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Commit c828a526 authored by nicolas.fernandez_ird.fr's avatar nicolas.fernandez_ird.fr :shinto_shrine:
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Update Snakemake-base env. (like geVarLi)

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Start_RQC.sh
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#!/bin/bash #!/bin/bash
rqc_version="v.2022.11" snakemake_base_version="v.2023.02"
rqc_version="v.2023.03"
###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 ___________________ Start_RQC.sh # Name ___________________ Start_RQC.sh
# Version ________________ v.2022.11 # Version ________________ v.2023.03
# Author _________________ Nicolas Fernandez # Author _________________ Nicolas Fernandez
# Affiliation ____________ IRD_U233_TransVIHMI # Affiliation ____________ IRD_U233_TransVIHMI
# Aim ____________________ Bash script running quality_control.smk snakefile # Aim ____________________ Bash script running quality_control.smk snakefile
# Date ___________________ 2021.10.12 # Date ___________________ 2021.10.12
# Latest modifications ___ 2022.11.18 # Latest modifications ___ 2023.03.01
# Use ____________________ bash Start_RQC.sh # Use ____________________ bash Start_RQC.sh
############################################################################### ###############################################################################
...@@ -32,7 +33,7 @@ ${blue}Author${nc} _________________ Nicolas Fernandez ...@@ -32,7 +33,7 @@ ${blue}Author${nc} _________________ Nicolas Fernandez
${blue}Affiliation${nc} ____________ IRD_U233_TransVIHMI ${blue}Affiliation${nc} ____________ IRD_U233_TransVIHMI
${blue}Aim${nc} ____________________ Bash script for ${red}R${nc}eads ${red}Q${nc}quality ${red}C${nc}ontrol ${blue}Aim${nc} ____________________ Bash script for ${red}R${nc}eads ${red}Q${nc}quality ${red}C${nc}ontrol
${blue}Date${nc} ___________________ 2021.10.12 ${blue}Date${nc} ___________________ 2021.10.12
${blue}Latest modifications${nc} ___ 2022.11.18 ${blue}Latest modifications${nc} ___ 2023.03.01
${blue}Run${nc} ____________________ bash Start_RQC.sh ${blue}Run${nc} ____________________ bash Start_RQC.sh
" "
...@@ -106,22 +107,29 @@ ${green}#####${nc} ${red}SETTINGS${nc} ${green}#####${nc} ...@@ -106,22 +107,29 @@ ${green}#####${nc} ${red}SETTINGS${nc} ${green}#####${nc}
${green}--------------------${nc} ${green}--------------------${nc}
" "
workdir=$(cd "$(dirname "${BASH_SOURCE[0]}" )" && pwd) # Get working directory workdir=$(cd "$(dirname "${BASH_SOURCE[0]}" )" && pwd) # Get working directory
fastq=$(expr $(ls -l ${workdir}/resources/reads/*.fastq.gz | wc -l)) # Get fastq.gz files count config_file="${workdir}/configuration/config.yaml" # Get configuration file
samples=$(expr ${fastq} \/ 2) # {fastq.gz count} / 2 = samples count (paired-end) fastq=$(expr $(ls -l ${workdir}/resources/reads/*.fastq.gz | wc -l)) # Get fastq.gz files count
conda_version=$(conda --version | sed "s/conda //") # Get conda version
snakemake_version=$(grep -o -E "snakemake_version: '.+'" ${workdir}/config/config.yaml | \ if [[ "${fastq}" == "0" ]] # Start GeVarLi with at least 1 sample
sed "s/snakemake_version: //" | sed "s/'//g") # Get snakemake version then
conda_frontend=$(grep -o -E "conda_frontend: '.+'" ${workdir}/config/config.yaml | \ echo -e "${red}¡${nc} No fastq file detected in ${ylo}resources/reads/${nc} ${red}!${nc}
sed "s/conda_frontend: //" | sed "s/'//g") # Get conda frontend ${red}SARS-CoV-2${nc} ${ylo}resources/data_test/${nc} fastq will be used as sample example
max_threads=$(grep -o -E "cpus: [0-9]+" ${workdir}/config/config.yaml | sed "s/cpus: //") # Get user config for max threads "
