From 04bbabd5889ba90e6e95c3badcbcff1dc16cd23c Mon Sep 17 00:00:00 2001
From: "Gervaise H. Henry" <gervaise.henry@utsouthwestern.edu>
Date: Tue, 25 Aug 2020 11:35:44 -0500
Subject: [PATCH] Allow override for input bagit #61
---
workflow/rna-seq.nf | 25 +++++++++++++++++++++----
1 file changed, 21 insertions(+), 4 deletions(-)
diff --git a/workflow/rna-seq.nf b/workflow/rna-seq.nf
index ac23518..f1a7c65 100644
--- a/workflow/rna-seq.nf
+++ b/workflow/rna-seq.nf
@@ -19,6 +19,9 @@ params.refHuVersion = "38.p12.v31"
params.refERCCVersion = "92"
params.outDir = "${baseDir}/../output"
+// Define override input variable
+params.inputBagForce = ""
+
// Parse input variables
deriva = Channel
.fromPath(params.deriva)
@@ -32,6 +35,8 @@ refHuVersion = params.refHuVersion
refERCCVersion = params.refERCCVersion
outDir = params.outDir
logsDir = "${outDir}/Logs"
+inputBagForce = params.inputBagForce
+
// Define fixed files
derivaConfig = Channel.fromPath("${baseDir}/conf/replicate_export_config.json")
@@ -119,6 +124,9 @@ process getBag {
output:
path ("Replicate_*.zip") into bagit
+ when:
+ params.inputBagForce == ""
+
script:
"""
hostname > ${repRID}.getBag.log
@@ -137,6 +145,15 @@ process getBag {
"""
}
+// Set inputBag to downloaded or forced input
+if (inputBagForce != "") {
+ inputBag = Channel
+ .fromPath(inputBagForce)
+ .ifEmpty { exit 1, "override inputBagit file not found: ${inputBagForce}" }
+} else {
+ inputBag = bagit
+}
+
/*
* getData: fetch study files from consortium with downloaded bdbag.zip
*/
@@ -146,7 +163,7 @@ process getData {
input:
path script_bdbagFetch
path cookies, stageAs: "deriva-cookies.txt" from bdbag
- path bagit
+ path inputBag
output:
path ("*.R{1,2}.fastq.gz") into fastqs
@@ -158,7 +175,7 @@ process getData {
"""
hostname > ${repRID}.getData.log
ulimit -a >> ${repRID}.getData.log
-
+
# link deriva cookie for authentication
echo -e "LOG: linking deriva cookie" >> ${repRID}.getData.log
mkdir -p ~/.bdbag
@@ -166,12 +183,12 @@ process getData {
echo -e "LOG: linked" >> ${repRID}.getData.log
# get bagit basename
- replicate=\$(basename "${bagit}" | cut -d "." -f1)
+ replicate=\$(basename "\${inputBag}" | cut -d "." -f1)
echo -e "LOG: bagit replicate name \${replicate}" >> ${repRID}.getData.log
# unzip bagit
echo -e "LOG: unzipping replicate bagit" >> ${repRID}.getData.log
- unzip ${bagit}
+ unzip ${inputBag}
echo -e "LOG: unzipped" >> ${repRID}.getData.log
# bagit fetch fastq's only and rename by repRID
--
GitLab