From 98b73813b6f113a9755b087b33c4f6dd98509d7a Mon Sep 17 00:00:00 2001 From: Stephen Kelly Date: Tue, 19 Apr 2022 13:00:05 -0400 Subject: [PATCH] add extra_sample_ids to workflow with facets --- cwl/workflow_with_facets.cwl | 6 ++++++ tests/test_workflow_with_facets.py | 32 +++++++++++++++--------------- 2 files changed, 22 insertions(+), 16 deletions(-) diff --git a/cwl/workflow_with_facets.cwl b/cwl/workflow_with_facets.cwl index 04f1950..f665238 100644 --- a/cwl/workflow_with_facets.cwl +++ b/cwl/workflow_with_facets.cwl @@ -286,6 +286,11 @@ inputs: type: - "null" - File[] + extra_sample_ids: + doc: Extra sample ids that should be included in case list files + type: + - string[] + - "null" steps: @@ -385,6 +390,7 @@ steps: data_clinical_file: data_clinical_file sample_summary_file: sample_summary_file facets_suite_txt_files: run_facets/facets_txt + extra_sample_ids: extra_sample_ids out: [ portal_meta_clinical_sample_file, # meta_clinical_sample.txt diff --git a/tests/test_workflow_with_facets.py b/tests/test_workflow_with_facets.py index 5c91d06..3a90079 100755 --- a/tests/test_workflow_with_facets.py +++ b/tests/test_workflow_with_facets.py @@ -152,10 +152,10 @@ def test_demo_dataset1(self): OFile(name = 'Proj_08390_G_data_cna_hg19.seg', size = 525, hash = 'e99e98d33598c423448cba44a37da712c9c933c5'), OFile(name = 'data_fusions.txt', size = 99, hash = 'c16f763b248813fcdde76f7486f1ddc4e9856038'), ODir(name = 'case_lists', items = [ - OFile(name = 'cases_all.txt', size = 188, hash = '3d3d54b5cbd98e751adf926d07884eeaed94aaef'), - OFile(name = 'cases_cnaseq.txt', size = 268, hash = '2a43c8ed31f69c12cf9a14044bab1aaa1b6ec7ee'), - OFile(name = 'cases_cna.txt', size = 200, hash = '117563761d7cb4690dea363f40b77ef1a0444fc1'), - OFile(name = 'cases_sequenced.txt', size = 213, hash = '78d1d0acb6928349b4448a73f2cdf1ed4edcb1a3'), + OFile(name = 'cases_all.txt', size = 188, hash = '8ff1cacffcaafbe3d40ec42989433f9447dff6cf'), + OFile(name = 'cases_cnaseq.txt', size = 268, hash = '2be82e138057f8eb1b315b5b3c6fe4859ce951e4'), + OFile(name = 'cases_cna.txt', size = 200, hash = '8f0ec24a0135bc6de006277a134efa4aaf5d2e82'), + OFile(name = 'cases_sequenced.txt', size = 213, hash = 'd3c860cb681ba952bf2f9d546a5a088a04a77261'), ]), OFile(name = 'report.html') ]) @@ -379,10 +379,10 @@ def test_demo_dataset2(self): OFile(name = 'Proj_08390_G_data_cna_hg19.seg', size = 878, hash = 'e1c85484cd13a88cea322de84cd35143c86a8ef3'), OFile(name = 'data_fusions.txt', size = 99, hash = 'c16f763b248813fcdde76f7486f1ddc4e9856038'), ODir(name = 'case_lists', items = [ - OFile(name = 'cases_all.txt', size = 188, hash = '3d3d54b5cbd98e751adf926d07884eeaed94aaef'), - OFile(name = 'cases_cnaseq.txt', size = 268, hash = '2a43c8ed31f69c12cf9a14044bab1aaa1b6ec7ee'), - OFile(name = 'cases_cna.txt', size = 200, hash = '117563761d7cb4690dea363f40b77ef1a0444fc1'), - OFile(name = 'cases_sequenced.txt', size = 213, hash = '78d1d0acb6928349b4448a73f2cdf1ed4edcb1a3'), + OFile(name = 'cases_all.txt', size = 188, hash = '8ff1cacffcaafbe3d40ec42989433f9447dff6cf'), + OFile(name = 'cases_cnaseq.txt', size = 268, hash = '2be82e138057f8eb1b315b5b3c6fe4859ce951e4'), + OFile(name = 'cases_cna.txt', size = 200, hash = '8f0ec24a0135bc6de006277a134efa4aaf5d2e82'), + OFile(name = 'cases_sequenced.txt', size = 213, hash = 'd3c860cb681ba952bf2f9d546a5a088a04a77261'), ]), OFile(name = 'report.html') ]) @@ -582,10 +582,10 @@ def test_run_worflow_one_maf(self): OFile(name = 'Proj_08390_G_data_cna_hg19.seg', size = 1459, hash = '76e2c8a0a9c4200e26b8fc4a60701bd7b1b86560'), OFile(name = 'data_fusions.txt', size = 99, hash = 'c16f763b248813fcdde76f7486f1ddc4e9856038'), ODir(name = 'case_lists', items = [ - OFile(name = 'cases_all.txt', size = 616, hash = 'b9e43289cec5603b0886b5e8507c8d019387c125'), - OFile(name = 'cases_cnaseq.txt', size = 696, hash = 'b87e2da8dce0fddbadec348efe2986519b2a794b'), - OFile(name = 'cases_cna.txt', size = 628, hash = '053481a8299e9430117f8e45e081aa7ec21033a6'), - OFile(name = 'cases_sequenced.txt', size = 641, hash = 'ef9f5aef03c2527bf576470168660557ca1c7cc9'), + OFile(name = 'cases_all.txt', size = 616, hash = 'd186ba8540f5e382147fee313cb95b52e5d933fe'), + OFile(name = 'cases_cnaseq.txt', size = 696, hash = '6d675d97c9ce8907101d894f2b0c8636b38071bd'), + OFile(name = 'cases_cna.txt', size = 628, hash = 'e87e642c8313133658a20c451396954a79fb7e81'), + OFile(name = 'cases_sequenced.txt', size = 641, hash = 'fd926ae050b8032f98df09330b8bdd340adc81a4'), ]), OFile(name = 'report.html') ]) @@ -829,10 +829,10 @@ def test_run_worflow_two_mafs(self): OFile(name = 'Proj_08390_G_data_cna_hg19.seg', size = 2703, hash = '8995133edb5b4547371b0fdea9925848eb480fbc'), OFile(name = 'data_fusions.txt', size = 99, hash = 'c16f763b248813fcdde76f7486f1ddc4e9856038'), ODir(name = 'case_lists', items = [ - OFile(name = 'cases_all.txt', size = 616, hash = 'b9e43289cec5603b0886b5e8507c8d019387c125'), - OFile(name = 'cases_cnaseq.txt', size = 696, hash = 'b87e2da8dce0fddbadec348efe2986519b2a794b'), - OFile(name = 'cases_cna.txt', size = 628, hash = '053481a8299e9430117f8e45e081aa7ec21033a6'), - OFile(name = 'cases_sequenced.txt', size = 641, hash = 'ef9f5aef03c2527bf576470168660557ca1c7cc9'), + OFile(name = 'cases_all.txt', size = 616, hash = 'd186ba8540f5e382147fee313cb95b52e5d933fe'), + OFile(name = 'cases_cnaseq.txt', size = 696, hash = '6d675d97c9ce8907101d894f2b0c8636b38071bd'), + OFile(name = 'cases_cna.txt', size = 628, hash = 'e87e642c8313133658a20c451396954a79fb7e81'), + OFile(name = 'cases_sequenced.txt', size = 641, hash = 'fd926ae050b8032f98df09330b8bdd340adc81a4'), ]), OFile(name = 'report.html') ])