Add variables to make scripts more generic

README.md

@@ -3,13 +3,13 @@
 - ASDP PIPELINE
 - Author: anne-sophie.denomme-pichon@u-bourgogne.fr
 - Version: 0.0.1
-- Licence: FIXME
+- Licence: AGPLv3
 - Description: How to launch scripts to get STR genotype from genomes on all the locus tested
 
-1. Create `genomes.list`
-2. Specify output file in `launch_pipeline.sh`. Warning, don't overwrite existing files
-3. Launch `launch_pipeline.sh`: `nohup ./launch_pipeline.sh &`. Dependencies:
-   - `genomes.list`
+1. Create `samples.list`
+2. Fill the configuration file `config.sh`. Warning, don't overwrite existing files
+3. Launch `launch_pipeline.sh` : `nohup ./launch_pipeline.sh samples.list &`. Dependencies :
+   - `samples.list`
    - `pipeline.sh`
    - `wrapper_delete.sh`
    - `wrapper_ehdn.sh`

launch_pipeline.sh

 #! /bin/sh
 
 ### ASDP PIPELINE ###
-## launch_pipeline.sh
-## Version : 0.0.1
-## Licence : FIXME
-## Description : script to launch the pipeline for STR detection
-## Usage : 
-## Output : FIXME
-## Requirements : FIXME
-
-## Author : anne-sophie.denomme-pichon@u-bourgogne.fr
-## Creation Date : 20191208
-## last revision date : 20200215
-## Known bugs : None
-
-/work/gad/shared/bin/parallel/parallel-20150522-1.el7.cern/bin/parallel \
-    --jobs 16 \
+## Version: 0.0.1
+## Licence: AGPLV3
+## Author: anne-sophie.denomme-pichon@u-bourgogne.fr
+## Description: script to launch the pipeline for STR detection. Receive multiple samples: one sample per line
+
+# $1 : first argument in the command line : a list containing one sample per line, for exemple samples.list
+SAMPLES="$1"
+
+# Check if sample is specified
+if [ -z "$SAMPLES" ]
+then
+    echo "List of samples is not specified"
+    echo "$(date +"%F_%H-%M-%S"): END"
+    exit 1
+fi
+
+# Source configuration file
+. "$(dirname "$0")/config.sh"
+
+# Parallel allow to parallelize the processing of multiple samples
+"$PARALLEL" \
+    --jobs "$PARALLEL_JOB_COUNT" \
     --line-buffer \
     "$(dirname "$0")/pipeline.sh" \
-    < genomes.list
+    < "$SAMPLES"
+
+
+

pipeline.sh

@@ -18,31 +18,34 @@ then
     exit 1
 fi
 
-INPUTFILE="/archive/gad/shared/bam_new_genome_temp/$SAMPLE.bam"
+# Source the configuration file
+. "$(dirname "$0")/config.sh"
+
+INPUTFILE="INPUTDIR/$SAMPLE.bam"
 DATE="$(date +"%F_%H-%M-%S")"
-OUTPUTDIR="/work/gad/shared/analyse/STR/pipeline/$SAMPLE"
+OUTPUTDIR="OUTPUTDIR/$SAMPLE"
 
 # Transfer bam and bai from archive to work
 mkdir -p "$OUTPUTDIR"
-qsub -pe smp 1 -q transfer -N "transfer_$SAMPLE" -v INPUTFILE="$INPUTFILE",OUTPUTDIR="$OUTPUTDIR",LOGFILE="$OUTPUTDIR/transfer_$DATE.log" wrapper_transfer.sh
+qsub -pe smp 1 -q "$TRANSFERQUEUE" -N "transfer_$SAMPLE" -v INPUTFILE="$INPUTFILE",OUTPUTDIR="$OUTPUTDIR",LOGFILE="$OUTPUTDIR/transfer_$DATE.log" wrapper_transfer.sh
 
 INPUTFILE="$OUTPUTDIR/$SAMPLE.bam"
 
 # Launch ExpansionHunter
 mkdir -p "$OUTPUTDIR/eh"
-qsub -pe smp 4 -q batch  -N "eh_$SAMPLE" -hold_jid "transfer_$SAMPLE" -v INPUTFILE="$INPUTFILE",OUTPUTPREFIX="$OUTPUTDIR/eh/$SAMPLE",LOGFILE="$OUTPUTDIR/eh/$DATE.log" wrapper_expansionhunter.sh
+qsub -pe smp 4 -q "$COMPUTEQUEUE"  -N "eh_$SAMPLE" -hold_jid "transfer_$SAMPLE" -v INPUTFILE="$INPUTFILE",OUTPUTPREFIX="$OUTPUTDIR/eh/$SAMPLE",LOGFILE="$OUTPUTDIR/eh/$DATE.log" wrapper_expansionhunter.sh
 