max_memory=$(grep -o -E "ram: [0-9]+" ${workdir}/config/config.yaml | sed "s/ram: //") # Get user config for max memory cp ${workdir}/resources/data_test/*.fastq.gz ${workdir}/resources/reads/ # use data_test/*.fastq.gz
memory_per_job=$(expr ${max_memory} \/ ${max_threads}) # Calcul maximum memory usage per job fi
mapper=$(grep -o -E "mapper: '.+'" ${workdir}/config/config.yaml | \
sed "s/mapper: //" | sed "s/'//g") # Get user config mapper samples=$(expr ${fastq} \/ 2) # {fastq.gz count} / 2 = samples count (paired-end)
subset=$(grep -o -E "subset: [0-9]+" ${workdir}/config/config.yaml | sed "s/subset: //") # Get user config subset conda_version=$(conda --version | sed "s/conda //") # Get conda version
time_stamp_start=$(date +"%Y-%m-%d %H:%M") # Get analyzes starting time snakemake_version=$(grep -o -E "snakemake_version: '.+'" ${config_file} | sed "s/snakemake_version: //" | sed "s/'//g") # Get snakemake version
SECONDS=0 # Initialize SECONDS counter conda_frontend=$(grep -o -E "frontend: '.+'" ${config_file} | sed "s/frontend: //" | sed "s/'//g") # Get conda frontend
max_threads=$(grep -o -E "cpus: [0-9]+" ${config_file} | sed "s/cpus: //") # Get user config for max threads
max_memory=$(grep -o -E "ram: [0-9]+" ${config_file} | sed "s/ram: //") # Get user config for max memory
memory_per_job=$(expr ${max_memory} \/ ${max_threads}) # Calcul maximum memory usage per job
aligner=$(grep -o -E "aligner: '.+'" ${config_file} | sed "s/aligner: //" | sed "s/'//g") # Get user config aligner
time_stamp_start=$(date +"%Y-%m-%d %H:%M") # Get analyzes starting time
time_stamp_archive=$(date +"%Y-%m-%d_%Hh%M") # Get analyzes time to archive (wo space)
SECONDS=0 # Initialize SECONDS counter
# Print some analyzes settings # Print some analyzes settings
echo -e " echo -e "
...@@ -136,38 +144,41 @@ ${blue}max Threads${nc} ____________ ${red}${max_threads}${nc} of ${ylo}${logica ...@@ -136,38 +144,41 @@ ${blue}max Threads${nc} ____________ ${red}${max_threads}${nc} of ${ylo}${logica
${blue}max Memory${nc} _____________ ${red}${max_memory}${nc} of ${ylo}${ram_gb}${nc} Gb available ${blue}max Memory${nc} _____________ ${red}${max_memory}${nc} of ${ylo}${ram_gb}${nc} Gb available
${blue}job Memory${nc} _____________ ${red}${memory_per_job}${nc} Gb per job ${blue}job Memory${nc} _____________ ${red}${memory_per_job}${nc} Gb per job
${blue}Mapper${nc} _________________ ${ylo}${mapper}${nc} ${blue}Aligner${nc} ________________ ${ylo}${aligner}${nc}
${blue}Subet${nc} __________________ ${ylo}${subset}${nc} reads
${blue}Start time${nc} _____________ ${time_stamp_start} ${blue}Start time${nc} _____________ ${time_stamp_start}
" "
############################################################################### ###############################################################################
###### RQC Base Conda Environment Installation ###### ###### Snakemake Installation ######
echo -e " echo -e "
${green}------------------------------------------------------------------------${nc} ${green}------------------------------------------------------------------------${nc}
${green}#####${nc} ${red}RQC-BASE CONDA ENVIRONMENT INSTALLATION${nc} ${green}#####${nc} ${green}#####${nc} ${red}SNAKEMAKE-BASE INSTALLATION${nc} ${green}#####${nc}
${green}---------------------------------------------------${nc} ${green}---------------------------------------${nc}
" "
# Test if 'rqc-base' environment exist # Test if latest 'snakemake-base' environment exist
if [[ $(conda info --envs | grep -o -E "^rqc-base_${rqc_version}") ]] if [[ $(conda info --envs | grep -o -E "^snakemake-base_${snakemake_base_version}") ]]
then then
echo -e " echo -e "
Conda environment ${ylo}rqc-base_${rqc_version}${nc} it's already created Conda environment ${ylo}snakemake-base_${snakemake_base_version}${nc} it's already created!
