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add extra_sample_ids to workflow with facets
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@stevekm
stevekm committed Apr 19, 2022
1 parent 8035ca7 commit 98b7381
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Showing 2 changed files with 22 additions and 16 deletions.
6 changes: 6 additions & 0 deletions cwl/workflow_with_facets.cwl
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Original file line number Diff line number Diff line change
Expand Up @@ -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:
Expand Down Expand Up @@ -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
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32 changes: 16 additions & 16 deletions tests/test_workflow_with_facets.py
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Original file line number Diff line number Diff line change
Expand Up @@ -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')
])
Expand Down Expand Up @@ -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')
])
Expand Down Expand Up @@ -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')
])
Expand Down Expand Up @@ -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')
])
Expand Down

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