diff --git a/Soma.json b/Soma.json index 12942ca..03109c8 100644 --- a/Soma.json +++ b/Soma.json @@ -7,7 +7,7 @@ "Soma.XferLabel":"", "Soma.SomaRepo":"/storage1/fs1/gtac-mgi/Active/CLE/assay/SOMA/process/git/cle-soma", "Soma.DataTransfer":"true", - "Soma.RmRunDir":"true", + "Soma.RmRunDir":"false", "Soma.JobGroup":"/cle/wdl/haloplex", "Soma.DragenEnv":"LSF_DOCKER_DRAGEN=y", "Soma.DragenDockerImage":"gtac-mgi-dragen(seqfu/oracle8-dragen-4.0.3:latest)", diff --git a/Soma.wdl b/Soma.wdl index b23d90a..5ce3d45 100644 --- a/Soma.wdl +++ b/Soma.wdl @@ -111,20 +111,20 @@ workflow Soma { jobGroup=JobGroup } - if (defined(DemuxSampleSheet)){ - if (DataTransfer) { - call data_transfer { - input: QcAll=batch_qc.QC_all, - #QcFile= OutputDir + '/' + basename(OutputDir) + '_Genoox.xlsx', - QcFile=batch_qc.QC_file, - BatchFastqDir= DemuxFastqDir + '/' + basename(OutputDir), - InputSpreadSheet=InputSpreadSheet, - XferLabel=XferLabel, - queue=Queue, - jobGroup=JobGroup - } + if (DataTransfer) { + call data_transfer { + input: QcAll=batch_qc.QC_all, + #QcFile= OutputDir + '/' + basename(OutputDir) + '_Genoox.xlsx', + QcFile=batch_qc.QC_file, + BatchFastqDir= DemuxFastqDir + '/' + basename(OutputDir), + InputSpreadSheet=InputSpreadSheet, + XferLabel=XferLabel, + queue=Queue, + jobGroup=JobGroup } + } + if (defined(DemuxSampleSheet)){ if (RmRunDir) { call remove_rundir { input: order_by=gather_files.done, diff --git a/Soma_alt.json b/Soma_alt.json index f410e34..ed4a6ea 100644 --- a/Soma_alt.json +++ b/Soma_alt.json @@ -7,10 +7,10 @@ "Soma.XferLabel":"", "Soma.SomaRepo":"/storage1/fs1/gtac-mgi/Active/CLE/assay/SOMA/process/git/cle-soma", "Soma.DataTransfer":"true", - "Soma.RmRunDir":"true", + "Soma.RmRunDir":"false", "Soma.JobGroup":"/cle/wdl/haloplex", "Soma.DragenEnv":"LSF_DOCKER_DRAGEN=y", "Soma.DragenDockerImage":"gtac-mgi-dragen(seqfu/oracle8-dragen-4.0.3:latest)", - "Soma.DragenQueue":"dragen", + "Soma.DragenQueue":"dragen-4", "Soma.Queue":"gtac-mgi" }