Keep rundir, dragen-4 renaming, data_xfer with fastq input

dhslab · Aug 22, 2023 · 30fcbaa · 30fcbaa
1 parent a9e93fa
commit 30fcbaa
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Showing 3 changed files with 15 additions and 15 deletions.
diff --git 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
@@ -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
@@ -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"
 }