From b073d7ba6bc8442e97cc17d4626f359e1c92492a Mon Sep 17 00:00:00 2001
From: "Gervaise H. Henry" <gervaise.henry@utsouthwestern.edu>
Date: Mon, 28 Dec 2020 14:26:45 -0600
Subject: [PATCH] Add delete entry sctrpt to upload processed file process
---
workflow/rna-seq.nf | 6 ++++--
1 file changed, 4 insertions(+), 2 deletions(-)
diff --git a/workflow/rna-seq.nf b/workflow/rna-seq.nf
index 85a504f..d3b3c6b 100644
--- a/workflow/rna-seq.nf
+++ b/workflow/rna-seq.nf
@@ -94,7 +94,8 @@ script_uploadInputBag = Channel.fromPath("${baseDir}/scripts/uploadInputBag.py")
script_uploadExecutionRun = Channel.fromPath("${baseDir}/scripts/uploadExecutionRun.py")
script_uploadQC = Channel.fromPath("${baseDir}/scripts/uploadQC.py")
script_uploadOutputBag = Channel.fromPath("${baseDir}/scripts/uploadOutputBag.py")
-script_deleteEntry = Channel.fromPath("${baseDir}/scripts/deleteEntry.py")
+script_deleteEntry_uploadQC = Channel.fromPath("${baseDir}/scripts/deleteEntry.py")
+script_deleteEntry_uploadProcessedFile = Channel.fromPath("${baseDir}/scripts/deleteEntry.py")
/*
* trackStart: track start of pipeline
@@ -1430,7 +1431,7 @@ process uploadQC {
tag "${repRID}"
input:
- path script_deleteEntry
+ path script_deleteEntry_uploadQC
path script_uploadQC
path credential, stageAs: "credential.json" from deriva_uploadQC
val executionRunRID from executionRunRID_uploadQC
@@ -1496,6 +1497,7 @@ process uploadProcessedFile {
publishDir "${outDir}/outputBag", mode: 'copy', pattern: "Replicate_${repRID}.outputBag.zip"
input:
+ path script_deleteEntry_uploadProcessedFile
path credential, stageAs: "credential.json" from deriva_uploadProcessedFile
path executionRunExportConfig
path multiqc
--
GitLab