" "
else else
echo -e " echo -e "
Conda environment ${ylo}rqc-base_${rqc_version}${nc} will be now created Conda environment ${red}snakemake-base${nc} ${ylo}${snakemake_base_version}${nc} will be now created, with:
# ${red}Mamba${nc} ver. ${ylo}1.0.0${nc} (to create snakemake-conda's environments faster)
# ${red}Snakemake${nc} ver. ${ylo}7.18.1${nc} (to run GeVarLi)
# ${red}Rename${nc} ver. ${ylo}1.601${nc} (to rename fastq files)
# ${red}Graphviz${nc} ver. ${ylo}6.0.1${nc} (to dot snakemake DAG)
" "
# Create a 'rqc-base' environment, with : conda env create -f ${workdir}/workflow/environments/${os}/snakemake-base_${snakemake_base_version}.yaml
# Mamba ver. 1.0.0 (to create snakemake-conda's environments faster)
# Snakemake ver. 7.18.1 (to run RQC)
# Rename ver. 1.601 (to rename fastq files)
# Graphviz ver. 6.0.1 (to dot snakemake DAG)
conda env create -f ${workdir}/workflow/envs/${os}/rqc-base_${rqc_version}.yaml
fi fi
# Remove old 'gevarli-base' environment
conda env remove --name rqc-base_v.2022.11
############################################################################### ###############################################################################
###### Conda Env. Activation ###### ###### Conda Env. Activation ######
echo -e " echo -e "
...@@ -176,10 +187,12 @@ ${green}#####${nc} ${red}CONDA ACTIVATION${nc} ${green}#####${nc} ...@@ -176,10 +187,12 @@ ${green}#####${nc} ${red}CONDA ACTIVATION${nc} ${green}#####${nc}
${green}----------------------------${nc} ${green}----------------------------${nc}
" "
echo -e "conda activate ${red}snakemake-base${nc} ${ylo}${snakemake_base_version}${nc}"
# intern shell source conda # intern shell source conda
source ~/miniconda3/etc/profile.d/conda.sh 2> /dev/null # local user source ~/miniconda3/etc/profile.d/conda.sh 2> /dev/null # local user
source /usr/local/miniconda3/etc/profile.d/conda.sh 2> /dev/null # HPC server source /usr/local/miniconda3/etc/profile.d/conda.sh 2> /dev/null # HPC server
conda activate rqc-base_${rqc_version} conda activate snakemake-base_${snakemake_base_version}
############################################################################### ###############################################################################
###### Rename samples ###### ###### Rename samples ######
...@@ -189,12 +202,18 @@ ${green}#####${nc} ${red}RENAME FASTQ FILES${nc} ${green}#####${nc} ...@@ -189,12 +202,18 @@ ${green}#####${nc} ${red}RENAME FASTQ FILES${nc} ${green}#####${nc}
${green}------------------------------${nc} ${green}------------------------------${nc}
" "
# Rename fastq files to remove "_001" Illumina pattern. # Rename fastq files to remove "_001" Illumina pattern (mandatory)
## De/comment (#) if you want keep Illumina barcode-ID and/or Illumina line-ID ## De/comment line (#) if you want keep Illumina barcode-ID and/or Illumina line-ID
#rename "s/_S\d+_/_/" ${workdir}/resources/reads/*.fastq.gz 2> /dev/null # Remove barcode-ID like {_S001_} echo -e "Removing ${red}'_S'${nc} index tag ID"
#rename "s/_L\d+_/_/" ${workdir}/resources/reads/*.fastq.gz 2> /dev/null # Remove line-ID ID like {_L001_} rename "s/_S\d+_/_/" ${workdir}/resources/reads/*.fastq.gz 2> /dev/null # Remove barcode-ID like {_S001_}
echo -e "Removing ${red}'_L'${nc} line tag ID"
rename "s/_L\d+_/_/" ${workdir}/resources/reads/*.fastq.gz 2> /dev/null # Remove line-ID ID like {_L001_}
echo -e "Removing ${red}'_001'${nc} illumina tag ID"
rename "s/_001.fastq.gz/.fastq.gz/" ${workdir}/resources/reads/*.fastq.gz 2> /dev/null # Remove end-name ID like {_001}.fastq.gz rename "s/_001.fastq.gz/.fastq.gz/" ${workdir}/resources/reads/*.fastq.gz 2> /dev/null # Remove end-name ID like {_001}.fastq.gz
echo -e "
If you want to keep Illumina ${blue}barcode-ID${nc} and/or Illumina ${blue}line-ID${nc}, please edit ${ylo}Start_GeVarLi.sh${nc} script (l.199).
