From 67be8b6ae48f260a1f9d5f4bb8d71d52938f64b6 Mon Sep 17 00:00:00 2001
From: Phil Ewels <phil.ewels@scilifelab.se>
Date: Wed, 21 Nov 2018 19:35:44 +0100
Subject: [PATCH] Remove legacy rseqc strandRule code.

Closes nf-core/rnaseq#119
---
 main.nf | 8 +-------
 1 file changed, 1 insertion(+), 7 deletions(-)

diff --git a/main.nf b/main.nf
index 6343dadfd..2ee09c5f9 100644
--- a/main.nf
+++ b/main.nf
@@ -554,7 +554,7 @@ if(params.aligner == 'star'){
         script:
         prefix = reads[0].toString() - ~/(_R1)?(_trimmed)?(_val_1)?(\.fq)?(\.fastq)?(\.gz)?$/
         def star_mem = task.memory ?: params.star_memory ?: false
-        def avail_mem = star_mem ? "--limitBAMsortRAM ${star_mem.toBytes() - 100000000}" : '' 
+        def avail_mem = star_mem ? "--limitBAMsortRAM ${star_mem.toBytes() - 100000000}" : ''
         seqCenter = params.seqCenter ? "--outSAMattrRGline ID:$prefix 'CN:$params.seqCenter'" : ''
         """
         STAR --genomeDir $index \\
@@ -712,12 +712,6 @@ process rseqc {
     file "*.{txt,pdf,r,xls}" into rseqc_results
 
     script:
-    def strandRule = ''
-    if (forward_stranded && !unstranded){
-        strandRule = params.singleEnd ? '-d ++,--' : '-d 1++,1--,2+-,2-+'
-    } else if (reverse_stranded && !unstranded){
-        strandRule = params.singleEnd ? '-d +-,-+' : '-d 1+-,1-+,2++,2--'
-    }
     """
     samtools index $bam_rseqc
     infer_experiment.py -i $bam_rseqc -r $bed12 > ${bam_rseqc.baseName}.infer_experiment.txt