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Commit d3003427 authored by Venkat Malladi's avatar Venkat Malladi
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Fix array rename.

parent fac677c3
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1 merge request!20Resolve "Use SampleIds/ Experiment Id as file names throughtout pipeline"
Pipeline #2819 failed with stages
in 3 minutes and 46 seconds
......@@ -76,15 +76,15 @@ def rename_reads(fastq, sample, paired):
if paired: # paired-end data
# Set file names
renamed_fastq[0] = cwd + '/' + sample + '_R1.fastq.gz'
renamed_fastq[1] = cwd + '/' + sample + '_R2.fastq.gz'
renamed_fastq.append(cwd + '/' + sample + '_R1.fastq.gz')
renamed_fastq.append(cwd + '/' + sample + '_R2.fastq.gz')
# Great symbolic links
os.symlink(fastq[0], renamed_fastq[0])
os.symlink(fastq[1], renamed_fastq[1])
else:
# Set file names
renamed_fastq[0] = cwd + '/' + sample + '_R1.fastq.gz'
renamed_fastq.append(cwd + '/' + sample + '_R1.fastq.gz')
# Great symbolic links
os.symlink(fastq[0], renamed_fastq[0])
......
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