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Commit 9262f8c5 authored by nicolas.fernandez_ird.fr's avatar nicolas.fernandez_ird.fr :shinto_shrine:
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Feat: ver. 2025.01 (Prepare for Snakedeploy)

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Run_GeVarLi.sh
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...@@ -10,13 +10,13 @@ ...@@ -10,13 +10,13 @@
### ### ### ###
###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 # Name ___________________ Run_GeVarLi.sh
# Version ________________ v.2024.10 # Version ________________ v.2025.01
# Author _________________ Nicolas Fernandez # Author _________________ Nicolas Fernandez
# Affiliation ____________ IRD_U233_TransVIHMI # Affiliation ____________ IRD_U233_TransVIHMI
# Aim ____________________ Bash script running gevarli.smk snakefile # Aim ____________________ Bash script running gevarli.smk snakefile
# Date ___________________ 2021.10.12 # Date ___________________ 2021.10.12
# Latest modifications ___ 2024.11.15 (Update Snakemake) # Latest modifications ___ 2025.01.08 (Prepare for Snakedeploy)
# Use ____________________ 'bash ./Run_GeVarLi.sh' # Use ____________________ 'bash Run_GeVarLi.sh'
############################################################################### ###############################################################################
### COLORS ### ### COLORS ###
...@@ -31,7 +31,7 @@ nc="\033[0m" # no color ...@@ -31,7 +31,7 @@ nc="\033[0m" # no color
############################################################################### ###############################################################################
### ABOUT ### ### ABOUT ###
############# #############
version="2024.11" # Version version="2025.01" # Version
workdir=$(cd "$(dirname "${BASH_SOURCE[0]}" )" && pwd) # Get working directory workdir=$(cd "$(dirname "${BASH_SOURCE[0]}" )" && pwd) # Get working directory
sample_test="SARS-CoV-2_Omicron-BA1_Covid-Seq-Lib-on-MiSeq_250000-reads" sample_test="SARS-CoV-2_Omicron-BA1_Covid-Seq-Lib-on-MiSeq_250000-reads"
...@@ -47,8 +47,8 @@ ${blue}Author${nc} _________________ Nicolas Fernandez ...@@ -47,8 +47,8 @@ ${blue}Author${nc} _________________ Nicolas Fernandez
${blue}Affiliation${nc} ____________ IRD_U233_TransVIHMI ${blue}Affiliation${nc} ____________ IRD_U233_TransVIHMI
${blue}Aim${nc} ____________________ Bash script for ${red}Ge${nc}nome assembling, ${red}Var${nc}iant calling and ${red}Li${nc}neage assignation ${blue}Aim${nc} ____________________ Bash script for ${red}Ge${nc}nome assembling, ${red}Var${nc}iant calling and ${red}Li${nc}neage assignation
${blue}Date${nc} ___________________ 2021.10.12 ${blue}Date${nc} ___________________ 2021.10.12
${blue}Latest modifications${nc} ___ 2024.10.01 (Dedicated installation scripts creation) ${blue}Latest modifications${nc} ___ 2025.01.08 (Prepare for Snakedeploy)
${blue}Use${nc} ____________________ '${ylo}./Run_GeVarLi.sh${nc}' ${blue}Use${nc} ____________________ '${ylo}bash Run_GeVarLi.sh${nc}'
" "
...@@ -158,9 +158,9 @@ ${green}#####${nc} ${red}CONDA ACTIVATION${nc} ${green}#####${nc} ...@@ -158,9 +158,9 @@ ${green}#####${nc} ${red}CONDA ACTIVATION${nc} ${green}#####${nc}
${green}----------------------------${nc} ${green}----------------------------${nc}
