From 96fc2b7191bdc9c481c548871d3901d6cc0a3cc7 Mon Sep 17 00:00:00 2001
From: "Gervaise H. Henry" <gervaise.henry@utsouthwestern.edu>
Date: Tue, 13 Apr 2021 21:19:47 -0500
Subject: [PATCH] Fix fetch fastq count
---
CHANGELOG.md | 3 ++-
rna-seq.nf | 3 ++-
2 files changed, 4 insertions(+), 2 deletions(-)
diff --git a/CHANGELOG.md b/CHANGELOG.md
index f111685..1feda59 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -37,6 +37,7 @@
* Change ambiguous species ci to wrong species
* Add test for DNAnexus env
* Add test for AWS env
+* Fix fetch fastq count
*Known Bugs*
* Override params (inputBag, fastq, species) aren't checked for integrity
@@ -44,7 +45,7 @@
* Check for outputBag in hatrac doesn't check for any uploaded by chaise
* CI container cache will fail if cache folder is not owned by CI runner user
* CI container cache will not error if container failed to pull
-* CI (container cache, version collection, and unit tests) will not work correctly if containers reffered to in nextflow.config aren't prefixed perfectly with: "container = "
+* CI (container cache, version collection, and unit tests) will not work correctly if containers referred to in nextflow.config aren't prefixed perfectly with: "container = "
* also, it is assumed that the containers are on dockerhub and don't have the "docker://" prefix
<hr>
diff --git a/rna-seq.nf b/rna-seq.nf
index 9f4be25..a1dcd02 100644
--- a/rna-seq.nf
+++ b/rna-seq.nf
@@ -269,7 +269,8 @@ process getData {
then
echo -e "LOG: fetching replicate bdbag" >> ${repRID}.getData.log
fastqCount=\$(sh ${script_bdbagFetch} \${replicate::-13} ${repRID})
- echo -e "LOG: fetched" >> ${repRID}.getData.log
+ fastqCount=\$(echo \${fastqCount} | tail -n1)
+ echo -e "LOG: \${fastqCount} fastqs fetched" >> ${repRID}.getData.log
else
echo -e "LOG: fastq override detected, not fetching fastqs" >> ${repRID}.getData.log
fastqCount="0"
--
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