From ac447cd6754a9b06e26f0321876a2393960b88a9 Mon Sep 17 00:00:00 2001 From: John Vivian Date: Tue, 2 May 2017 13:14:33 -0700 Subject: [PATCH] Fix None bug for deleting ids (resolves #80) --- src/toil_rnaseq/rnaseq_cgl_pipeline.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/src/toil_rnaseq/rnaseq_cgl_pipeline.py b/src/toil_rnaseq/rnaseq_cgl_pipeline.py index d956a38..7d971fe 100644 --- a/src/toil_rnaseq/rnaseq_cgl_pipeline.py +++ b/src/toil_rnaseq/rnaseq_cgl_pipeline.py @@ -366,7 +366,7 @@ def consolidate_output(job, config, kallisto_output, rsem_star_output, fastqc_ou copy_files(file_paths=[os.path.join(work_dir, config.uuid + '.tar.gz')], output_dir=config.output_dir) # Delete intermediates - ids_to_delete = [x for x in [rsem_id, hugo_id, star_id, kallisto_output, fastqc_output] if x is not None] + ids_to_delete = [x for x in [rsem_id, hugo_id, star_id, kallisto_output, fastqc_output]] job.addChildJobFn(cleanup_ids, ids_to_delete) @@ -377,7 +377,7 @@ def cleanup_ids(job, ids_to_delete): :param JobFunctionWrappingJob job: passed automatically by Toil :param list ids_to_delete: list of FileStoreIDs to delete """ - [job.fileStore.deleteGlobalFile(x) for x in ids_to_delete] + [job.fileStore.deleteGlobalFile(x) for x in ids_to_delete if x is not None] # Pipeline specific functions