"
############################################################################### ###############################################################################
###### Call snakemake pipelines ###### ###### Call snakemake pipelines ######
...@@ -220,7 +239,7 @@ for snakefile in ${snakefile_list} ; do ...@@ -220,7 +239,7 @@ for snakefile in ${snakefile_list} ; do
echo -e "${blue}-- ${snakefile} --${nc}" ; echo -e "${blue}-- ${snakefile} --${nc}" ;
snakemake \ snakemake \
--directory ${workdir}/ \ --directory ${workdir}/ \
--snakefile ${workdir}/workflow/rules/${snakefile}.smk \ --snakefile ${workdir}/workflow/snakefiles/${snakefile}.smk \
--config os=${os} \ --config os=${os} \
--rerun-incomplete \ --rerun-incomplete \
--unlock ; --unlock ;
...@@ -241,7 +260,7 @@ for snakefile in ${snakefile_list} ; do ...@@ -241,7 +260,7 @@ for snakefile in ${snakefile_list} ; do
echo -e "${blue}-- ${snakefile} --${nc}" ; echo -e "${blue}-- ${snakefile} --${nc}" ;
snakemake \ snakemake \
--directory ${workdir}/ \ --directory ${workdir}/ \
--snakefile ${workdir}/workflow/rules/${snakefile}.smk \ --snakefile ${workdir}/workflow/snakefiles/${snakefile}.smk \
--cores ${max_threads} \ --cores ${max_threads} \
--config os=${os} \ --config os=${os} \
--rerun-incomplete \ --rerun-incomplete \
...@@ -266,7 +285,7 @@ for snakefile in ${snakefile_list} ; do ...@@ -266,7 +285,7 @@ for snakefile in ${snakefile_list} ; do
echo -e "${blue}-- ${snakefile} --${nc}" ; echo -e "${blue}-- ${snakefile} --${nc}" ;
snakemake \ snakemake \
--directory ${workdir}/ \ --directory ${workdir}/ \
--snakefile ${workdir}/workflow/rules/${snakefile}.smk \ --snakefile ${workdir}/workflow/snakefiles/${snakefile}.smk \
--cores ${max_threads} \ --cores ${max_threads} \
--config os=${os} \ --config os=${os} \
--rerun-incomplete \ --rerun-incomplete \
...@@ -295,7 +314,7 @@ for snakefile in ${snakefile_list} ; do ...@@ -295,7 +314,7 @@ for snakefile in ${snakefile_list} ; do
echo -e "${blue}-- ${snakefile} --${nc}" ; echo -e "${blue}-- ${snakefile} --${nc}" ;
snakemake \ snakemake \
--directory ${workdir}/ \ --directory ${workdir}/ \
--snakefile ${workdir}/workflow/rules/${snakefile}.smk \ --snakefile ${workdir}/workflow/snakefiles/${snakefile}.smk \
--cores ${max_threads}\ --cores ${max_threads}\
--config os=${os} \ --config os=${os} \
--rerun-incomplete \ --rerun-incomplete \
...@@ -326,7 +345,7 @@ for snakefile in ${snakefile_list} ; do ...@@ -326,7 +345,7 @@ for snakefile in ${snakefile_list} ; do
echo -e "${blue}-- ${snakefile} --${nc}" ; echo -e "${blue}-- ${snakefile} --${nc}" ;
snakemake \ snakemake \
--directory ${workdir}/ \ --directory ${workdir}/ \
--snakefile ${workdir}/workflow/rules/${snakefile}.smk \ --snakefile ${workdir}/workflow/snakefiles/${snakefile}.smk \
--cores ${max_threads} \ --cores ${max_threads} \
--max-threads ${max_threads} \ --max-threads ${max_threads} \
--config os=${os} \ --config os=${os} \
...@@ -362,7 +381,7 @@ for snakefile in ${snakefile_list} ; do ...@@ -362,7 +381,7 @@ for snakefile in ${snakefile_list} ; do
for extention in ${extention_list} ; do for extention in ${extention_list} ; do
snakemake \ snakemake \
--directory ${workdir}/ \ --directory ${workdir}/ \
--snakefile ${workdir}/workflow/rules/${snakefile}.smk \ --snakefile ${workdir}/workflow/snakefiles/${snakefile}.smk \
--${graph} \ --${graph} \
| dot -T${extention} \ | dot -T${extention} \
2> /dev/null \ 2> /dev/null \
...@@ -374,7 +393,7 @@ done ...@@ -374,7 +393,7 @@ done