" "
echo -e "conda activate ${ylo}workflow-base_v.${version}${nc}" workflowbase_version="2024.11"
echo -e "conda activate ${ylo}workflow-base_v.${workflowbase_version}${nc}"
conda activate workflow-base_v.${version} conda activate workflow-base_v.${workflowbase_version}
############################################################################### ###############################################################################
...@@ -179,6 +179,7 @@ yq_version=$(yq --version | sed 's/yq //') # Yq version ...@@ -179,6 +179,7 @@ yq_version=$(yq --version | sed 's/yq //') # Yq version
rename_version="1.601" # Rename version (ver. 1.601 from 2024-02) rename_version="1.601" # Rename version (ver. 1.601 from 2024-02)
graphviz_version="11.0.0" # GraphViz version (ver. 11.0.0 from 2024-02) graphviz_version="11.0.0" # GraphViz version (ver. 11.0.0 from 2024-02)
#graphviz_version=$#(dot -V | sed 's/dot - graphviz version //') # GraphViz version (ver. 11.0.0 from 2024-02) #graphviz_version=$#(dot -V | sed 's/dot - graphviz version //') # GraphViz version (ver. 11.0.0 from 2024-02)
nextclade_version=""
fastq=$(expr $(ls -l ${workdir}/resources/reads/*.fastq.gz 2> /dev/null | wc -l)) # Get fastq.gz files count fastq=$(expr $(ls -l ${workdir}/resources/reads/*.fastq.gz 2> /dev/null | wc -l)) # Get fastq.gz files count
if [[ "${fastq}" == "0" ]] # If no sample, if [[ "${fastq}" == "0" ]] # If no sample,
...@@ -241,9 +242,7 @@ ${blue}Samples processed${nc} ______ ${red}${samples}${nc} samples (${ylo}${fast ...@@ -241,9 +242,7 @@ ${blue}Samples processed${nc} ______ ${red}${samples}${nc} samples (${ylo}${fast
${blue}Snakemake version${nc} ______ ${ylo}${snakemake_version}${nc} ${blue}Snakemake version${nc} ______ ${ylo}${snakemake_version}${nc}
${blue}Conda version${nc} __________ ${ylo}${conda_version}${nc} ${blue}Conda version${nc} __________ ${ylo}${conda_version}${nc}
${blue}Conda frontend${nc} _________ ${ylo}${conda_frontend}${nc}
${blue}Mamba version${nc} __________ ${ylo}${mamba_version}${nc} ${blue}Mamba version${nc} __________ ${ylo}${mamba_version}${nc}
${blue}Nextclade version${nc} ______ ${ylo}${nextclade_version}${nc}
${blue}Quality Ccontrol${nc} _______ [ ${red}${quality}${nc} ] ${blue}Quality Ccontrol${nc} _______ [ ${red}${quality}${nc} ]
${blue}Trimming${nc} _______________ [ ${red}${trimming}${nc} ] ${blue}Trimming${nc} _______________ [ ${red}${trimming}${nc} ]
...@@ -258,6 +257,7 @@ ${blue}Reference genome${nc} _______ ${ylo}${reference}${nc} ...@@ -258,6 +257,7 @@ ${blue}Reference genome${nc} _______ ${ylo}${reference}${nc}
${blue}Aligner${nc} ________________ ${ylo}${aligner}${nc} ${blue}Aligner${nc} ________________ ${ylo}${aligner}${nc}
${blue}Min coverage${nc} ___________ ${red}${min_cov}${nc} X ${blue}Min coverage${nc} ___________ ${red}${min_cov}${nc} X
${blue}Min allele frequency${nc} ___ ${red}${min_freq}${nc} ${blue}Min allele frequency${nc} ___ ${red}${min_freq}${nc}
${blue}Nextclade dataset${nc} ______ ${red}${nextclade_dataset}${nc} ${blue}Nextclade dataset${nc} ______ ${red}${nextclade_dataset}${nc}
" "
...@@ -324,22 +324,26 @@ fi ...@@ -324,22 +324,26 @@ fi
############################################################################### ###############################################################################
