From 4e976b0e8917b0538a213af9e1606ac282a9f769 Mon Sep 17 00:00:00 2001
From: "Gervaise H. Henry" <gervaise.henry@utsouthwestern.edu>
Date: Mon, 28 Dec 2020 12:33:16 -0600
Subject: [PATCH] Send delete entry script to upload qc process
---
.gitlab-ci.yml | 2 +-
workflow/rna-seq.nf | 3 +++
2 files changed, 4 insertions(+), 1 deletion(-)
diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index 9874485..ea38a76 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -358,7 +358,7 @@ uploadProcessedFile:
cookie=$(cat credential.json | grep -A 1 '\"staging.gudmap.org\": {' | grep -o '\"cookie\": \".*\"') &&
cookie=${cookie:11:-1} &&
if [ "${exist}" != "[]" ]; then
- rids=$(echo $exist | grep -o '\"RID\":\".\{7\}' | sed 's/^.\{7\}//')
+ rids=$(echo ${exist} | grep -o '\"RID\":\".\{7\}' | sed 's/^.\{7\}//')
for rid in ${rids}; do
singularity run 'docker://gudmaprbk/deriva1.3:1.0.0' python3 ./workflow/scripts/deleteEntry.py -r ${rid} -t Processed_File -o $staging.gudmap.org -c ${cookie}
echo old processed file RID deleted - ${rid}
diff --git a/workflow/rna-seq.nf b/workflow/rna-seq.nf
index d311523..94ad34a 100644
--- a/workflow/rna-seq.nf
+++ b/workflow/rna-seq.nf
@@ -94,6 +94,7 @@ script_uploadInputBag = Channel.fromPath("${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")
/*
* trackStart: track start of pipeline
@@ -1429,6 +1430,7 @@ process uploadQC {
tag "${repRID}"
input:
+ path script_deleteEntry
path script_uploadQC
path credential, stageAs: "credential.json" from deriva_uploadQC
val executionRunRID from executionRunRID_uploadQC
@@ -1438,6 +1440,7 @@ process uploadQC {
val rawCount from rawReadsInfer_uploadQC
val finalCount from assignedReadsInfer_uploadQC
+
output:
path ("qcRID.csv") into qcRID_fl
--
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