 # Launch Tredparse
 mkdir -p "$OUTPUTDIR/tredparse"
-qsub -pe smp 4 -q batch -N "tredparse_$SAMPLE" -hold_jid "transfer_$SAMPLE" -v INPUTFILE="$INPUTFILE",OUTPUTDIR="$OUTPUTDIR/tredparse",LOGFILE="$OUTPUTDIR/tredparse/$DATE.log" wrapper_tredparse.sh
+qsub -pe smp 4 -q "$COMPUTEQUEUE" -N "tredparse_$SAMPLE" -hold_jid "transfer_$SAMPLE" -v INPUTFILE="$INPUTFILE",OUTPUTDIR="$OUTPUTDIR/tredparse",LOGFILE="$OUTPUTDIR/tredparse/$DATE.log" wrapper_tredparse.sh
 
 # Launch GangSTR
 mkdir -p "$OUTPUTDIR/gangstr"
-qsub -pe smp 4 -q batch -N "gangstr_$SAMPLE" -hold_jid "transfer_$SAMPLE" -v INPUTFILE="$INPUTFILE",OUTPUTPREFIX="$OUTPUTDIR/gangstr/$SAMPLE",LOGFILE="$OUTPUTDIR/gangstr/$DATE.log" wrapper_gangstr.sh
+qsub -pe smp 4 -q "$COMPUTEQUEUE" -N "gangstr_$SAMPLE" -hold_jid "transfer_$SAMPLE" -v INPUTFILE="$INPUTFILE",OUTPUTPREFIX="$OUTPUTDIR/gangstr/$SAMPLE",LOGFILE="$OUTPUTDIR/gangstr/$DATE.log" wrapper_gangstr.sh
 
 # Launch ehdn profile
 mkdir -p "$OUTPUTDIR/ehdn"
-qsub -pe smp 4 -q batch -N "ehdn_$SAMPLE" -hold_jid "transfer_$SAMPLE" -v INPUTFILE="$INPUTFILE",OUTPUTPREFIX="$OUTPUTDIR/ehdn/$SAMPLE",LOGFILE="$OUTPUTDIR/ehdn/$DATE.log" wrapper_ehdn.sh
+qsub -pe smp 4 -q "$COMPUTEQUEUE" -N "ehdn_$SAMPLE" -hold_jid "transfer_$SAMPLE" -v INPUTFILE="$INPUTFILE",OUTPUTPREFIX="$OUTPUTDIR/ehdn/$SAMPLE",LOGFILE="$OUTPUTDIR/ehdn/$DATE.log" wrapper_ehdn.sh
 
 # Delete transfered bam and bai
-qsub -pe smp 1 -q batch -N "delete_$SAMPLE" -hold_jid "eh_$SAMPLE,tredparse_$SAMPLE,gangstr_$SAMPLE,ehdn_$SAMPLE" -sync y -v SAMPLE="$SAMPLE",LOGFILE="$OUTPUTDIR/delete_$DATE.log" wrapper_delete.sh
+qsub -pe smp 1 -q "$COMPUTEQUEUE" -N "delete_$SAMPLE" -hold_jid "eh_$SAMPLE,tredparse_$SAMPLE,gangstr_$SAMPLE,ehdn_$SAMPLE" -sync y -v SAMPLE="$SAMPLE",LOGFILE="$OUTPUTDIR/delete_$DATE.log" wrapper_delete.sh

wrapper_delete.sh

@@ -7,6 +7,8 @@
 ## Description: a wrapper for qsubing bam deletion for STR pipeline
 ## Usage: qsub -pe smp 1 -v SAMPLE=<sample>,[LOGFILE=<path to the log file>] wrapper_delete.sh
 
+# Source the configuration file
+. "$(dirname "$0")/config.sh"
 
 # Log file path option
 if [ -z "$LOGFILE" ]
@@ -30,8 +32,8 @@ fi
 echo "command : rm \
     $SAMPLE"
 rm \
-    "/work/gad/shared/analyse/STR/pipeline/$SAMPLE/$SAMPLE.bam" \
-    "/work/gad/shared/analyse/STR/pipeline/$SAMPLE/$SAMPLE.bai"
+    "$OUTPUTDIR/$SAMPLE/$SAMPLE.bam" \
+    "$OUTPUTDIR/$SAMPLE/$SAMPLE.bai"
 
 delete_exitcode=$?
 