### RENAME SAMPLES ### ### RENAME SYMLINKS ###
###################### #######################
echo -e " echo -e "
${green}------------------------------------------------------------------------${nc} ${green}------------------------------------------------------------------------${nc}
${green}#####${nc} ${red}RENAME FASTQ FILES${nc} ${green}#####${nc} ${green}#####${nc} ${red}RENAME FASTQ SYMLINKS${nc} ${green}#####${nc}
${green}------------------------------${nc} ${green}---------------------------------${nc}
" "
# Rename fastq files to remove "_001" Illumina pattern (mandatory) # Remove tags from symlinks:
## De/comment line (#) if you want keep Illumina barcode-ID and/or Illumina line-ID ## barcode-ID like {_S001_}
echo -e "Removing ${red}'_S'${nc} index tag ID" ## line-ID ID like {_L001_}
rename "s/_S\d+_/_/" ${workdir}/resources/reads/*.fastq.gz 2> /dev/null # Remove barcode-ID like {_S001_} ## end-name ID like {_001}.fastq.gz
echo -e "Removing ${red}'_L'${nc} line tag ID" mkdir -p ${workdir}/resources/symlinks/
rename "s/_L\d+_/_/" ${workdir}/resources/reads/*.fastq.gz 2> /dev/null # Remove line-ID ID like {_L001_} for fastq in ${workdir}/resources/reads/*.fastq.gz; do
echo -e "Removing ${red}'_001'${nc} illumina tag ID" symlinks=$(echo $(basename "${fastq}") | \
rename "s/_001.fastq.gz/.fastq.gz/" ${workdir}/resources/reads/*.fastq.gz 2> /dev/null # Remove end-name ID like {_001}.fastq.gz sed -E "s/_S\d+_//" | \
sed -E "s/_L\d+_//" | \
sed -E "s/_001.fastq.gz/.fastq.gz/")
ln -s "${fastq}" "${workdir}/resources/symlinks/${symlinks}"
done
echo -e " echo -e "
If you want to keep Illumina ${blue}barcode-ID${nc} and/or Illumina ${blue}line-ID${nc}, please edit ${ylo}Run_GeVarLi.sh${nc} script (l.335). If you want to keep Illumina ${blue}barcode-ID${nc} and/or Illumina ${blue}line-ID${nc}, please edit ${ylo}Run_GeVarLi.sh${nc} script (l.335).
...@@ -355,9 +359,6 @@ ${green}#####${nc} ${red}SNAKEMAKE PIPELINES${nc} ${green}#####${nc} ...@@ -355,9 +359,6 @@ ${green}#####${nc} ${red}SNAKEMAKE PIPELINES${nc} ${green}#####${nc}
${green}-------------------------------${nc} ${green}-------------------------------${nc}
" "
# MODULES
snakefiles_list="indexing_genomes gevarli"
echo -e " echo -e "
${blue}## Unlocking Working Directory ##${nc} ${blue}## Unlocking Working Directory ##${nc}
${blue}---------------------------------${nc} ${blue}---------------------------------${nc}
...@@ -367,14 +368,11 @@ ${blue}---------------------------------${nc} ...@@ -367,14 +368,11 @@ ${blue}---------------------------------${nc}
# Re-run all jobs the output of which is recognized as incomplete. # Re-run all jobs the output of which is recognized as incomplete.
# Remove a lock on the working directory. # Remove a lock on the working directory.
for snakefile in ${snakefiles_list} ; do snakemake \
echo -e "${blue}-- ${snakefile} --${nc}" ; --directory ${workdir}/ \
snakemake \ --snakefile ${workdir}/workflow/Snakefile \
--directory ${workdir}/ \ --rerun-incomplete \
--snakefile ${workdir}/workflow/snakefiles/${snakefile}.smk \ --unlock
--rerun-incomplete \
--unlock ;
done
echo -e " echo -e "
${blue}## Let's Run! ##${nc} ${blue}## Let's Run! ##${nc}
...@@ -390,22 +388,17 @@ ${blue}----------------${nc} ...@@ -390,22 +388,17 @@ ${blue}----------------${nc}
