From 6b6268c33da30ec0c5ce883f907acadb53685487 Mon Sep 17 00:00:00 2001
From: "Gervaise H. Henry" <gervaise.henry@utsouthwestern.edu>
Date: Tue, 19 Jan 2021 20:12:36 -0600
Subject: [PATCH] Don't parse manual ends from file.csv anymore
---
CHANGELOG.md | 1 +
workflow/rna-seq.nf | 4 ++--
2 files changed, 3 insertions(+), 2 deletions(-)
diff --git a/CHANGELOG.md b/CHANGELOG.md
index b285b5d..9d5d0b5 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -11,6 +11,7 @@
* Update input bag export config to only fetch fastq's that match *[_.]R[1-2].fastq.gz naming convention
* Remove check for multiple fastq check in parse metadata (redundant and no longer valid)
* Handle blank submitted endness better
+* Don't use file.csv from inputBag to parse manual endness, use counted from getData
*Known Bugs*
* Override params (inputBag, fastq, species) aren't checked for integrity
diff --git a/workflow/rna-seq.nf b/workflow/rna-seq.nf
index 7702207..c98d141 100644
--- a/workflow/rna-seq.nf
+++ b/workflow/rna-seq.nf
@@ -344,8 +344,8 @@ process parseMetadata {
fi
# ganually get endness
- endsManual=\$(python3 ${script_parseMeta} -r ${repRID} -m "${file}" -p endsManual)
- echo -e "LOG: endedness manually detected: \${endsManual}" >> ${repRID}.parseMetadata.log
+ endsManual=${fastqCount}
+ echo -e "LOG: endedness manually detected: ${fastqCount}" >> ${repRID}.parseMetadata.log
# get strandedness metadata
stranded=\$(python3 ${script_parseMeta} -r ${repRID} -m "${experimentSettings}" -p stranded)
--
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