From 0bb07de440dffa189535a97f3941c14b64277e5b Mon Sep 17 00:00:00 2001
From: "Gervaise H. Henry" <gervaise.henry@utsouthwestern.edu>
Date: Thu, 28 Jan 2021 21:32:47 -0600
Subject: [PATCH] Move spike/stranded override to infer (like species), not
submitter
---
workflow/rna-seq.nf | 24 ++++++++++++------------
1 file changed, 12 insertions(+), 12 deletions(-)
diff --git a/workflow/rna-seq.nf b/workflow/rna-seq.nf
index b0e2c66..dbcfbc0 100644
--- a/workflow/rna-seq.nf
+++ b/workflow/rna-seq.nf
@@ -320,8 +320,6 @@ process parseMetadata {
path experiment from experimentMeta
path (fastq) from fastqs_parseMetadata.collect()
val fastqCount
- val strandedForce
- val spikeForce
output:
path "design.csv" into metadata_fl
@@ -379,11 +377,6 @@ process parseMetadata {
then
stranded="_No value_"
fi
- if [ "${strandedForce}" != "" ]
- then
- stranded=${strandedForce}
- echo -e "LOG: spike-in metadata forced: \${stranded}" >> ${repRID}.parseMetadata.log
- fi
# get spike-in metadata
spike=\$(python3 ${script_parseMeta} -r ${repRID} -m "${experimentSettings}" -p spike)
@@ -392,11 +385,6 @@ process parseMetadata {
then
spike="_No value_"
fi
- if [ "${spikeForce}" != "" ]
- then
- spike=${spikeForce}
- echo -e "LOG: spike-in metadata forced: \${spike}" >> ${repRID}.parseMetadata.log
- fi
if [ "\${spike}" == "f" ]
then
spike="false"
@@ -952,6 +940,8 @@ process inferMetadata {
path bam from sampleBam.collect()
path bai from sampleBai.collect()
path alignSummary from alignSampleQC_inferMetadata.collect()
+ val strandedForce
+ val spikeForce
val fastqCountError_inferMetadata
val fastqReadError_inferMetadata
val fastqFileError_inferMetadata
@@ -990,6 +980,11 @@ process inferMetadata {
spike="false"
fi
echo -e "LOG: inference of strandedness results is: \${spike}" >> ${repRID}.inferMetadata.log
+ if [ "${spikeForce}" != "" ]
+ then
+ spike=${spikeForce}
+ echo -e "LOG: spike-in metadata forced: \${spike}" >> ${repRID}.parseMetadata.log
+ fi
speciesError=false
speciesError_details=""
@@ -1062,6 +1057,11 @@ process inferMetadata {
stranded="unstranded"
fi
echo -e "LOG: stradedness set to: \${stranded}" >> ${repRID}.inferMetadata.log
+ if [ "${strandedForce}" != "" ]
+ then
+ stranded=${strandedForce}
+ echo -e "LOG: spike-in metadata forced: \${stranded}" >> ${repRID}.inferMetadata.log
+ fi
else
ends=""
stranded=""
--
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