for snakefile in ${snakefile_list} ; do for snakefile in ${snakefile_list} ; do
snakemake \ snakemake \
--directory ${workdir} \ --directory ${workdir} \
--snakefile ${workdir}/workflow/rules/${snakefile}.smk \ --snakefile ${workdir}/workflow/snakefiles/${snakefile}.smk \
--summary > ${workdir}/results/10_Reports/files-summaries/${snakefile}_files-summary.txt \ --summary > ${workdir}/results/10_Reports/files-summaries/${snakefile}_files-summary.txt \
2> /dev/null ; 2> /dev/null ;
done done
...@@ -420,7 +439,7 @@ Author _________________ Nicolas Fernandez ...@@ -420,7 +439,7 @@ Author _________________ Nicolas Fernandez
Affiliation ____________ IRD_U233_TransVIHMI Affiliation ____________ IRD_U233_TransVIHMI
Aim ____________________ Bash script for RQC Aim ____________________ Bash script for RQC
Date ___________________ 2021.10.12 Date ___________________ 2021.10.12
Latest modifications ___ 2022.11.18 Latest modifications ___ 2023.03.01
Run ____________________ bash Start_RQC.sh Run ____________________ bash Start_RQC.sh
Operating System _______ ${os} Operating System _______ ${os}
...@@ -456,8 +475,9 @@ cd ${workdir}/results/ ...@@ -456,8 +475,9 @@ cd ${workdir}/results/
tar -zcf 10_Reports_archive.tar.gz 10_Reports tar -zcf 10_Reports_archive.tar.gz 10_Reports
# Gzip results directory # Gzip results directory
mkdir -p ${workdir}/archives/ 2> /dev/null
cd ${workdir}/ cd ${workdir}/
tar -zcf Results_${time_stamp_archive}_${reference}_${aligner}-${min_cov}X_${samples}sp_archive.tar.gz results tar -zcf archives/Results_${time_stamp_archive}_${samples}sp_archive.tar.gz results/
echo -e " echo -e "
${green}------------------------------------------------------------------------${nc} ${green}------------------------------------------------------------------------${nc}
......
config/config.yaml → configuration/config.yaml
+ 37
− 33
View file @ c828a526
--- ---
###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 ___________________ config.yaml # Name ___________________ config.yaml
# Version ________________ v.2022.11 # Version ________________ v.2023.03
# Author _________________ Nicolas Fernandez # Author _________________ Nicolas Fernandez
# Affiliation ____________ IRD_U233_TransVIHMI # Affiliation ____________ IRD_U233_TransVIHMI
# Aim ____________________ Configuration yaml file for quality_control.smk snakefile # Aim ____________________ Configuration yaml file for quality_control.smk snakefile
# Date ___________________ 2021.10.12 # Date ___________________ 2021.10.12
# Latest modifications ___ 2022.11.18 # Latest modifications ___ 2023.03.01
# Use ____________________ Edit default settings # Use ____________________ Edit default settings
############################################################################### ###############################################################################
...@@ -21,41 +21,15 @@ resources: ...@@ -21,41 +21,15 @@ resources:
## '.' # Local (i.e. GeVarLi root directory) ## '.' # Local (i.e. GeVarLi root directory)
## '/scratch' # HPC (set it to match your HPC usage) ## '/scratch' # HPC (set it to match your HPC usage)
conda_frontend: 'mamba' # Conda frontend (conda or mamba)
# conda_version: '22.9.0' # Conda version (upgrade from "4.12.0")
# mamba_version: '1.0.0' # Mamba version (faster than conda)
# snakemake_version: '7.18.1' # Snakemake version (upgrade from "6.12.3")
# rename_version: '1.601' # Rename version (to rename fastq files)
# graphviz_version: '6.0.1' # GraphViz version (to do dot snakemake DAG)
### ENVIRONNEMENTS -----------------------------------------------------------------------------------
conda:
