From 8ab63c9501e9b783eb29fa928a44fabb373c1596 Mon Sep 17 00:00:00 2001
From: "Gervaise H. Henry" <gervaise.henry@utsouthwestern.edu>
Date: Mon, 14 Dec 2020 10:14:57 -0600
Subject: [PATCH] Add optional upload param
---
workflow/rna-seq.nf | 14 ++++++++++++++
1 file changed, 14 insertions(+)
diff --git a/workflow/rna-seq.nf b/workflow/rna-seq.nf
index 1056f77..788a910 100644
--- a/workflow/rna-seq.nf
+++ b/workflow/rna-seq.nf
@@ -18,6 +18,7 @@ params.refMoVersion = "38.p6.vM22"
params.refHuVersion = "38.p12.v31"
params.refERCCVersion = "92"
params.outDir = "${baseDir}/../output"
+params.upload = true
params.email = ""
@@ -51,6 +52,7 @@ refHuVersion = params.refHuVersion
refERCCVersion = params.refERCCVersion
outDir = params.outDir
logsDir = "${outDir}/Logs"
+upload = params.upload
inputBagForce = params.inputBagForce
fastqsForce = params.fastqsForce
speciesForce = params.speciesForce
@@ -1284,6 +1286,9 @@ process uploadInputBag {
output:
path ("inputBagRID.csv") into inputBagRID_fl
+ when:
+ upload
+
script:
"""
hostname > ${repRID}.uploadInputBag.log
@@ -1350,6 +1355,9 @@ process uploadExecutionRun {
output:
path ("executionRunRID.csv") into executionRunRID_fl
+ when:
+ upload
+
script:
"""
hostname > ${repRID}.uploadExecutionRun.log
@@ -1431,6 +1439,9 @@ process uploadQC {
output:
path ("qcRID.csv") into qcRID_fl
+ when:
+ upload
+
script:
"""
hostname > ${repRID}.uploadQC.log
@@ -1572,6 +1583,9 @@ process uploadOutputBag {
output:
path ("outputBagRID.csv") into outputBagRID_fl
+ when:
+ upload
+
script:
"""
hostname > ${repRID}.uploadOutputBag.log
--
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