wrapper_ehdn.sh

@@ -7,6 +7,8 @@
 ## Description: a wrapper for qsubing ExpansionHunter denovo script for STR detection
 ## Usage: qsub -pe smp 1 -v INPUTFILE=<path to the bam file>,OUTPUTPREFIX=<output prefix>,[LOGFILE=<path to the log file>] wrapper_ehdn.sh
 
+# Source the configuration file
+. "$(dirname "$0")/config.sh"
 
 # Log file path option
 if [ -z "$LOGFILE" ]
@@ -35,21 +37,27 @@ then
     exit 1
 fi
 
-# Create .bam and .bai symbolic links
+# Create .bam and .bai symbolic links (EHDN expects .bam.bai)
 TMPDIR="$(mktemp -d)"
 ln -s "$INPUTFILE" "$TMPDIR/$(basename "$INPUTFILE")"
-ln -s "$(echo "$INPUTFILE" | sed 's/\.bam$/.bai/')" "$TMPDIR/$(basename "$INPUTFILE").bai"
+if [ -f "$INPUTFILE.bai" ]
+then
+    ln -s "$INPUTFILE.bai" "$TMPDIR/$(basename "$INPUTFILE").bai"
+else
+    ln -s "$(echo "$INPUTFILE" | sed 's/\.bam$/.bai/')" "$TMPDIR/$(basename "$INPUTFILE").bai"
+fi
 
 # Launch script command and check exit code
-echo "command : /work/gad/shared/bin/expansionhunterdenovo/ExpansionHunterDenovo-v0.8.0-linux_x86_64/bin/ExpansionHunterDenovo-v0.8.0 profile \
-    --reads "$TMPDIR/$(basename "$INPUTFILE")" \
-    --reference /work/gad/shared/pipeline/hg19/index/hg19_essential.fa \
+echo "command : $EHDN profile \
+    --reads $TMPDIR/$(basename "$INPUTFILE") \
+    --reference $REF \
     --output-prefix $OUTPUTPREFIX \
     --min-anchor-mapq 50 \
     --max-irr-mapq 40"
-/work/gad/shared/bin/expansionhunterdenovo/ExpansionHunterDenovo-v0.8.0-linux_x86_64/bin/ExpansionHunterDenovo-v0.8.0 profile \
+
+"$EHDN" profile \
     --reads "$TMPDIR/$(basename "$INPUTFILE")" \
-    --reference /work/gad/shared/pipeline/hg19/index/hg19_essential.fa \
+    --reference "$REF" \
     --output-prefix "$OUTPUTPREFIX" \
     --min-anchor-mapq 50 \
     --max-irr-mapq 40

wrapper_ehdn_outlier.sh

@@ -6,11 +6,8 @@
 ## Author: anne-sophie.denomme-pichon@u-bourgogne.fr
 ## Description: script to generate automatically a manifest and multisampleprofile in a tsv format, then do outlier analyses for a single patient
 
-
-EHDN="/work/gad/shared/bin/expansionhunterdenovo/ExpansionHunterDenovo-v0.8.0-linux_x86_64/bin/ExpansionHunterDenovo-v0.8.0"
-EHDN_OUTLIER="/work/gad/shared/bin/expansionhunterdenovo/ExpansionHunterDenovo-v0.8.0-linux_x86_64/scripts/outlier.py"
-REFERENCE="/work/gad/shared/pipeline/hg19/index/hg19_essential.fa"
-WORKDIR="/work/gad/shared/analyse/STR/pipeline"
+# Source the configuration file
+. "$(dirname "$0")/config.sh"
 
 # Log file path option
 if [ -z "$LOGFILE" ]
@@ -31,20 +28,20 @@ then
 fi
 
 # Generate manifest for one patient with all samples (to write lines in the file)
-cd "$WORKDIR"
+cd "$OUTPUTDIR"
 for dijen in dijen*
 do
     # Check if str_profile.json exists
-    if [ -f "$WORKDIR/$dijen/ehdn/$dijen.str_profile.json" ]
+    if [ -f "$OUTPUTDIR/$dijen/ehdn/$dijen.str_profile.json" ]
     then
         if [ "x$dijen" = "x$CASE" ]
         then
-        echo -e "$dijen\tcase\t$WORKDIR/$dijen/ehdn/$dijen.str_profile.json"
+        echo -e "$dijen\tcase\t$OUTPUTDIR/$dijen/ehdn/$dijen.str_profile.json"
         else
-        echo -e "$dijen\tcontrol\t$WORKDIR/$dijen/ehdn/$dijen.str_profile.json"
+        echo -e "$dijen\tcontrol\t$OUTPUTDIR/$dijen/ehdn/$dijen.str_profile.json"
         fi
     fi
-done > "$WORKDIR/$CASE/ehdn/$CASE.manifest.tsv"
+done > "$OUTPUTDIR/$CASE/ehdn/$CASE.manifest.tsv"
 
 ehdn_outlier_exitcode=$?
 