osx: # Conda OSX environement yaml files:
bowtie2: '../envs/osx/bowtie2_v.2.4.5.yaml' # Bowtie2 ver. 2.4.5
bwa: '../envs/osx/bwa_v.0.7.17.yaml' # BWA ver. 0.7.17
fastq-screen: '../envs/osx/fastq-screen_v.0.15.2.yaml' # Fastq-Screen ver. 0.15.2
fastqc: '../envs/osx/fastqc_v.0.11.9.yaml' # FastQC ver. 0.11.9
rqc-base: '../envs/osx/rqc-base_v.2022.11' # RQC-Base ver. 2022.11
multiqc: '../envs/osx/multiqc_v.1.12.yaml' # MultiQC ver. 1.12
linux: # Conda Linux environement yaml files:
bowtie2: '../envs/linux/bowtie2_v.2.4.5.yaml' # Bowtie2 ver. 2.4.5
bwa: '../envs/linux/bwa_v.0.7.17.yaml' # BWA ver. 0.7.17
fastq-screen: '../envs/linux/fastq-screen_v.0.15.2.yaml' # Fastq-Screen ver. 0.15.2
fastqc: '../envs/linux/fastqc_v.0.11.9.yaml' # FastQC ver. 0.11.9
rqc-base: '../envs/linux/rqc-base_v.2022.11' # RQC-Base ver. 2022.11
multiqc: '../envs/linux/multiqc_v.1.12.yaml' # MultiQC ver. 1.12
### FASTQSCREEN -------------------------------------------------------------------------------------- ### FASTQSCREEN --------------------------------------------------------------------------------------
fastq-screen: fastq-screen:
config: 'config/fastq-screen_bwa.conf' # Path to the fastq-screen configuration file config: 'configuration/fastq-screen_bwa.conf' # Path to the fastq-screen configuration file
# Available options: # Available options:
#- 'config/fastq-screen_bwa.conf' # Default fastq-screen configuration file for bwa users #- 'configuration/fastq-screen_bwa.conf' # Default fastq-screen configuration file for bwa users
#- 'config/fastq-screen_bowtie2.conf' # Default fastq-screen configuration file for bowtie2 users #- 'configuration/fastq-screen_bowtie2.conf' # Default fastq-screen configuration file for bowtie2 users
#- 'config/fastq-screen_custom.conf' # Your cutom fastq-screen configuration file #- 'configuration/fastq-screen_custom.conf' # Your cutom fastq-screen configuration file
subset: 10000 # Don't use whole sequences, but a subset reads (default: "1000") [INT] (0=all) subset: 10000 # Don't use whole sequences, but a subset reads (default: "1000") [INT] (0=all)
mapper: 'bwa' # Mapper used by fastq-screen for alignments (default "bwa") aligner: 'bwa' # Mapper used by fastq-screen for alignments (default "bwa")
# Available options: # Available options:
#- 'bwa' # Burrows-Wheeler Aligner (default, somme small genomes indexes provided, see "fastq-screen_bwa.conf") #- 'bwa' # Burrows-Wheeler Aligner (default, somme small genomes indexes provided, see "fastq-screen_bwa.conf")
#- 'bowtie2' # Bowtie2 (somme small genomes indexes provided, see "fastq-screen_bowtie2.conf") #- 'bowtie2' # Bowtie2 (somme small genomes indexes provided, see "fastq-screen_bowtie2.conf")
...@@ -84,6 +58,36 @@ bowtie2: ...@@ -84,6 +58,36 @@ bowtie2:
#- '' # (default) #- '' # (default)
#- '--large-index' # Force generated index to be "large", even if reference has fewer than 4 billion nucleotides #- '--large-index' # Force generated index to be "large", even if reference has fewer than 4 billion nucleotides
### ENVIRONNEMENTS -----------------------------------------------------------------------------------
# conda_version: '22.9.0' # Conda version (upgrade from "4.12.0")
# mamba_version: '1.0.0' # Mamba version (faster than conda)
# snakemake_version: '7.18.1' # Snakemake version (upgrade from "6.12.3")
# rename_version: '1.601' # Rename version (to rename fastq files)
# graphviz_version: '6.0.1' # GraphViz version (to do dot snakemake DAG)
conda:
