ~ ##
@@ -41,20 +41,19 @@ The Covid-19 epidemic has highlighted the disparities that remain between contin
- Sickle-trim (_quality trimming_)
- Reads mapping
- (_bam files_)
- -
- -
-- Variants calling
- - (_vcf files_)
+ - (_bed files_)
+ - Visualization (IGV)
+- Variants calling and filtering (_vcf files_)
- Genome coverage (_statistics reports_)
- Consensus sequences (_fasta file_)
- Genomes classification
- - Nextclade
- - Pangolin
+ - Nextclade (_consensus quality and lineages reports_)
+ - Pangolin (_lineages reports_)
### Version ###
-*V.2023.03*
+*V.2023.04*
### Rulegraph ###
@@ -189,8 +188,8 @@ _Option-2: Edit **fastq-screen.conf** file in **./configuration/** directory_
First run will auto-created _(only once)_:
- Snakemake-Base conda environment _(Snakemake, Mamba, Rename, GraphViz)_
- - GeVarLi-conda environments _(tools used by GeVarLi)_
- - Indexes for BWA and BOWTIE2 aligners _(for each fasta genomes in resources)_
+ - GeVarLi-Tools conda environments _(tools used by GeVarLi)_
+ - Indexes for BWA and BOWTIE2 aligners _(for each fasta genomes in resources/ directory)_
_This may take some time, depending on your internet connection and your computer_
@@ -205,10 +204,10 @@ _Some [temp] tagged files are removed by default, to save disk usage_
├── 📂 archives/
│ └── 📦 Results_{YYYY-MM-DD_HHhMM}_{REFERENCE}_{ALIGNER}_{MINCOV}_{SAMPLES}_archive.tar.gz
└── 📂 results/
- ├── 🧬 All_consensus_sequences.fasta
- ├── 📊 All_genome_coverages.tsv
- ├── 📊 All_nextclade_lineages.tsv
- ├── 📊 All_pangolin_lineages.tsv
+ ├── 🧬 All_{REFERENCE}_consensus_sequences.fasta
+ ├── 📊 All_{REFERENCE}_genome_coverages.tsv
+ ├── 📊 All_{REFERENCE}_nextclade_lineages.tsv
+ ├── 📊 All_{REFERENCE}_pangolin_lineages.tsv
├── 🌠All_readsQC_reports.html
├── 📂 00_Quality_Control/
│ ├── 📂 fastq-screen/
@@ -229,40 +228,40 @@ _Some [temp] tagged files are removed by default, to save disk usage_
│    ├── 📄 multiqc_general_stats.txt
|    └── 📄 multiqc_sources.txt
├── 📂 01_Trimmidapt
- │ ├── 📂 cutad{SAMPLE}_cutadapt-removed_R{1/2}.fastq.gz # [temp]
- │ │ └── 📦 {S
+ │ ├── 📂 cutadapt/
+ │ │ └── 📦 {SAMPLE}_cutadapt-removed_R{1/2}.fastq.gz # [temp]
│ └── 📂 sickle/
│ ├── 📦 {SAMPLE}_sickle-trimmed_R{1/2}.fastq.gz # [temp]
│ └── 📦 {SAMPLE}_sickle-trimmed_SE.fastq.gz # [temp]
├── 📂 02_Mapping/
- │ ├── 🧠{SAMPLE}_{ALIGNER}_mark-dup.bam
- │ ├── ðŸ—‚ï¸ {SAMPLE}_{ALIGNER}_mark-dup.bam.bai
- │ ├── 🧠{SAMPLE}_{ALIGNER}_mark-dup.primerclipped.bam
- │ ├── ðŸ—‚ï¸ {SAMPLE}_{ALIGNER}_mark-dup.primerclipped.bam.bai
+ │ ├── 🧠{SAMPLE}_{REFERENCE}_{ALIGNER}_mark-dup.bam
+ │ ├── ðŸ—‚ï¸ {SAMPLE}_{REFERENCE}_{ALIGNER}_mark-dup.bam.bai
