From 805f538383a975a972fa590715fc67d09aafb37b Mon Sep 17 00:00:00 2001 From: John Vivian Date: Fri, 1 Jul 2016 10:57:24 -0700 Subject: [PATCH] Fix single-end labelling logic (resolves #336) --- src/toil_scripts/rnaseq_cgl/rnaseq_cgl_pipeline.py | 8 ++------ 1 file changed, 2 insertions(+), 6 deletions(-) diff --git a/src/toil_scripts/rnaseq_cgl/rnaseq_cgl_pipeline.py b/src/toil_scripts/rnaseq_cgl/rnaseq_cgl_pipeline.py index 8c35c281..1db71ae9 100644 --- a/src/toil_scripts/rnaseq_cgl/rnaseq_cgl_pipeline.py +++ b/src/toil_scripts/rnaseq_cgl/rnaseq_cgl_pipeline.py @@ -815,10 +815,9 @@ def consolidate_output(job, job_vars, output_ids_and_values): # I/O if improper_pair: uuid = 'IMPROPERLY_PAIRED.{}'.format(uuid) - input_args['uuid'] = uuid if single_end: uuid = 'SINGLE-END.{}'.format(uuid) - input_args['uuid'] = uuid + input_args['uuid'] = uuid out_tar = os.path.join(work_dir, uuid + '.tar.gz') # Consolidate separate tarballs into one as streams (avoids unnecessary untaring) with tarfile.open(os.path.join(work_dir, out_tar), 'w:gz') as f_out: @@ -877,10 +876,7 @@ def upload_to_s3(job, job_vars): else: read_from_filestore(job, work_dir, ids, 'uuid.tar.gz') uuid_tar = os.path.join(work_dir, 'uuid.tar.gz') - if 'R.fastq' in ids: - k.key = os.path.join(bucket_dir, uuid + 'single-end' + '.tar.gz') - else: - k.key = os.path.join(bucket_dir, uuid + '.tar.gz') + k.key = os.path.join(bucket_dir, uuid + '.tar.gz') k.set_contents_from_filename(uuid_tar)