frontend: 'mamba' # Conda frontend (conda or mamba)
# Available options:
#- 'mamba' # mamba (default)
#- 'conda' # conda
osx: # Conda OSX environement yaml files:
snakemake-base: '../environments/osx/snakemake-base_v.2023.02.yaml' # Snakemake-Base ver. 2023.02
#rqc-tools: '../environments/osx/rqc-tools_v.2023.03' # RQC-Tools ver. 2023.03
bowtie2: '../environments/osx/bowtie2_v.2.4.5.yaml' # Bowtie2 ver. 2.4.5
bwa: '../environments/osx/bwa_v.0.7.17.yaml' # BWA ver. 0.7.17
fastq-screen: '../environments/osx/fastq-screen_v.0.15.2.yaml' # Fastq-Screen ver. 0.15.2
fastqc: '../environments/osx/fastqc_v.0.11.9.yaml' # FastQC ver. 0.11.9
multiqc: '../environments/osx/multiqc_v.1.12.yaml' # MultiQC ver. 1.12
linux: # Conda Linux environement yaml files:
snakemake-base: '../environments/linux/snakemake-base_v.2023.02.yaml' # Snakemake-Base ver. 2023.02
#rqc-tools: '../environments/linux/rqc-tools_v.2023.03' # RQC-Tools ver. 2023.03
bowtie2: '../environments/linux/bowtie2_v.2.4.5.yaml' # Bowtie2 ver. 2.4.5
bwa: '../environments/linux/bwa_v.0.7.17.yaml' # BWA ver. 0.7.17
fastq-screen: '../environments/linux/fastq-screen_v.0.15.2.yaml' # Fastq-Screen ver. 0.15.2
fastqc: '../environments/linux/fastqc_v.0.11.9.yaml' # FastQC ver. 0.11.9
multiqc: '../environments/linux/multiqc_v.1.12.yaml' # MultiQC ver. 1.12
### OPERATING-SYSTEM --------------------------------------------------------------------------------- ### OPERATING-SYSTEM ---------------------------------------------------------------------------------
os: 'osx' # Operating System (default: "osx") os: 'osx' # Operating System (default: "osx")
# Available options: # Available options:
......
config/fastq-screen_bwa.conf → configuration/fastq-screen_bwa.conf
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...@@ -26,13 +26,13 @@ DATABASE Vectors resources/indexes/bwa/UniVec_wo_phiX_and_kanamycin ...@@ -26,13 +26,13 @@ DATABASE Vectors resources/indexes/bwa/UniVec_wo_phiX_and_kanamycin
#### Putative Hosts (Large genomes) ----- #### Putative Hosts (Large genomes) -----
### Gorilla g4 ### Gorilla g4
#DATABASE Gorilla resources/indexes/bwa/Gorilla-gorilla_g4 DATABASE Gorilla resources/indexes/bwa/Gorilla-gorilla_g4
### Chimpanzee t3 ### Chimpanzee t3
#DATABASE Chimpanzee resources/indexes/bwa/Pan_troglodytes_t3 DATABASE Chimpanzee resources/indexes/bwa/Pan_troglodytes_t3
### Human - Homo-sapiens_h38_NC-000001.11 ### Human - Homo-sapiens_h38_NC-000001.11
#DATABASE Human resources/indexes/bwa/Homo-sapiens_h38_NC000001-11 DATABASE Human resources/indexes/bwa/Homo-sapiens_h38_NC000001-11
### Bat v1 ### Bat v1
#DATABASE Bat resources/indexes/bwa/Pteropus-vampyrus_v1 DATABASE Bat resources/indexes/bwa/Pteropus-vampyrus_v1
#### Main Viruses (Small genomes) ----- #### Main Viruses (Small genomes) -----
...@@ -52,18 +52,18 @@ DATABASE HIV resources/indexes/bwa/HIV-1_HXB2_K03455-1 ...@@ -52,18 +52,18 @@ DATABASE HIV resources/indexes/bwa/HIV-1_HXB2_K03455-1
### E. coli (Bacteria) - QC_Echerichia-coli_CP060121.1 ### E. coli (Bacteria) - QC_Echerichia-coli_CP060121.1
DATABASE Ecoli resources/indexes/bwa/Echerichia-coli_CP060121-1 DATABASE Ecoli resources/indexes/bwa/Echerichia-coli_CP060121-1
### S. cerevisiae (Yeast) - sequence ### S. cerevisiae (Yeast) - sequence
#DATABASE Scerevisiae resources/indexes/bwa/Saccharomyces-cerevisiae DATABASE Scerevisiae resources/indexes/bwa/Saccharomyces-cerevisiae
