From e84344600fe0ade64f9b79aceb17f99494a095b6 Mon Sep 17 00:00:00 2001
From: Venkat Malladi <venkat.malladi@utsouthwestern.edu>
Date: Tue, 19 Jun 2018 13:54:56 -0500
Subject: [PATCH] Fix check design file.
---
workflow/main.nf | 10 +++++-----
1 file changed, 5 insertions(+), 5 deletions(-)
diff --git a/workflow/main.nf b/workflow/main.nf
index 04866eb..1d1d6af 100644
--- a/workflow/main.nf
+++ b/workflow/main.nf
@@ -56,12 +56,12 @@ process checkDesignFile {
if (pairedEnd) {
"""
- python3 $baseDir/scripts/check_design.py -d $designFile -f $readsList -p
+ python3 $baseDir/scripts/check_design.py -d $designFile -f $readsList -p -a
"""
}
else {
"""
- python $baseDir/scripts/check_design.py -d $designFile -f $readsList
+ python $baseDir/scripts/check_design.py -d $designFile -f $readsList -a
"""
}
@@ -75,7 +75,7 @@ if (pairedEnd) {
} else {
rawReads = designFilePaths
.splitCsv(sep: '\t', header: true)
- .map { row -> [ row.sample_id, [row.fastq_read1], row.experiment_id, row.biosample, row.factor, row.treatment, row.replicate, ] }
+ .map { row -> [ row.sample_id, [row.fastq_read1], row.experiment_id, row.biosample, row.factor, row.treatment, row.replicate ] }
}
// Trim raw reads using trimgalore
@@ -116,12 +116,12 @@ process alignReads {
input:
- set sampleId, reads, experimentId, biosample, factor, treatment, replicate, from trimmedReads
+ set sampleId, reads, experimentId, biosample, factor, treatment, replicate from trimmedReads
file index from bwaIndex.first()
output:
- set sampleId, file('*.bam'), experimentId, biosample, factor, treatment, replicate, into mappedReads
+ set sampleId, file('*.bam'), experimentId, biosample, factor, treatment, replicate into mappedReads
file '*.srt.bam.flagstat.qc' into mappedReadsStats
--
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