From c42cd0ff6a683421b39ec45a797e453cae28a787 Mon Sep 17 00:00:00 2001
From: Peng Lian <Peng.Lian@UTSouthwestern.edu>
Date: Wed, 2 Mar 2022 12:21:18 -0600
Subject: [PATCH] Fix bug, is empty
---
workflow/main.nf | 11 +++++++++--
1 file changed, 9 insertions(+), 2 deletions(-)
diff --git a/workflow/main.nf b/workflow/main.nf
index ef33763..2cfa261 100644
--- a/workflow/main.nf
+++ b/workflow/main.nf
@@ -23,9 +23,13 @@ indel="$params.genome/GoldIndels.vcf.gz"
knownindel=file(indel)
dbsnp=file(dbsnp)
-repoDir=workflow.projectDir
+
if (params.repoDir) {
- repoDir=params.repoDir
+ repoDir=params.repoDir
+} else if (workflow.projectDir) {
+ repoDir=workflow.projectDir
+} else {
+ repoDir="$baseDir"
}
// params genome is the directory
@@ -90,12 +94,15 @@ process ralign {
errorStrategy 'ignore'
label 'ralign'
publishDir "$params.output", mode: 'copy'
+
input:
set pair_id, file(fqs) from trimread
+
output:
set pair_id, file("${pair_id}.bam") into aligned
set pair_id, file("${pair_id}.bam") into aligned2
file("${pair_id}.alignerout.txt") into hsatout
+
script:
"""
bash $repoDir/process_scripts/alignment/rnaseqalign.sh -a $params.align -p ${pair_id} -r ${index_path} ${fqs}
--
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