### C. elegans (Nematode) - sequence ### C. elegans (Nematode) - sequence
#DATABASE Celegans resources/indexes/bwa/Caenorhabditis-elegans DATABASE Celegans resources/indexes/bwa/Caenorhabditis-elegans
### D. melanogaster (Fruit fly) - sequence ### D. melanogaster (Fruit fly) - sequence
#DATABASE Dmelanogaster resources/indexes/bwa/Drosophila-melanogaster DATABASE Dmelanogaster resources/indexes/bwa/Drosophila-melanogaster
### D. rerio (Zebrafish) - sequence ### D. rerio (Zebrafish) - sequence
#DATABASE Drerio resources/indexes/bwa/Danio-rerio DATABASE Drerio resources/indexes/bwa/Danio-rerio
### X. laevis (Xenope) - sequence ### X. laevis (Xenope) - sequence
#DATABASE Xlaevis resources/indexes/bwa/Xenopus-laevis DATABASE Xlaevis resources/indexes/bwa/Xenopus-laevis
### G. gallus - sequence ### G. gallus - sequence
#DATABASE Ggallus ressources/indexes/bwa/Gallus-gallus DATABASE Ggallus ressources/indexes/bwa/Gallus-gallus
### Mouse m39 ### Mouse m39
#DATABASE Mouse resources/indexes/bwa/Mus-musculus_m39 DATABASE Mouse resources/indexes/bwa/Mus-musculus_m39
### Arabidopsis t10 (Plant) - sequence from NCBI (ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/001/735/GCF_000001735.3_TAIR10/GCF_000001735.3_TAIR10_genomic.fna.gz) ### Arabidopsis t10 (Plant) - sequence from NCBI (ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/001/735/GCF_000001735.3_TAIR10/GCF_000001735.3_TAIR10_genomic.fna.gz)
#DATABASE Arabidopsis resources/indexes/bwa/Arabidopsis-thaliana_t10_NC003070-9 DATABASE Arabidopsis resources/indexes/bwa/Arabidopsis-thaliana_t10_NC003070-9
resources/data_test/.gitkeep 0 → 100644
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Git: keep this non empty file!
\ No newline at end of file
workflow/envs/linux/rqc-base_v.2022.11.yaml → workflow/environments/linux/snakemake-base_v.2023.02.yaml
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name: rqc-base_v.2022.11 name: snakemake-base_v.2023.02
channels: channels:
- bioconda - bioconda
- conda-forge - conda-forge
......
workflow/envs/osx/rqc-base_v.2022.11.yaml → workflow/environments/osx/snakemake-base_v.2023.02.yaml
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name: rqc-base_v.2022.11 name: snakemake-base_v.2023.02
channels: channels:
- bioconda - bioconda
- conda-forge - conda-forge
......
workflow/rules/indexing_genomes.smk → workflow/snakefiles/indexing_genomes.smk
+ 2
− 2
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...@@ -4,13 +4,13 @@ ...@@ -4,13 +4,13 @@
# Affiliation ____________ IRD_U233_TransVIHMI # Affiliation ____________ IRD_U233_TransVIHMI
# Aim ____________________ Snakefile with indexing genomes rules # Aim ____________________ Snakefile with indexing genomes rules
# Date ___________________ 2022.09.28 # Date ___________________ 2022.09.28
# Latest modifications ___ 2022.11.18 # Latest modifications ___ 2023.03.01
# Use ____________________ snakemake -s indexing_genomes.smk --use-conda # Use ____________________ snakemake -s indexing_genomes.smk --use-conda
############################################################################### ###############################################################################
###### CONFIGURATION ###### ###### CONFIGURATION ######
configfile: "config/config.yaml" configfile: "configuration/config.yaml"
############################################################################### ###############################################################################
###### FUNCTIONS ###### ###### FUNCTIONS ######
......
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