modif master

Master.sh

@@ -19,14 +19,6 @@
 #$ -V
 
 
-function jumpto
-{
-    label=$1
-    cmd=$(sed -n "/$label:/{:a;n;p;ba};" $0 | grep -v ':$')
-    eval "$cmd"
-    exit
-}
-
 #Logging
 logbasename=$(date +"%F_%H-%M-%S")
 vcfbasename=$(date +"%F")
@@ -72,11 +64,6 @@ REF=`grep "reference" $PHARMCONFIG | cut -f2`
 PYTHONPATH=$PIPELINEBASE/common:/work/gad/shared/bin/lib/python_2.7/lib/python2.7/site-packages:/work/gad/shared/bin/miniconda2/lib/python2.7/site-packages/
 export PYTHONPATH
 
-# Varcall status file
-if [ -z ${STATUSFILE} ]
-then
-   STATUSFILE=$ANALYSISDIR/status.tsv
-fi
 
 # Sample list
 samples=`find -L $ANALYSISDIR/ -maxdepth 1 -mindepth 1 -type d | xargs -l basename`
@@ -88,92 +75,6 @@ then
 fi
 find -L $ANALYSISDIR/ -maxdepth 1 -mindepth 1 -type d | xargs -l basename >> $ANALYSISDIR/batch.list
 
-# 0 : Check status file
-if [ ! -e $STATUSFILE ]
-then
-    echo "No status file found : Jumping to configuration step"
-    jumpto configure
-else
-    echo "### Getting last analysis status ###"
-
-    # delete .failed files
-    failedfile=($ANALYSISDIR/*.failed)
-    if [ -e ${failedfile[0]} ]
-    then
-        rm $ANALYSISDIR/*.failed
-    fi
-
-    # get the status
-    HLAscan=`grep "process_HLAscan" $STATUSFILE | cut -f2`
-    varcallSNP=`grep "process_varcallSNP" $STATUSFILE | cut -f2`
-    varcallCNV=`grep "process_varcallCNV" $STATUSFILE | cut -f2`
-    createHTML=`grep "process_createHTML" $STATUSFILE | cut -f2`
-    mergeVCF=`grep "mergeVCF" $STATUSFILE | cut -f2`
-
-    if [ "$HLAscan" == "FAIL" ]
-    then
-	    echo "HLAscan step failed : jumping to HLAscan step"
-	    jumpto HLAscan
-    else
-	    echo "HLAscan step was OK"
-    fi
-    if [ "$varcallSNP" == "FAIL" ]
-    then
-	    echo "Variant calling SNP first step failed : jumping to variant calling SNP first step"
-	    jumpto varcallSNP
-    else
-	    echo "Variant calling SNP first step was OK"
-    fi
-    if [ "$varcallCNV" == "FAIL" ]
-    then
-	    echo "Variant calling CNV second step failed : jumping to variant calling CNV second step"
-	    jumpto varcallCNV
-    else
-	    echo "Variant calling CNV second step was OK"
-    fi
-    if [ "$createHTML" == "FAIL" ]
-    then
-      echo "CreateHTML step failed : jumping to variant create HTML step"
-      jumpto createHTML
-    else
-      echo "CreateHTML step was OK"
-    fi
-    if [ "$mergeVCF" == "FAIL" ]
-    then
-      echo "MergeVCF step failed : jumping to merge step"
-      jumpto MergeVCF
-    else
-      echo "MerfeVCF step was OK"
-    fi
-
-    echo "pipeline was correctly executed, no need to relaunch a step"
-    exit 0
-fi
-
-configure:
-# Configure variant calling analysis
-echo "### Configuration step ###"
-echo "Start : $(date +"%F_%H-%M-%S")"
-
-varcallfiles=($ANALYSISDIR/*/*.Master.list)
-if [ -e ${varcallfiles[0]} ]
-then
-    rm $ANALYSISDIR/*/*.Master.list
-fi
-
-situation=0
-
-# case no family file
-if [ "$situation" -eq "0" ]
-then
-    echo "No family file"
-    for currentSample in $samples
-    do
-        echo $currentSample >> $ANALYSISDIR/$currentSample/$currentSample.Master.list
-    done
-fi
-
-HLAscan:
 # HLA genotyping
 echo "### Execute HLAscan ###"
 echo "Start : $(date +"%F_%H-%M-%S")"
@@ -184,7 +85,6 @@ do
 done
 echo "End : $(date +"%F_%H-%M-%S")"
 
-varcallSNP:
 # Variant calling first step
 echo "### Variant calling SNP first step ###"
 echo "Start : $(date +"%F_%H-%M-%S")"
@@ -195,7 +95,6 @@ do
 done
 echo "End : $(date +"%F_%H-%M-%S")"
 
-varcallCNV:
 # Variant calling second step
 echo "### Variant calling CNV second step ###"
 echo "Start : $(date +"%F_%H-%M-%S")"
@@ -207,7 +106,6 @@ do
 done
 echo "End : $(date +"%F_%H-%M-%S")"
 
-createHTML:
 # Generate a HTML report_vcf
 echo "### Generate HTML report ###"
 echo "Start : $(date +"%F_%H-%M-%S")"
@@ -218,7 +116,6 @@ do
 done
 echo "End : $(date +"%F_%H-%M-%S")"
 
-MergeVCF:
 #merge vcf fies
 echo "### Merge VCF files"
 echo "Start : $(date +"%F_%H-%M-%S")"