@@ -58,7 +55,7 @@ fi
 # Generate multisampleprofile for one patient with all samples
 "$EHDN" merge \
     --reference "$REFERENCE" \
-    --manifest "$WORKDIR/$CASE/ehdn/$CASE.manifest.tsv" \
+    --manifest "$OUTPUTDIR/$CASE/ehdn/$CASE.manifest.tsv" \
     --output-prefix "$CASE/ehdn/$CASE"
 
 ehdn_outlier_exitcode=$?
@@ -72,9 +69,9 @@ fi
 
 # Run locus-based comparison analysis
 "$EHDN_OUTLIER" locus \
-    --manifest "$WORKDIR/$CASE/ehdn/$CASE.manifest.tsv" \
-    --multisample-profile "$WORKDIR/$CASE/ehdn/$CASE.multisample_profile.json" \
-    --output "$WORKDIR/$CASE/ehdn/$CASE.outlier_locus.tsv"
+    --manifest "$OUTPUTDIR/$CASE/ehdn/$CASE.manifest.tsv" \
+    --multisample-profile "$OUTPUTDIR/$CASE/ehdn/$CASE.multisample_profile.json" \
+    --output "$OUTPUTDIR/$CASE/ehdn/$CASE.outlier_locus.tsv"
 
 ehdn_outlier_exitcode=$?
 
@@ -88,9 +85,9 @@ fi
 
 # Run motif_based comparison analysis
 "$EHDN_OUTLIER" motif \
-    --manifest "$WORKDIR/$CASE/ehdn/$CASE.manifest.tsv" \
-    --multisample-profile "$WORKDIR/$CASE/ehdn/$CASE.multisample_profile.json" \
-    --output "$WORKDIR/$CASE/ehdn/$CASE.outlier_motif.tsv"
+    --manifest "$OUTPUTDIR/$CASE/ehdn/$CASE.manifest.tsv" \
+    --multisample-profile "$OUTPUTDIR/$CASE/ehdn/$CASE.multisample_profile.json" \
+    --output "$OUTPUTDIR/$CASE/ehdn/$CASE.outlier_motif.tsv"
 
 ehdn_outlier_exitcode=$?
 

wrapper_expansionhunter.sh

@@ -7,6 +7,8 @@
 ## Description: a wrapper for qsubing ExpansionHunter script for STR detection
 ## Usage: qsub -pe smp 1 -v INPUTFILE=<path to the bam file>,OUTPUTPREFIX=<output prefix>,[LOGFILE=<path to the log file>] wrapper_expansionhunter.sh
 
+# Source the configuration file
+. "$(dirname "$0")/config.sh"
 
 # Log file path option
 if [ -z "$LOGFILE" ]
@@ -35,21 +37,27 @@ then
     exit 1
 fi
 
-# Create .bam and .bai symbolic links
+# Create .bam and .bai symbolic links (EH expects .bam.bai)
 TMPDIR="$(mktemp -d)"
 ln -s "$INPUTFILE" "$TMPDIR/$(basename "$INPUTFILE")"
-ln -s "$(echo "$INPUTFILE" | sed 's/\.bam$/.bai/')" "$TMPDIR/$(basename "$INPUTFILE").bai"
+if [ -f "$INPUTFILE.bai" ]
+then
+    ln -s "$INPUTFILE.bai" "$TMPDIR/$(basename "$INPUTFILE").bai"
+else
+    ln -s "$(echo "$INPUTFILE" | sed 's/\.bam$/.bai/')" "$TMPDIR/$(basename "$INPUTFILE").bai"
+fi
 