# If defined in the rule, run job in a conda environment. # If defined in the rule, run job in a conda environment.
# Print out the shell commands that will be executed. # Print out the shell commands that will be executed.
for snakefile in ${snakefiles_list} ; do snakemake \
echo -e "${blue}-- ${snakefile} --${nc}" ; --directory ${workdir}/ \
snakemake \ --snakefile ${workdir}/workflow/Snakefile\
--directory ${workdir}/ \ --cores ${max_threads} \
--snakefile ${workdir}/workflow/snakefiles/${snakefile}.smk \ --max-threads ${max_threads} \
--cores ${max_threads} \ --resources mem_gb=${max_memory} \
--max-threads ${max_threads} \ --rerun-incomplete \
--resources mem_gb=${max_memory} \ --keep-going \
--rerun-incomplete \ --use-conda \
--keep-going \ --quiet host
--use-conda ; # Possible choices: all, host, progress, rules
# --quiet host \
# --quiet progress \
# --quiet rules ;
done
############################################################################### ###############################################################################
### CONCATENATE RESULTS ### ### CONCATENATE RESULTS ###
...@@ -477,27 +470,23 @@ mkdir -p ${workdir}/results/10_Reports/files-summaries/ 2> /dev/null ...@@ -477,27 +470,23 @@ mkdir -p ${workdir}/results/10_Reports/files-summaries/ 2> /dev/null
graph_list="dag rulegraph filegraph" graph_list="dag rulegraph filegraph"
extention_list="pdf png" extention_list="pdf png"
for snakefile in ${snakefiles_list} ; do for graph in ${graph_list} ; do
for graph in ${graph_list} ; do for extention in ${extention_list} ; do
for extention in ${extention_list} ; do snakemake \
snakemake \ --directory ${workdir}/ \
--directory ${workdir}/ \ --snakefile ${workdir}/workflow/Snakefile \
--snakefile ${workdir}/workflow/snakefiles/${snakefile}.smk \ --${graph} \
--${graph} \ | dot -T${extention} \
| dot -T${extention} \ 2> /dev/null \
2> /dev/null \ 1> ${workdir}/results/10_Reports/graphs/${graph}.${extention} ;
1> ${workdir}/results/10_Reports/graphs/${snakefile}_${graph}.${extention} ;
done ;
done ; done ;
done done
for snakefile in ${snakefiles_list} ; do snakemake \
snakemake \ --directory ${workdir} \
--directory ${workdir} \ --snakefile ${workdir}/workflow/Snakefile \
--snakefile ${workdir}/workflow/snakefiles/${snakefile}.smk \ --summary > ${workdir}/results/10_Reports/files-summaries/files-summary.txt \
--summary > ${workdir}/results/10_Reports/files-summaries/${snakefile}_files-summary.txt \ 2> /dev/null
2> /dev/null ;
done
cp ${config_file} ${workdir}/results/10_Reports/config.log 2> /dev/null cp ${config_file} ${workdir}/results/10_Reports/config.log 2> /dev/null
...@@ -512,14 +501,15 @@ ${green}------------------------${nc} ...@@ -512,14 +501,15 @@ ${green}------------------------${nc}
" "
# Save and deactive environments # Save and deactive environments
mkdir -p ${workdir}/results/10_Reports/conda_env/ 2> /dev/null mkdir -p ${workdir}/results/10_Reports/conda_envs/ 2> /dev/null
cp ${workdir}/workflow/environments/*.yaml ${workdir}/results/10_Reports/conda_env/ cp ${workdir}/workflow/envs/*.yaml ${workdir}/results/10_Reports/conda_envs/
conda deactivate conda deactivate
# Cleanup # Cleanup
find ${workdir}/results/ -type f -empty -delete # Remove empty file (like empty log) find ${workdir}/results/ -type f -empty -delete # Remove empty file (like empty log)
