# HG changeset patch # User chrisw # Date 1550090587 18000 # Node ID 35ed7314038dafaa560f8b65c1eeb59f31e229b5 # Parent f43dd6f7c687dd7741bc963c27605586dfae32b9 Uploaded diff -r f43dd6f7c687 -r 35ed7314038d Snakefile --- a/Snakefile Wed Feb 13 15:37:51 2019 -0500 +++ b/Snakefile Wed Feb 13 15:43:07 2019 -0500 @@ -25,7 +25,7 @@ import re -FASTQ_PATT=re.compile(r'([^_\.]+)_(\d+)\.((fastq)|fq)(\.gz)?$') +FASTQ_PATT=re.compile(r'([^_\.]+)(_(\d+))?\.((fastq)|fq)(\.gz)?$') import os def prep_for_galaxy_run(): try: @@ -34,7 +34,9 @@ pass fastqs = config['inputs'].split(',') m = FASTQ_PATT.search(fastqs[0]) - run_acc = m.group(1) + run_acc = 'sample' + if m is not None: + run_acc = m.group(1) study_acc = run_acc if 'study' in config: study_acc = config['study']