From 7972b21c7c13d8f9c64bdebe06704a511c6de8b8 Mon Sep 17 00:00:00 2001
From: Jeremy Mathews <Jeremy.Mathews@utsouthwestern.edu>
Date: Thu, 7 Nov 2019 16:14:23 -0600
Subject: [PATCH] Resolve 37-Design File Check
---
CHANGELOG.md | 1 +
workflow/main.nf | 8 ++++++--
workflow/scripts/check_design.py | 4 ++--
3 files changed, 9 insertions(+), 4 deletions(-)
diff --git a/CHANGELOG.md b/CHANGELOG.md
index 599997e..4e1b76a 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -1,5 +1,6 @@
# v1.3.0 (in development)
**User Facing**
+* Check Design File for spaces in name and file contents
**Background**
* Add Nextflow Tower integration into CI (GHH's profile)
diff --git a/workflow/main.nf b/workflow/main.nf
index 8862991..3784116 100755
--- a/workflow/main.nf
+++ b/workflow/main.nf
@@ -87,7 +87,11 @@ process checkDesignFile {
"""
hostname
ulimit -a
- python3 ${baseDir}/scripts/check_design.py -d ${designLocation} -f ${fastqList}
+ noSpaceDesign=\$(echo "${designLocation}" | tr -d ' ')
+ if [[ "\${noSpaceDesign}" != "${designLocation}" ]]; then
+ mv "${designLocation}" "\${noSpaceDesign}"
+ fi
+ python3 ${baseDir}/scripts/check_design.py -d \${noSpaceDesign} -f ${fastqList}
"""
}
@@ -353,4 +357,4 @@ process multiqc {
multiqc -c ${multiqcConf} .
"""
-}
\ No newline at end of file
+}
diff --git a/workflow/scripts/check_design.py b/workflow/scripts/check_design.py
index c5c679e..4a4d84c 100755
--- a/workflow/scripts/check_design.py
+++ b/workflow/scripts/check_design.py
@@ -97,7 +97,7 @@ def main():
logger.addHandler(handler)
# Read files as dataframes
- design_df = pd.read_csv(args.design, sep=',')
+ design_df = pd.read_csv(args.design, sep=',', converters={'Sample': str.strip, 'fastq_R1': str.strip, 'fastq_R2': str.strip})
fastq_df = pd.read_csv(args.fastq, sep='\t', names=['name', 'path'])
# Check design file
@@ -107,4 +107,4 @@ def main():
new_design_df.to_csv('design.checked.csv', header=True, sep=',', index=False)
if __name__ == '__main__':
- main()
\ No newline at end of file
+ main()
--
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