commit

Pipeline/panBrass.nf

@@ -184,18 +184,18 @@ process prepareChrSize {
     tuple val(nameInputChannel), file(correspondanceChromosomeFileInputChannel), file(chrFastaFileInputChannel)
 
     output:
-    path "${nameInputChannel}.{chr.size}"
+    path "${nameInputChannel}.chr.size.txt"
 
     // copy the prepareChrSize output files located in the work folder and paste them in a folder of my choice
     //publishDir "$prepareChrSizeOutputDir", mode: 'copy'
-    publishDir "$prepareChrSizeOutputDir", mode: 'copy', pattern: '*.chr.size'
+    publishDir "$prepareChrSizeOutputDir", mode: 'copy', pattern: '*.chr.size.txt'
 
     script:
     """
     #echo $nameInputChannel $correspondanceChromosomeFileInputChannel $chrFastaFileInputChannel
     #head -5 $correspondanceChromosomeFileInputChannel
     #head -5 $chrFastaFileInputChannel
-    python3 /panbrass/scripts/PrepareChrSizeFile/src/PrepareChrSizeFile.py --fasta $chrFastaFileInputChannel --rename $correspondanceChromosomeFileInputChannel --chr_size_output ${nameInputChannel}.chr.size
+    python3 /panbrass/scripts/PrepareChrSizeFile/src/PrepareChrSizeFile.py --fasta $chrFastaFileInputChannel --rename $correspondanceChromosomeFileInputChannel --chr_size_output ${nameInputChannel}.chr.size.txt
     """
 }
 

scripts/PrepareChrSizeFile/src/PrepareChrSizeFile.py

@@ -20,5 +20,5 @@ with gzip.open(args['fasta'],'rt') as handle:
     for record in SeqIO.parse(handle, "fasta"):
         if (record.id in conv):
             # On l'ecrit dans le fichier
-            os.write(conv[record.id] + "\t" + str(len(record)) + "\n")
+            os.write(conv[record.id] + " " + str(len(record)) + "\n")
 os.close()
\ No newline at end of file