From 1e8d161ea6c8870d8d33446f65e95f176b7ef074 Mon Sep 17 00:00:00 2001
From: "Gervaise H. Henry" <gervaise.henry@utsouthwestern.edu>
Date: Tue, 2 Mar 2021 11:12:30 -0600
Subject: [PATCH] Don't donwload fastqs if overridden
---
CHANGELOG.md | 2 ++
rna-seq.nf | 20 ++++++++++++++++----
2 files changed, 18 insertions(+), 4 deletions(-)
diff --git a/CHANGELOG.md b/CHANGELOG.md
index 1025ae0..c90e24a 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -29,6 +29,8 @@
* Add new CI py tests for override and integration
* Fix fastq file and species error status detail bub (#118)
* Make compatible with XPACK-DNANEXUS
+* Don't download fastq's if fastq override present
+* Override fastq count to override counts
*Known Bugs*
* Override params (inputBag, fastq, species) aren't checked for integrity
diff --git a/rna-seq.nf b/rna-seq.nf
index 923eccc..f761977 100644
--- a/rna-seq.nf
+++ b/rna-seq.nf
@@ -264,9 +264,14 @@ process getData {
echo -e "LOG: unzipped" >> ${repRID}.getData.log
# bag fetch fastq's only and rename by repRID
- echo -e "LOG: fetching replicate bdbag" >> ${repRID}.getData.log
- fastqCount=\$(sh ${script_bdbagFetch} \${replicate::-13} ${repRID})
- echo -e "LOG: fetched" >> ${repRID}.getData.log
+ if [ "${fastqsForce}" != "" ]
+ then
+ echo -e "LOG: fetching replicate bdbag" >> ${repRID}.getData.log
+ fastqCount=\$(sh ${script_bdbagFetch} \${replicate::-13} ${repRID})
+ echo -e "LOG: fetched" >> ${repRID}.getData.log
+ else
+ echo -e "LOG: fastq override detected, not fetching fastqs" >> ${repRID}.getData.log
+ fi
if [ "\${fastqCount}" == "0" ]
then
@@ -277,9 +282,10 @@ process getData {
}
// Split fastq count into channel
+fastqCountTemp = Channel.create()
fastqCount = Channel.create()
fastqCount_fl.splitCsv(sep: ",", header: false).separate(
- fastqCount
+ fastqCountTemp
)
// Set raw fastq to downloaded or forced input and replicate them for multiple process inputs
@@ -293,6 +299,9 @@ if (fastqsForce != "") {
fastqs_parseMetadata
fastqs_fastqc
}
+ fastqsForce.count().into{
+ fastqCount
+ }
} else {
fastqs.collect().into {
fastqs_seqwho
@@ -300,6 +309,9 @@ if (fastqsForce != "") {
fastqs_parseMetadata
fastqs_fastqc
}
+ fastqCountTemp.into {
+ fastqCount
+ }
}
/*
--
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