From 1c689b38dd492a62f901b26ad7ff3908f5579e2f Mon Sep 17 00:00:00 2001 From: RoanKanninga Date: Sat, 16 Apr 2016 08:25:38 +0200 Subject: [PATCH 1/2] set workflow dependencies right --- compute5/NGS_DNA/workflow.csv | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/compute5/NGS_DNA/workflow.csv b/compute5/NGS_DNA/workflow.csv index 57841fb7..5f9661ec 100755 --- a/compute5/NGS_DNA/workflow.csv +++ b/compute5/NGS_DNA/workflow.csv @@ -30,8 +30,8 @@ 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,s24_VcfToTable -s25a_QC_Stats,protocols/QCStats.sh,s14a_CollectMultipleMetrics;s14b_CollectHSMetrics;s14c_CollectGCBiasMetrics;s14d_CollectBamIndexMetrics;s25_InSilicoConcordance -s26_QCReport,protocols/QCReport.sh,s12_SequenomConcordanceCheck;s25_InSilicoConcordance -s27_CountAllFinishedFiles,protocols/CountAllFinishedFiles.sh,s26_QCReport;s10b_DellyAnnotator +s25a_InSilicoConcordance,protocols/InSilicoConcordance.sh,s24_VcfToTable +s25b_QC_Stats,protocols/QCStats.sh,s14a_CollectMultipleMetrics;s14b_CollectHSMetrics;s14c_CollectGCBiasMetrics;s14d_CollectBamIndexMetrics;s25a_InSilicoConcordance +s26_QCReport,protocols/QCReport.sh,s25b_QC_Stats +s27_CountAllFinishedFiles,protocols/CountAllFinishedFiles.sh,s26_QCReport s28_CopyToResultsDir,protocols/CopyToResultsDir.sh,s27_CountAllFinishedFiles From fbcd08dcfcba94530f58850a459da2776311ce28 Mon Sep 17 00:00:00 2001 From: RoanKanninga Date: Sat, 16 Apr 2016 09:44:03 +0200 Subject: [PATCH 2/2] fixing gd or gaf group in CopyToResultsDir --- compute5/NGS_DNA/protocols/CopyToResultsDir.sh | 13 ++++++++++++- 1 file changed, 12 insertions(+), 1 deletion(-) diff --git a/compute5/NGS_DNA/protocols/CopyToResultsDir.sh b/compute5/NGS_DNA/protocols/CopyToResultsDir.sh index 0fc6f1c6..f86f6bd9 100755 --- a/compute5/NGS_DNA/protocols/CopyToResultsDir.sh +++ b/compute5/NGS_DNA/protocols/CopyToResultsDir.sh @@ -205,8 +205,19 @@ then elif [[ "${host}" == *"gd-node"* || "${host}" == "zinc-finger.gcc.rug.nl" ]] then + + if [[ "${logsDir}" == *"/groups/umcg-gd"* ]] + then + . ${EBROOTAUTOMATED}/parameters_gd.csv + elif [[ "${logsDir}" == *"/groups/umcg-gaf"* ]] + then + . ${EBROOTAUTOMATED}/parameters_gaf.csv + else + echo "unknown groupname please run in gaf or gd" + fi + touch ${logsDir}/${project}.pipeline.finished - . $EBROOTAUTOMATED/zinc-finger.gcc.rug.nl.cfg + . ${EBROOTAUTOMATED}/zinc-finger.gcc.rug.nl.cfg . $EBROOTAUTOMATED/sharedConfig.cfg echo "pipeline is finished, user ${ONTVANGER} has been mailed" printf "The results can be found: ${projectResultsDir}\n\nCheers from the GCC :)"| mail -s "NGS_DNA pipeline is finished for project ${project} on `date +%d/%m/%Y` `date +%H:%M`" ${ONTVANGER}