From b08a7fc521b0ff747cfd4df041d7716121fb2250 Mon Sep 17 00:00:00 2001
From: "Gervaise H. Henry" <gervaise.henry@utsouthwestern.edu>
Date: Thu, 17 Dec 2020 16:05:30 -0600
Subject: [PATCH] Change process output bag name to uploadProcessedFiles

---
 .gitlab-ci.yml              |  2 +-
 workflow/conf/aws.config    |  2 +-
 workflow/conf/biohpc.config |  2 +-
 workflow/nextflow.config    |  2 +-
 workflow/rna-seq.nf         | 26 +++++++++++++-------------
 5 files changed, 17 insertions(+), 17 deletions(-)

diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index f9d856b..f6051c0 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -341,7 +341,7 @@ uploadQC:
     rid=$(singularity run 'docker://gudmaprbk/deriva1.3:1.0.0' python3 ./workflow/scripts/uploadQC.py -r 17-BTFJ -e  -p "Single Read" -s forward -l 35 -w 5 -f 1 -n 'This is a test mRNA QC' -o dev.gudmap.org -c ${cookie} -u F) &&
     echo ${rid} test mRNA QC created
 
-outputBag:
+uploadProcessedFile:
   stage: unit
   only:
     - push
diff --git a/workflow/conf/aws.config b/workflow/conf/aws.config
index 2b484e6..3e3cbb6 100644
--- a/workflow/conf/aws.config
+++ b/workflow/conf/aws.config
@@ -96,7 +96,7 @@ process {
     cpus = 1
     memory = '1 GB'
   }
-  withName: outputBag {
+  withName: uploadProcessedFile {
     cpus = 1
     memory = '1 GB'
   }
diff --git a/workflow/conf/biohpc.config b/workflow/conf/biohpc.config
index 042447a..ca9f0e4 100755
--- a/workflow/conf/biohpc.config
+++ b/workflow/conf/biohpc.config
@@ -67,7 +67,7 @@ process {
   withName: uploadQC {
     executor = 'local'
   }
-  withName: outputBag {
+  withName: uploadProcessedFile {
     executor = 'local'
   }
   withName: uploadOutputBag {
diff --git a/workflow/nextflow.config b/workflow/nextflow.config
index 6d91804..0aca0d8 100644
--- a/workflow/nextflow.config
+++ b/workflow/nextflow.config
@@ -76,7 +76,7 @@ process {
   withName:uploadQC {
     container = 'gudmaprbk/deriva1.3:1.0.0'
   }
-  withName:outputBag {
+  withName:uploadProcessedFile {
     container = 'gudmaprbk/deriva1.3:1.0.0'
   }
   withName:uploadOutputBag {
diff --git a/workflow/rna-seq.nf b/workflow/rna-seq.nf
index 25f4a24..bf91e37 100644
--- a/workflow/rna-seq.nf
+++ b/workflow/rna-seq.nf
@@ -37,10 +37,10 @@ deriva.into {
   deriva_getBag
   deriva_getRefInfer
   deriva_getRef
-  deriva_outputBag
   deriva_uploadInputBag
   deriva_uploadExecutionRun
   deriva_uploadQC
+  deriva_uploadProcessedFile
   deriva_uploadOutputBag
 }
 bdbag = Channel
@@ -353,12 +353,12 @@ endsManual.into {
 studyRID.into {
   studyRID_aggrQC
   studyRID_uploadInputBag
-  studyRID_outputBag
+  studyRID_uploadProcessedFile
   studyRID_uploadOutputBag
 }
 expRID.into {
   expRID_aggrQC
-  expRID_outputBag
+  expRID_uploadProcessedFile
 }
 
 
@@ -757,8 +757,8 @@ spikeInfer.into{
 speciesInfer.into {
   speciesInfer_getRef
   speciesInfer_aggrQC
-  speciesInfer_outputBag
   speciesInfer_uploadExecutionRun
+  speciesInfer_uploadProcessedFile
 }
 
 
@@ -974,7 +974,7 @@ dedupBam.into {
   dedupBam_countData
   dedupBam_makeBigWig
   dedupBam_dataQC
-  dedupBam_outputBag
+  dedupBam_uploadProcessedFile
 }
 
 /*
@@ -1417,8 +1417,8 @@ executionRunRID_fl.splitCsv(sep: ",", header: false).separate(
 
 //
 executionRunRID.into {
-  executionRunRID_outputBag
   executionRunRID_uploadQC
+  executionRunRID_uploadProcessedFile
   executionRunRID_uploadOutputBag
 }
 
@@ -1488,22 +1488,22 @@ qcRID_fl.splitCsv(sep: ",", header: false).separate(
 /*
  *ouputBag: create ouputBag
 */
-process outputBag {
+process uploadProcessedFile {
   tag "${repRID}"
   publishDir "${outDir}/outputBag", mode: 'copy', pattern: "Replicate_${repRID}.outputBag.zip"
 
   input:
-    path credential, stageAs: "credential.json" from deriva_outputBag
+    path credential, stageAs: "credential.json" from deriva_uploadProcessedFile
     path executionRunExportConfig
     path multiqc
     path multiqcJSON
-    tuple path (bam),path (bai) from dedupBam_outputBag
+    tuple path (bam),path (bai) from dedupBam_uploadProcessedFile
     path bigwig
     path counts
-    val species from speciesInfer_outputBag
-    val studyRID from studyRID_outputBag
-    val expRID from expRID_outputBag
-    val executionRunRID from executionRunRID_outputBag
+    val species from speciesInfer_uploadProcessedFile
+    val studyRID from studyRID_uploadProcessedFile
+    val expRID from expRID_uploadProcessedFile
+    val executionRunRID from executionRunRID_uploadProcessedFile
 
   output:
     path ("${repRID}_Output_Bag.zip") into outputBag
-- 
GitLab