From 96a89c3aad023d383e8aff893e1dc6f85167cbfc Mon Sep 17 00:00:00 2001
From: "Gervaise H. Henry" <gervaise.henry@utsouthwestern.edu>
Date: Fri, 6 Mar 2020 17:14:35 -0600
Subject: [PATCH] TEST remove count process
---
workflow/rna-seq.nf | 22 ----------------------
1 file changed, 22 deletions(-)
diff --git a/workflow/rna-seq.nf b/workflow/rna-seq.nf
index 378c8f2..16aca0e 100755
--- a/workflow/rna-seq.nf
+++ b/workflow/rna-seq.nf
@@ -404,25 +404,3 @@ process makeBigWig {
"""
}
-/*
- *Run featureCounts and get the counts, tpm, and fpkm
-*/
-process makeFeatureCounts {
- tag "${repRID}"
- publishDir "${outDir}/featureCounts", mode: 'copy', pattern: "${repRID}*.featureCounts*"
- publishDir "${logsDir}", mode: 'copy', pattern: "${repRID}.makeFetureCounts.{out,err}"
-
- input:
- path script_calculateTPM
- tuple val (repRID1), path (bam), path (bai) from featureCountsIn
- tuple val (repRID2), path (genome), path (gtf) from featureCountsRef
-
- output:
- tuple val ("${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"
- """
-}
--
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