Merge pull request #238 from RoanKanninga/master

increase walltime + changed number of cores SpikePhiX protocol
molgenis · Jun 22, 2015 · 874e678 · 874e678
2 parents b6c37e4 + 8ec4df3
commit 874e678
Show file tree

Hide file tree

Showing 2 changed files with 6 additions and 4 deletions.
diff --git a/compute5/NGS_DNA-2.1.1/protocols/SpikePhiX.sh b/compute5/NGS_DNA-2.1.1/protocols/SpikePhiX.sh
@@ -1,4 +1,4 @@
-#MOLGENIS nodes=1 ppn=1 mem=1gb walltime=02:30:00
+#MOLGENIS nodes=1 ppn=8 mem=1gb walltime=12:30:00
 
 #Parameter mapping
 #string seqType
@@ -17,6 +17,8 @@ echo "srBarcodeFqGz: ${srBarcodeFqGz}"
 
 sleep 10 
 
+module load pigz/2.3.3
+
 # Spike phiX only once
 samp=`tail -10 ${peEnd1BarcodeFqGz}`
 phiX=`tail -10 ${phiXEnd1Gz}`
@@ -33,8 +35,8 @@ else
 	elif [ $seqType == "PE" ]
 	then
 		echo "Append phiX reads"
-		zcat ${peEnd1BarcodeFqGz} ${phiXEnd1Gz} | gzip -c - > ${peEnd1BarcodeFqGz}.tmp
-		zcat ${peEnd2BarcodeFqGz} ${phiXEnd2Gz} | gzip -c - > ${peEnd2BarcodeFqGz}.tmp
+		zcat ${peEnd1BarcodeFqGz} ${phiXEnd1Gz} | ${PIGZ_HOME}/pigz > ${peEnd1BarcodeFqGz}.tmp
+		zcat ${peEnd2BarcodeFqGz} ${phiXEnd2Gz} | ${PIGZ_HOME}/pigz > ${peEnd2BarcodeFqGz}.tmp
 		mv ${peEnd1BarcodeFqGz}.tmp ${peEnd1BarcodeFqGz}
 		mv ${peEnd2BarcodeFqGz}.tmp ${peEnd2BarcodeFqGz}
 	fi

diff --git a/compute5/NGS_DNA-2.1.1/workflow.csv b/compute5/NGS_DNA-2.1.1/workflow.csv
@@ -24,7 +24,7 @@ s21b_IndelFiltration,protocols/IndelFiltration.sh,s20_SplitIndelsAndSNPs
 s22_dbNSFPAnnotation,protocols/dbNSFPAnnotation.sh,s21a_SnpFiltration
 s23_MergeIndelsAndSnps,protocols/MergeIndelsAndSnps.sh,s21b_IndelFiltration;s22_dbNSFPAnnotation
 s24_VcfToTable,protocols/VcfToTable.sh,s23_MergeIndelsAndSnps
-s25_InSilicoConcordance,protocols/InSilicoConcordance.sh,s16_VariantCalling;s24_VcfToTable
+s25_InSilicoConcordance,protocols/InSilicoConcordance.sh,s24_VcfToTable
 s26_QCReport,protocols/QCReport.sh,s12_SequenomConcordanceCheck;s25_InSilicoConcordance
 s27_CountAllFinishedFiles,protocols/CountAllFinishedFiles.sh,s26_QCReport
 s28_CopyToResultsDir,protocols/CopyToResultsDir.sh,s27_CountAllFinishedFiles