From 415fa4622fe0608440e55c80ae9fae1815217a9f Mon Sep 17 00:00:00 2001
From: s181706 <jonathan.gesell@utsouthwestern.edu>
Date: Thu, 23 Jan 2020 16:41:52 -0600
Subject: [PATCH] Added requested samtools flags for removing
unmapped/double-mapped reads.
---
workflow/rna-seq.nf | 4 ++--
1 file changed, 2 insertions(+), 2 deletions(-)
diff --git a/workflow/rna-seq.nf b/workflow/rna-seq.nf
index 0c4077e..ff34829 100755
--- a/workflow/rna-seq.nf
+++ b/workflow/rna-seq.nf
@@ -233,7 +233,7 @@ process trimData {
* alignReads: aligns the reads to a reference database
*/
process alignReads {
- tag "align-${repRID}"
+ tag "${repRID}"
publishDir "${outDir}/aligned", mode: "copy", pattern: "${repRID}.{unal,sorted}.{gz,bam,bai}"
publishDir "${logsDir}", mode: 'copy', pattern: "${repRID}.align.{out,err}"
@@ -253,7 +253,7 @@ process alignReads {
hisat2 -p `nproc` --add-chrname --un-gz ${repRID}.unal.gz -S ${repRID}.sam -x ${referenceDir_alignReads} ${stranded_alignReads} --no-mixed --no-discordant -1 ${fqs[0]} -2 ${fqs[1]} 1>${repRID}.align.out 2>${repRID}.align.err;
else hisat2 -p `nproc` --add-chrname --un-gz ${repRID}.unal.gz -S ${repRID}.sam -x ${referenceDir_alignReads} ${stranded_alignReads} -U ${fqs[0]} 1>${repRID}.align.out 2>${repRID}.align.err;
fi;
- samtools view -1 --threads `nproc` -o ${repRID}.bam ${repRID}.sam 1>>${repRID}.align.out 2>>${repRID}.align.err;
+ samtools view -1 -@ `nproc` -F 4 -F 8 -F 256 -o ${repRID}.bam ${repRID}.sam 1>>${repRID}.align.out 2>>${repRID}.align.err;
samtools sort -@ `nproc` -O BAM -o ${repRID}.sorted.bam ${repRID}.bam 1>>${repRID}.align.out 2>>${repRID}.align.err;
samtools index -@ `nproc` -b ${repRID}.sorted.bam ${repRID}.sorted.bai 1>>${repRID}.align.out 2>>${repRID}.align.err;
"""
--
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