From 978710b76e5b215cad60fb929d3dc1b163b2ac09 Mon Sep 17 00:00:00 2001
From: Peng Lian <Peng.Lian@UTSouthwestern.edu>
Date: Wed, 2 Mar 2022 23:46:36 -0600
Subject: [PATCH] Bugfix for permission issue

---
 workflow/main.nf | 16 +++++++++-------
 1 file changed, 9 insertions(+), 7 deletions(-)

diff --git a/workflow/main.nf b/workflow/main.nf
index 9f39593..fd9460a 100644
--- a/workflow/main.nf
+++ b/workflow/main.nf
@@ -49,7 +49,9 @@ process checkdesignfile {
 	stdout spltnames
 	script:
 	"""
-	$repoDir/process_scripts/design_file/checkdesignfile.sh ${params.pairs} design.ori.txt
+  # convert dos \r to unix format
+  sed -i 's/\x0D$//' design.ori.txt
+	bash $repoDir/process_scripts/design_file/checkdesignfile.sh ${params.pairs} design.ori.txt
 	"""
 }
 
@@ -86,7 +88,7 @@ process trim {
   set pair_id, file("${pair_id}.trim.R*.fastq.gz") into trimread
   script:
   """
-  $repoDir/process_scripts/preproc_fastq/trimgalore.sh -f -p ${pair_id} ${fqs}
+  bash $repoDir/process_scripts/preproc_fastq/trimgalore.sh -f -p ${pair_id} ${fqs}
   """
 }
 
@@ -105,7 +107,7 @@ process ralign {
   
   script:
   """
-  $repoDir/process_scripts/alignment/rnaseqalign.sh -a $params.align -p ${pair_id} -r ${index_path} ${fqs}
+  bash $repoDir/process_scripts/alignment/rnaseqalign.sh -a $params.align -p ${pair_id} -r ${index_path} ${fqs}
   """
 }
 
@@ -120,7 +122,7 @@ process alignqc {
   set file("${pair_id}_fastqc.zip"),file("${pair_id}_fastqc.html") into fastqc
   script:
   """
-  $repoDir/process_scripts/alignment/bamqc.sh -p ${pair_id} -b ${bam} -y rna
+  bash $repoDir/process_scripts/alignment/bamqc.sh -p ${pair_id} -b ${bam} -y rna
   """
 }
 
@@ -135,7 +137,7 @@ process markdups {
   set pair_id, file("${pair_id}.dedup.bam") into deduped2
   script:
   """
-  $repoDir/process_scripts/alignment/markdups.sh -a $params.markdups -b $sbam -p $pair_id
+  bash $repoDir/process_scripts/alignment/markdups.sh -a $params.markdups -b $sbam -p $pair_id
   """
 }
 
@@ -154,7 +156,7 @@ process geneabund {
   file("${pair_id}.fpkm.txt") into fpkm
   script:
   """
-  $repoDir/process_scripts/genect_rnaseq/geneabundance.sh -s $params.stranded -g ${gtf_file} -p ${pair_id} -b ${sbam}
+  bash $repoDir/process_scripts/genect_rnaseq/geneabundance.sh -s $params.stranded -g ${gtf_file} -p ${pair_id} -b ${sbam}
   """
 }
 
@@ -177,6 +179,6 @@ process statanal {
   file("geneset.shiny.gmt") into gmtfile
   script:
   """
-  $repoDir/process_scripts/genect_rnaseq/statanal.sh -d $params.dea
+  bash $repoDir/process_scripts/genect_rnaseq/statanal.sh -d $params.dea
   """
 }
-- 
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