Merge branch '37-CheckDesignFile' into 'develop'

Resolve 37-Design File Check

Closes #37

See merge request !58

CHANGELOG.md

 # 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)

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
+}

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()