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Commit c5469a84 authored by MORICE Jérôme's avatar MORICE Jérôme
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......@@ -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
"""
}
......
......@@ -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
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