Merge pull request #503 from RoanKanninga/master

set workflow dependencies right

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}

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