find ${workdir}/results/ -type d -empty -delete # Remove empty directory find ${workdir}/results/ -type d -empty -delete # Remove empty directory
rm -f ${workdir}/resources/reads/${sample_test}_R*.fastq.gz 2> /dev/null rm -f ${workdir}/resources/reads/${sample_test}_R*.fastq.gz 2> /dev/null
rm -rf ${workdir}/resources/symlinks/ 2> /dev/null
# Timer # Timer
time_stamp_end=$(date +"%Y-%m-%d %H:%M") # Get date / hour ending analyzes time_stamp_end=$(date +"%Y-%m-%d %H:%M") # Get date / hour ending analyzes
...@@ -542,8 +532,8 @@ Author _________________ Nicolas Fernandez ...@@ -542,8 +532,8 @@ Author _________________ Nicolas Fernandez
Affiliation ____________ IRD_U233_TransVIHMI Affiliation ____________ IRD_U233_TransVIHMI
Aim ____________________ Bash script for GeVarLi Aim ____________________ Bash script for GeVarLi
Date ___________________ 2021.10.12 Date ___________________ 2021.10.12
Latest modifications ___ 2024.10.01 (Dedicated installation scripts creation) Latest modifications ___ 2025.01.08 (Prepare for Snakedeploy)
Run ____________________ ./Run_GeVarLi.sh Run ____________________ 'bash Run_GeVarLi.sh'
Operating System _______ ${os} Operating System _______ ${os}
Shell __________________ ${shell} Shell __________________ ${shell}
...@@ -567,9 +557,8 @@ Samples processed _______ ${samples} samples (${ylo}${fastq} fastq files) ...@@ -567,9 +557,8 @@ Samples processed _______ ${samples} samples (${ylo}${fastq} fastq files)
Snakemake version _______ ${snakemake_version} Snakemake version _______ ${snakemake_version}
Conda version ___________ ${conda_version} Conda version ___________ ${conda_version}
Conda frontend __________ ${conda_frontend}
Mamba version ___________ ${mamba_version} Mamba version ___________ ${mamba_version}
Nextclade version _______ ${nextclade_version}
Quality Ccontrol ________ [ ${quality} ] Quality Ccontrol ________ [ ${quality} ]
Trimming ________________ [ ${trimming} ] Trimming ________________ [ ${trimming} ]
...@@ -584,16 +573,17 @@ Reference genome ________ ${reference} ...@@ -584,16 +573,17 @@ Reference genome ________ ${reference}
Aligner _________________ ${aligner} Aligner _________________ ${aligner}
Min coverage ____________ ${min_cov} X Min coverage ____________ ${min_cov} X
Min allele frequency ____ ${min_freq} Min allele frequency ____ ${min_freq}
Nextclade dataset _______ ${nextclade_dataset} Nextclade dataset _______ ${nextclade_dataset}
" > ${workdir}/results/10_Reports/settings.log " > ${workdir}/results/10_Reports/settings.log
# Gzip reports directory # Gzip reports directory
cd ${workdir}/results/ cd ${workdir}/results/
tar -zcf 10_Reports_archive.tar.gz 10_Reports tar -zcf 10_Reports_archive.tar.gz 10_Reports
cd ${workdir}
# Gzip results directory # Gzip results directory
#mkdir -p ${workdir}/archives/ 2> /dev/null #mkdir -p ${workdir}/archives/ 2> /dev/null
#cd ${workdir}/
#tar -zcf archives/Results_${time_stamp_archive}_${reference}_${aligner}-${min_cov}X_${samples}sp_archive.tar.gz results/ #tar -zcf archives/Results_${time_stamp_archive}_${reference}_${aligner}-${min_cov}X_${samples}sp_archive.tar.gz results/
echo -e " echo -e "
......
