From 387290a12641aaae63c1e405519ea44b5a7a948b Mon Sep 17 00:00:00 2001
From: s181706 <jonathan.gesell@utsouthwestern.edu>
Date: Sun, 15 Mar 2020 15:01:35 -0500
Subject: [PATCH] Added paired end and stranded features to featureCounts.
---
workflow/rna-seq.nf | 10 ++++++++--
1 file changed, 8 insertions(+), 2 deletions(-)
diff --git a/workflow/rna-seq.nf b/workflow/rna-seq.nf
index 2f21f7f..12c9f2a 100755
--- a/workflow/rna-seq.nf
+++ b/workflow/rna-seq.nf
@@ -188,6 +188,7 @@ metadata.splitCsv(sep: ",", header: false).separate(
endsManual.into {
endsManual_trimData
endsManual_alignData
+ endsManual_featureCounts
}
stranded.into {
stranded_alignData
@@ -392,14 +393,19 @@ process makeFeatureCounts {
path script_calculateTPM
tuple val (repRID1), path (bam), path (bai) from featureCountsIn
tuple val (repRID2), path (genome), path (gtf) from featureCountsRef
+ val endsManual_featureCounts
output:
tuple val ("${repRID}"), path ("${repRID}.featureCounts.summary"), path ("${repRID}.featureCounts"), path ("${bam}.featureCounts.sam") into featureCountsOut
script:
"""
- featureCounts -R SAM -p -G ${genome} -T `nproc` -a ${gtf} -o ${repRID}.featureCounts ${repRID}.sorted.deduped.bam
- Rscript calculateTPM.R --count "${repRID}.featureCounts"
+ if [ "${endsManual_featureCounts }" == "se" ]; then
+ featureCounts -R SAM -p -G ${genome} -T `nprioc` -s 1 -a ${gtf} -o ${repRID}.featureCounts ${repRID}.sorted.deduped.bam;
+ elif [ "${endsManual_featureCounts }" == "pe" ]; then
+ featureCounts -R SAM -p -G ${genome} -T `nproc` -s 1 -p -a ${gtf} -o ${repRID}.featureCounts ${repRID}.sorted.deduped.bam;
+ fi;
+ Rscript calculateTPM.R --count "${repRID}.featureCounts";
"""
}
--
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