 # Launch script command and check exit code
-echo "command : /work/gad/shared/bin/expansionhunter/ExpansionHunter-v3.1.2-linux_x86_64/bin/ExpansionHunter \
-    --reads "$TMPDIR/$(basename "$INPUTFILE")" \
-    --reference /work/gad/shared/pipeline/hg19/index/hg19_essential.fa \
-    --variant-catalog /work/gad/shared/bin/expansionhunter/ExpansionHunter-v3.1.2-linux_x86_64/variant_catalog/hg19/variant_catalog.json \
+echo "command : $EH \
+    --reads $TMPDIR/$(basename "$INPUTFILE") \
+    --reference $REF \
+    --variant-catalog $EH_VARIANT_CATALOG \
     --output-prefix $OUTPUTPREFIX"
-/work/gad/shared/bin/expansionhunter/ExpansionHunter-v3.1.2-linux_x86_64/bin/ExpansionHunter \
+
+"$EH" \
     --reads "$TMPDIR/$(basename "$INPUTFILE")" \
-    --reference /work/gad/shared/pipeline/hg19/index/hg19_essential.fa \
-    --variant-catalog /work/gad/shared/bin/expansionhunter/ExpansionHunter-v3.1.2-linux_x86_64/variant_catalog/hg19/variant_catalog.json \
+    --reference "$REF" \
+    --variant-catalog "$EH_VARIANT_CATALOG" \
     --output-prefix "$OUTPUTPREFIX"
 
 expansionhunter_exitcode=$?

wrapper_gangstr.sh

@@ -7,6 +7,9 @@
 ## Description: a wrapper for qsubing GangSTR script for STR detection
 ## Usage: qsub -pe smp 1 -v INPUTFILE=<path to the bam file>,OUTPUTPREFIX=<output prefix>,[LOGFILE=<path to the log file>] wrapper_gangstr.sh
 
+# Source the configuration file
+. "$(dirname "$0")/config.sh"
+
 # Log file path option
 if [ -z "$LOGFILE" ]
 then
@@ -35,20 +38,20 @@ then
 fi
 
 # Launch script command and check exit code
-echo "command : /work/gad/shared/bin/gangstr/GangSTR-2.4/bin/GangSTR \
-    --bam "$INPUTFILE" \
-    --ref /work/gad/shared/pipeline/hg19/index/hg19_essential.fa \
-    --regions /work/gad/shared/bin/gangstr/STRregions/hg19_ver13_1.bed \
-    --out "$OUTPUTPREFIX" \
-    --verbose
+echo "command : $GANGSTR \
+    --bam $INPUTFILE \
+    --ref $REF \
+    --regions $GANGSTR_REGIONS \
+    --out $OUTPUTPREFIX \
+    --verbose"
 
 #    --insertmean "$INSERTMEAN" \
 #    --insertsdev "$INSERTDEV""
 
-/work/gad/shared/bin/gangstr/GangSTR-2.4/bin/GangSTR \
+"$GANGSTR" \
     --bam "$INPUTFILE" \
-    --ref /work/gad/shared/pipeline/hg19/index/hg19_essential.fa \
-    --regions /work/gad/shared/bin/gangstr/STRregions/hg19_ver13_1.bed \
+    --ref "$REF" \
+    --regions "$GANGSTR_REGIONS" \
     --out "$OUTPUTPREFIX" \
     --verbose
 

wrapper_tredparse.sh

@@ -7,6 +7,8 @@
 ## Description: a wrapper for qsubing Tredparse script for STR detection
 ## Usage: qsub -pe smp 1 -v INPUTFILE=<path to the bam file>,OUTPUTDIR=<output directory>,[LOGFILE=<path to the log file>] wrapper_tredparse.sh
 
+# Source the configuration file
+. "$(dirname "$0")/config.sh"
 
 # Log file path option
 if [ -z "$LOGFILE" ]
@@ -35,13 +37,15 @@ then
     exit 1
 fi
 
-# Enable the virtualenv
-TREDPARSE="/work/gad/shared/bin/tredparse/Tredparse-20190901"
-. "$TREDPARSE/bin/activate"
+# Enable the virtualenv if any
+if [ -n "$TREDPARSE_VENV" ]
+then
+    . "$TREDPARSE_VENV"
+fi
 
 # Launch script command and check exit code
-echo "command : "$TREDPARSE/bin/tred.py" "$INPUTFILE" --workdir "$OUTPUTDIR" --ref hg19"
-"$TREDPARSE/bin/tred.py" "$INPUTFILE" --workdir "$OUTPUTDIR" --ref hg19
+echo "command : $TREDPARSE $INPUTFILE --workdir $OUTPUTDIR --ref hg19"
+"$TREDPARSE" "$INPUTFILE" --workdir "$OUTPUTDIR" --ref hg19
 
 tredparse_exitcode=$?