configuration/config.yaml
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− 25
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...@@ -36,12 +36,12 @@ resources: ...@@ -36,12 +36,12 @@ resources:
############################################################################### ###############################################################################
modules: # GeVarLi modules analysis modules: # GeVarLi modules analysis
# Available options, set at least one: # Available options, set at least one:
- 'quality' # Perform reads quality control (FastQC, Fastq-Screen, MultiQC) default: ON #- 'quality' # Perform reads quality control (FastQC, Fastq-Screen, MultiQC) default: ON
#- 'trimming' # Keep trimmed reads files after alignment (Cutadapt / Sickle-trim) default: OFF #- 'trimming' # Keep trimmed reads files after alignment (Cutadapt / Sickle-trim) default: OFF
#- 'cleapping' # Perform reads clipping (Bamclipper) default: OFF #- 'cleapping' # Perform reads clipping (Bamclipper) default: OFF
- 'consensus' # Perform reads mapping to reference (BWA, Bowtie2, Minimap2) default: ON - 'consensus' # Perform reads mapping to reference (BWA, Bowtie2, Minimap2) default: ON
- 'covstats' # Perform coverage statistics (Fagstat, Covstats) default: ON #- 'covstats' # Perform coverage statistics (Fagstat, Covstats) default: ON
- 'nextclade' # Perform nextclade clade assignation (Nexclade) default: ON #- 'nextclade' # Perform nextclade clade assignation (Nexclade) default: ON
#- 'pangolin' # Perform pangolin lineage assignation (Pangolin) default: OFF #- 'pangolin' # Perform pangolin lineage assignation (Pangolin) default: OFF
###- 'gisaid' # Perform gisaid submission (GisAid : TODO) default: OFF ###- 'gisaid' # Perform gisaid submission (GisAid : TODO) default: OFF
...@@ -51,7 +51,7 @@ consensus: ...@@ -51,7 +51,7 @@ consensus:
reference: # Your reference, in fasta format (default: "SARS-CoV-2_Wuhan_MN-908947-3") reference: # Your reference, in fasta format (default: "SARS-CoV-2_Wuhan_MN-908947-3")
# Available options (not exhaustive), set one: # Available options (not exhaustive), set one:
- 'SARS-CoV-2_Wuhan_MN-908947-3' # SARS-CoV-2 (Nextclade and Pangolin) - 'SARS-CoV-2_Wuhan_MN-908947-3' # SARS-CoV-2 (Nextclade and Pangolin)
#- 'Monkeypox-virus_Zaire_AF-380138-1' # Monkeypox (Nextclade and Pangolin) - 'Monkeypox-virus_Zaire_AF-380138-1' # Monkeypox (Nextclade and Pangolin)
#- 'Monkeypox-virus_UK_MT-903345-1' # Monkeypox (Nextclade and Pangolin) #- 'Monkeypox-virus_UK_MT-903345-1' # Monkeypox (Nextclade and Pangolin)
#- 'Swinepox-virus_India_MW-036632-1' # Swinepox (Nextclade) #- 'Swinepox-virus_India_MW-036632-1' # Swinepox (Nextclade)
#- 'Ebola-virus_Zaire_AF-272001-1' # Ebola (na) #- 'Ebola-virus_Zaire_AF-272001-1' # Ebola (na)
...@@ -96,8 +96,8 @@ consensus: ...@@ -96,8 +96,8 @@ consensus:
aligner: # Select your favorite aligner (default: 'bwa') aligner: # Select your favorite aligner (default: 'bwa')
# Available options, set one: # Available options, set one:
- 'bwa' # Better, Faster, (Stronger, Harder...) - 'bwa' # Better, Faster, (Stronger, Harder...)