+ │ ├── 🧠{SAMPLE}_{REFERENCE}_{ALIGNER}_mark-dup.primerclipped.bam
+ │ ├── ðŸ—‚ï¸ {SAMPLE}_{REFERENCE}_{ALIGNER}_mark-dup.primerclipped.bam.bai
│ ├── 🧠{SAMPLE}_{ALIGNER}-mapped.sam # [temp]
- │ ├── 🧠{SAMPLE}_{ALIGNER}_sorted-by-names.bam # [temp]
- │ ├── 🧠{SAMPLE}_{ALIGNER}_fixed-mate.bam # [temp]
- │ └── 🧠{SAMPLE}_{ALIGNER}_sorted.bam # [temp]
+ │ ├── 🧠{SAMPLE}_{REFERENCE}_{ALIGNER}_sorted-by-names.bam # [temp]
+ │ ├── 🧠{SAMPLE}_{REFERENCE}_{ALIGNER}_fixed-mate.bam # [temp]
+ │ └── 🧠{SAMPLE}_{REFERENCE}_{ALIGNER}_sorted.bam # [temp]
├── 📂 03_Coverage/
- │ ├── 📊 {SAMPLE}_{ALIGNER}_{MINCOV}_coverage-stats.tsv
- │ ├── ðŸ›ï¸ {SAMPLE}_{ALIGNER}_genome-cov.bed # [temp]
- │ ├── ðŸ›ï¸ {SAMPLE}_{ALIGNER}_{MINCOV}_min-cov-filt.bed # [temp]
- │ └── ðŸ›ï¸ {SAMPLE}_{ALIGNER}_{MINCOV}_low-cov-mask.bed # [temp]
+ │ ├── 📊 {SAMPLE}_{REFERENCE}_{ALIGNER}_{MINCOV}_coverage-stats.tsv
+ │ ├── ðŸ›ï¸ {SAMPLE}_{REFERENCE}_{ALIGNER}_genome-cov.bed # [temp]
+ │ ├── ðŸ›ï¸ {SAMPLE}_{REFERENCE}_{ALIGNER}_{MINCOV}_min-cov-filt.bed # [temp]
+ │ └── ðŸ›ï¸ {SAMPLE}_{REFERENCE}_{ALIGNER}_{MINCOV}_low-cov-mask.bed # [temp]
├── 📂 04_Variants/
- │ ├── 🧬 {SAMPLE}_{ALIGNER}_{MINCOV}_masked-ref.fasta
- │ ├── ðŸ—‚ï¸ {SAMPLE}_{ALIGNER}_{MINCOV}_masked-ref.fasta.fai
- │ ├── 🧠{SAMPLE}_{ALIGNER}_{MINCOV}_indel-qual.bam
- │ ├── ðŸ—‚ï¸ {SAMPLE}_{ALIGNER}_{MINCOV}_indel-qual.bai
- │ ├── ðŸ§®ï¸ {SAMPLE}_{ALIGNER}_{MINCOV}_variant-call.vcf
- │ ├── ðŸ§®ï¸ {SAMPLE}_{ALIGNER}_{MINCOV}_variant-filt.vcf
- │ ├── 📦 {SAMPLE}_{ALIGNER}_{MINCOV}_variant-filt.vcf.bgz # [temp]
- │ └── ðŸ—‚ï¸ {SAMPLE}_{ALIGNER}_{MINCOV}_variant-filt.vcf.bgz.tbi # [temp]
+ │ ├── 🧬 {SAMPLE}_{REFERENCE}_{ALIGNER}_{MINCOV}_masked-ref.fasta
+ │ ├── ðŸ—‚ï¸ {SAMPLE}_{REFERENCE}_{ALIGNER}_{MINCOV}_masked-ref.fasta.fai
+ │ ├── 🧠{SAMPLE}_{REFERENCE}_{ALIGNER}_{MINCOV}_indel-qual.bam
+ │ ├── ðŸ—‚ï¸ {SAMPLE}_{REFERENCE}_{ALIGNER}_{MINCOV}_indel-qual.bai
+ │ ├── ðŸ§®ï¸ {SAMPLE}_{REFERENCE}_{ALIGNER}_{MINCOV}_variant-call.vcf
+ │ ├── ðŸ§®ï¸ {SAMPLE}_{REFERENCE}_{ALIGNER}_{MINCOV}_variant-filt.vcf
+ │ ├── 📦 {SAMPLE}_{REFERENCE}_{ALIGNER}_{MINCOV}_variant-filt.vcf.bgz # [temp]
+ │ └── ðŸ—‚ï¸ {SAMPLE}_{REFERENCE}_{ALIGNER}_{MINCOV}_variant-filt.vcf.bgz.tbi # [temp]
├── 📂 05_Consensus/
- │ └── 🧬 {SAMPLE}_{ALIGNER}_{MINCOV}_consensus.fasta
+ │ └── 🧬 {SAMPLE}_{REFERENCE}_{ALIGNER}_{MINCOV}_consensus.fasta
├── 📂 06_Lineages/
- │ ├── 📊 {SAMPLE}_{ALIGNER}_{MINCOV}_nextclade-report.tsv
- │ ├── 📊 {SAMPLE}_{ALIGNER}_{MINCOV}_pangolin-report.csv
- │ └── 📂 {SAMPLE}_{ALIGNER}_{MINCOV}_nextclade-all/
+ │ ├── 📊 {SAMPLE}_{REFERENCE}_{ALIGNER}_{MINCOV}_nextclade-report.tsv
