From 8a91ad1ba1e23e07445ede54ed2a7f0087835c8a Mon Sep 17 00:00:00 2001
From: "Gervaise H. Henry" <gervaise.henry@utsouthwestern.edu>
Date: Tue, 19 Jan 2021 09:52:31 -0600
Subject: [PATCH] Allow unexpected values for stranded/spike/species
---
CHANGELOG.md | 2 ++
workflow/rna-seq.nf | 2 +-
workflow/scripts/parse_meta.py | 14 +-------------
3 files changed, 4 insertions(+), 14 deletions(-)
diff --git a/CHANGELOG.md b/CHANGELOG.md
index f7c6e74..deaa3b9 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -3,6 +3,8 @@
**Background**
* Add memory limit per thread for samtools sort
+* Remove parsing restrictions for submitted stranded/spike/species
+* Pass unidentified ends instead of overwriting it as unknown
*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 abec019..fcf77a3 100644
--- a/workflow/rna-seq.nf
+++ b/workflow/rna-seq.nf
@@ -338,7 +338,7 @@ process parseMetadata {
then
endsMeta="pe"
else
- endsMeta="unknown"
+ endsMeta=\${endsRaw}
fi
if [ "\${endsRaw}" == "" ]
then
diff --git a/workflow/scripts/parse_meta.py b/workflow/scripts/parse_meta.py
index 12cc7c7..c2c71e0 100644
--- a/workflow/scripts/parse_meta.py
+++ b/workflow/scripts/parse_meta.py
@@ -43,7 +43,7 @@ def main():
# Check experiment RID metadata from 'Experiment.csv'
if (args.parameter == "expRID"):
if (len(metaFile.Experiment_RID.unique()) > 1):
- print("There are multiple experoment RID's in the metadata: " +
+ print("There are multiple experiment RID's in the metadata: " +
" ".join(metaFile.Experiment_RID.unique()))
exit(1)
else:
@@ -79,10 +79,6 @@ def main():
stranded = "stranded"
elif (metaFile.Has_Strand_Specific_Information.unique() == "no"):
stranded = "unstranded"
- else:
- print("Stranded metadata not match expected options: " +
- metaFile.Has_Strand_Specific_Information.unique())
- exit(1)
print(stranded)
# Get spike-in metadata from 'Experiment Settings.csv'
@@ -91,10 +87,6 @@ def main():
spike = "yes"
elif (metaFile.Used_Spike_Ins.unique() == "no"):
spike = "no"
- else:
- print("Spike-ins metadata not match expected options: " +
- metaFile.Used_Spike_Ins.unique())
- exit(1)
print(spike)
# Get species metadata from 'Experiment.csv'
@@ -103,10 +95,6 @@ def main():
species = "Mus musculus"
elif (metaFile.Species.unique() == "Homo sapiens"):
species = "Homo sapiens"
- else:
- print("Species metadata not match expected options: " +
- metaFile.Species.unique())
- exit(1)
print(species)
# Get read length metadata from 'Experiment Settings.csv'
--
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