diff --git a/runner/operator/access/v2_1_0/cnv/__init__.py b/runner/operator/access/v2_1_0/cnv/__init__.py index 2f82900d3..5c483a375 100755 --- a/runner/operator/access/v2_1_0/cnv/__init__.py +++ b/runner/operator/access/v2_1_0/cnv/__init__.py @@ -46,8 +46,10 @@ def get_sample_inputs(self): for run in runs: bams.append(find_request_bams(run)) - # TUMOR Unfiltered - unfiltered_tumor_bams = [b["fgbio_collapsed_bam"] for b in bams if is_tumor_bam(b["fgbio_collapsed_bam"].file_name)] + # TUMOR Unfiltered + unfiltered_tumor_bams = [ + b["fgbio_collapsed_bam"] for b in bams if is_tumor_bam(b["fgbio_collapsed_bam"].file_name) + ] sample_ids = [] tumor_bams = [] diff --git a/runner/operator/access/v2_1_0/msi/__init__.py b/runner/operator/access/v2_1_0/msi/__init__.py index ecacc6888..6bcd47557 100755 --- a/runner/operator/access/v2_1_0/msi/__init__.py +++ b/runner/operator/access/v2_1_0/msi/__init__.py @@ -12,7 +12,13 @@ from runner.operator.operator import Operator from runner.run.objects.run_creator_object import RunCreator from runner.models import Port, RunStatus -from runner.operator.access import get_request_id, get_request_id_runs, create_cwl_file_object, find_request_bams, is_tumor_bam +from runner.operator.access import ( + get_request_id, + get_request_id_runs, + create_cwl_file_object, + find_request_bams, + is_tumor_bam, +) logger = logging.getLogger(__name__) @@ -56,7 +62,7 @@ def get_sample_inputs(self): for run in runs: bams.append(find_request_bams(run)) - # TUMOR Uncollapsed + # TUMOR Uncollapsed standard_tumor_bams = [b["uncollapsed_bam"] for b in bams if is_tumor_bam(b["fgbio_collapsed_bam"].file_name)] # Dictionary that associates tumor bam with standard bam with tumor_sample_id