#- 'bowtie2' # Depreciated (slower),"sensitivity" requiried (see below "Bowtie2" options) - 'bowtie2' # Depreciated (slower),"sensitivity" requiried (see below "Bowtie2" options)
#- 'minimap2' # A versatile sequence alignment program - 'minimap2' # A versatile sequence alignment program
caller: 'ivar' caller: 'ivar'
############################################################################### ###############################################################################
...@@ -275,24 +275,24 @@ fastq_screen: ...@@ -275,24 +275,24 @@ fastq_screen:
############################################################################### ###############################################################################
conda: conda:
yaml: # Conda environement yaml files: envs: # Conda environement yaml files:
bamclipper: '../environments/bamclipper_v.1.0.0.yaml' # Bamclipper ver. 1.0.0 bamclipper: 'envs/bamclipper_v.1.0.0.yaml' # Bamclipper ver. 1.0.0
bcftools: '../environments/bcftools_v.1.20.yaml' # Bcftools ver. 1.20 bcftools: 'envs/bcftools_v.1.20.yaml' # Bcftools ver. 1.20
bedtools: '../environments/bedtools_v.2.31.1.yaml' # Bedtools ver. 2.31.1 bedtools: 'envs/bedtools_v.2.31.1.yaml' # Bedtools ver. 2.31.1
bowtie2: '../environments/bowtie2_v.2.5.4.yaml' # Bowtie2 ver. 2.5.4 bowtie2: 'envs/bowtie2_v.2.5.4.yaml' # Bowtie2 ver. 2.5.4
bwa: '../environments/bwa_v.0.7.18.yaml' # BWA ver. 0.7.18 bwa: 'envs/bwa_v.0.7.18.yaml' # BWA ver. 0.7.18
cutadapt: '../environments/cutadapt_v.4.9.yaml' # Cutadapt ver. 4.9 cutadapt: 'envs/cutadapt_v.4.9.yaml' # Cutadapt ver. 4.9
fastq_screen: '../environments/fastq-screen_v.0.15.3.yaml' # Fastq-Screen ver. 0.15.3 (with BWA ver. 0.7.18) fastq_screen: 'envs/fastq-screen_v.0.15.3.yaml' # Fastq-Screen ver. 0.15.3 (with BWA ver. 0.7.18)
fastqc: '../environments/fastqc_v.0.12.1.yaml' # FastQC ver. 0.12.1 fastqc: 'envs/fastqc_v.0.12.1.yaml' # FastQC ver. 0.12.1
gawk: '../environments/gawk_v.5.3.0.yaml' # Awk (GNU) ver. 5.3.0 gawk: 'envs/gawk_v.5.3.0.yaml' # Awk (GNU) ver. 5.3.0
ivar: '../environments/ivar_v.1.4.3.yaml' # iVar ver. 1.4.3 (with Samtools ver. 1.20) ivar: 'envs/ivar_v.1.4.3.yaml' # iVar ver. 1.4.3 (with Samtools ver. 1.20)
minimap2: '../environments/minimap2_v.2.28.yaml' # Minimap2 ver. 2.28 minimap2: 'envs/minimap2_v.2.28.yaml' # Minimap2 ver. 2.28
multiqc: '../environments/multiqc_v.1.23.yaml' # MultiQC ver. 1.23 (with Pandoc ver. 3.3) multiqc: 'envs/multiqc_v.1.23.yaml' # MultiQC ver. 1.23 (with Pandoc ver. 3.3)
nextclade: '../environments/nextclade_v.3.9.1.yaml' # Nextclade ver. 3.9.1 nextclade: 'envs/nextclade_v.3.9.1.yaml' # Nextclade ver. 3.9.1
pangolin: '../environments/pangolin_v.4.3.yaml' # Pangolin ver. 4.3 pangolin: 'envs/pangolin_v.4.3.yaml' # Pangolin ver. 4.3
samtools: '../environments/samtools_v.1.20.yaml' # Samtools ver. 1.20 samtools: 'envs/samtools_v.1.20.yaml' # Samtools ver. 1.20
sickle_trim: '../environments/sickle-trim_v.1.33.yaml' # Sickle-trim ver. 1.33 sickle_trim: 'envs/sickle-trim_v.1.33.yaml' # Sickle-trim ver. 1.33
tsv2vcf: '../environments/tsv2vcf_v.1.1.yaml' # tsv2vcf ver. 1.1 (bcftools biopython numpy) tsv2vcf: 'envs/tsv2vcf_v.1.1.yaml' # tsv2vcf ver. 1.1 (bcftools biopython numpy)
workflow_base: '../environments/workflow-base_v.2024.11.yaml' # Workflow-Base ver. 2024.11 workflow_base: 'envs/workflow-base_v.2024.11.yaml' # Workflow-Base ver. 2024.11
############################################################################### ###############################################################################
version.txt
+ 1
− 1
View file @ 9262f8c5
2024.11 2025.01
workflow/Snakefile
+ 1454
− 4
View file @ 9262f8c5
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