Mercurial > repos > chrisw > monorail_test
changeset 31:de65ca585930 draft
Uploaded
| author | chrisw |
|---|---|
| date | Thu, 14 Nov 2019 07:42:04 +0000 |
| parents | db147d9348fe |
| children | 13df910d0683 |
| files | Snakefile |
| diffstat | 1 files changed, 7 insertions(+), 7 deletions(-) [+] |
line wrap: on
line diff
--- a/Snakefile Thu Nov 14 07:07:58 2019 +0000 +++ b/Snakefile Thu Nov 14 07:42:04 2019 +0000 @@ -99,13 +99,13 @@ if i == 2: open('%s/%s_%s_%s_%s_%d.fastq' % (config['temp'], run_acc, study_acc, genome, method, 2), "w").close() #create expected file structure for annotated exon bed file & reference index - ref = config['ref'] - config['ref'] = os.path.abspath('.') - os.makedirs('%s/%s' % (config['ref'], genome)) - os.symlink(ref, '%s/%s/star_idx' % (config['ref'], genome)) - os.makedirs('%s/%s/gtf' % (config['ref'], genome)) - os.symlink(config['exon_bed'], 'exons.tmp') - os.symlink('../../exons.tmp', '%s/%s/gtf/%s' % (config['ref'], genome, config.get('bw_bed', 'exons.bed'))) + #ref = config['ref'] + #config['ref'] = os.path.abspath('.') + #os.makedirs('%s/%s' % (config['ref'], genome)) + #os.symlink(ref, '%s/%s/star_idx' % (config['ref'], genome)) + #os.makedirs('%s/%s/gtf' % (config['ref'], genome)) + #os.symlink(config['exon_bed'], 'exons.tmp') + #os.symlink('../../exons.tmp', '%s/%s/gtf/%s' % (config['ref'], genome, config.get('bw_bed', 'exons.bed'))) #TODO may need to add additional symlinking for HISAT2 unmapped alignments return([run_acc, study_acc, genome, method])