+ │ ├── 📊 {SAMPLE}_{REFERENCE}_{ALIGNER}_{MINCOV}_pangolin-report.csv
+ │ └── 📂 {SAMPLE}_{REFERENCE}_{ALIGNER}_{MINCOV}_nextclade-all/
 │ ├── 🧬 nextclade.aligned.fasta
 │ ├── 📊 nextclade.csv
 │ ├── 📊 nextclade.errors.csv
diff --git a/Start_GeVarLi.sh b/Start_GeVarLi.sh
index 287d5e1..e7fd319 100755
--- a/Start_GeVarLi.sh
+++ b/Start_GeVarLi.sh
@@ -124,7 +124,7 @@ Conda environment ${red}snakemake-base_v.${snakemake_base_version}${nc} will be
# ${red}Rename${nc}: Rename fastq files (ver. 1.601)
# ${red}Graphviz${nc}: Dot snakemake DAG (ver. 7.1.0)
"
- conda env create -f ${workdir}/workflow/environments/${os}/snakemake-base_v.${snakemake_base_version}.yaml
+q conda env create -f ${workdir}/workflow/environments/${os}/snakemake-base_v.${snakemake_base_version}.yaml
fi
# Remove old 'gevarli' and 'snakemake' environments
@@ -437,7 +437,7 @@ for directory in ${workdir}/results/02_Mapping/*/ ; do
awk "NR==1 || NR%2==0" ${workdir}/results/All_${reference}_genome_coverages.tsv \
2> /dev/null \
1> ${workdir}/results/GENCOV.tmp \
- && mv ${workdir}/results/GENCOV.tmp ${workdir}/results/All_genome_coverages.tsv \
+ && mv ${workdir}/results/GENCOV.tmp ${workdir}/results/All_${reference}_genome_coverages.tsv \
2> /dev/null ;
# Concatenate PANGOLIN
cat ${workdir}/results/06_Lineages/${reference}/*_pangolin-report.csv \
diff --git a/configuration/config.yaml b/configuration/config.yaml
index 8679e8d..9d4d9df 100755
--- a/configuration/config.yaml
+++ b/configuration/config.yaml
@@ -30,8 +30,8 @@ consensus:
reference: # Your reference, in fasta format (default: SARS-CoV-2_Wuhan_MN-908947-3)
# Available options (not exhaustive), choose one:
- 'SARS-CoV-2_Wuhan_MN-908947-3' # SARS-CoV-2 (Nextclade and Pangolin)
- #- 'Monkeypox-virus_Zaire_AF-380138-1' # Monkeypox (Nextclade)
- #- 'Monkeypox-virus_UK_MT-903345-1' # Monkeypox (Nextclade)
+ #- 'Monkeypox-virus_Zaire_AF-380138-1' # Monkeypox (Nextclade and Pangolin)
+ #- 'Monkeypox-virus_UK_MT-903345-1' # Monkeypox (Nextclade and Pangolin)
#- 'Swinepox-virus_India_MW-036632-1' # Swinepox (Nextclade)
#- 'Ebola-virus_Zaire_AF-272001-1' # Ebola (na)
#- 'Ebola-virus_Sudan_MH-121162-1' # Ebola (Nextclade)
@@ -142,7 +142,7 @@ conda:
frontend: # Conda frontend (default: mamba)
# Available options, choose one:
- 'mamba' # mamba (faster)
- #- 'conda' # conda
+ #- 'conda' # conda (iTrop)
osx: # Conda OSX environement yaml files:
snakemake_base: '../environments/osx/snakemake-base_v.2023.04.yaml' # Snakemake-Base ver. 2023.04
gevarli_tools: '../environments/osx/gevarli-tools_v.2023.04.yaml' # GeVarLi-Tools ver. 2023.04
--
GitLab