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add handling for extra sample ids in portal workflow
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@stevekm
stevekm committed Apr 19, 2022
1 parent d66a777 commit 8035ca7
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Showing 2 changed files with 192 additions and 17 deletions.
71 changes: 67 additions & 4 deletions cwl/portal-workflow.cwl
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Original file line number Diff line number Diff line change
Expand Up @@ -154,8 +154,38 @@ inputs:
type:
- "null"
- File[]
extra_sample_ids:
doc: Extra sample ids that should be included in case list files
type:
- string[]
- "null"

steps:
update_extra_sample_ids:
doc: if no extra sample ids were passed in, convert the null value to an empty list to make downstream processes easier
in:
sample_ids: extra_sample_ids
out: [ extra_sample_ids ]
run:
class: ExpressionTool
inputs:
sample_ids:
type:
- "null"
- string[]
outputs:
extra_sample_ids:
type: string[]
expression: |
${
var sample_ids = [];
if (inputs.sample_ids === null) {
return {'extra_sample_ids': sample_ids};
} else {
return {'extra_sample_ids': inputs.sample_ids};
}
}

# meta_clinical_sample.txt (cbio_clinical_sample_meta_filename; meta_clinical_sample_file)
generate_meta_clinical_sample:
run: generate_cBioPortal_file.cwl
Expand Down Expand Up @@ -281,6 +311,13 @@ steps:
data_clinical_file: data_clinical_file
out:
[output_file]
update_cases_all:
run: updateCaseList.cwl
in:
sample_ids: update_extra_sample_ids/extra_sample_ids
case_list: generate_cbio_cases_all/output_file
output_filename: cbio_cases_all_filename
out: [output_file]

# cases_cnaseq.txt
generate_cases_cnaseq:
Expand All @@ -293,6 +330,13 @@ steps:
data_clinical_file: data_clinical_file
out:
[output_file]
update_cases_cnaseq:
run: updateCaseList.cwl
in:
sample_ids: update_extra_sample_ids/extra_sample_ids
case_list: generate_cases_cnaseq/output_file
output_filename: cbio_cases_cnaseq_filename
out: [output_file]

# cases_cna.txt
generate_cases_cna:
Expand All @@ -305,6 +349,13 @@ steps:
data_clinical_file: data_clinical_file
out:
[output_file]
update_cases_cna:
run: updateCaseList.cwl
in:
sample_ids: update_extra_sample_ids/extra_sample_ids
case_list: generate_cases_cna/output_file
output_filename: cbio_cases_cna_filename
out: [output_file]

# cases_sequenced.txt (cbio_cases_sequenced_filename)
generate_cases_sequenced:
Expand All @@ -317,6 +368,14 @@ steps:
data_clinical_file: data_clinical_file
out:
[output_file]
update_cases_sequenced:
run: updateCaseList.cwl
in:
sample_ids: update_extra_sample_ids/extra_sample_ids
case_list: generate_cases_sequenced/output_file
output_filename: cbio_cases_sequenced_filename
out: [output_file]


# data_CNA.txt (cbio_cna_data_filename)
# data_CNA.ascna.txt (cbio_cna_ascna_data_filename)
Expand Down Expand Up @@ -445,10 +504,14 @@ steps:
make_case_list_dir:
run: put_in_dir.cwl
in:
cases_all: generate_cbio_cases_all/output_file
cases_cnaseq: generate_cases_cnaseq/output_file
cases_cna: generate_cases_cna/output_file
cases_sequenced: generate_cases_sequenced/output_file
# cases_all: generate_cbio_cases_all/output_file
# cases_cnaseq: generate_cases_cnaseq/output_file
# cases_cna: generate_cases_cna/output_file
# cases_sequenced: generate_cases_sequenced/output_file
cases_all: update_cases_all/output_file
cases_cnaseq: update_cases_cnaseq/output_file
cases_cna: update_cases_cna/output_file
cases_sequenced: update_cases_sequenced/output_file
output_directory_name:
valueFrom: ${ return "case_lists"; }
files:
Expand Down
138 changes: 125 additions & 13 deletions tests/test_portal-workflow_cwl.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -86,8 +86,8 @@ def test_run_worflow_one_maf(self):

expected_output = {
'portal_case_list_dir': ODir(name='case_lists', items=[
OFile(name='cases_all.txt', size=604, hash='b8abebd686a5a4e3897af9546ee3e9e5fee8cf25'),
OFile(name='cases_cnaseq.txt', size=684, hash='3bc39070fa15b305c9b1f4a041b75c6a0ddbba9a'),
OFile(name='cases_all.txt', size=604, hash='a7bad4f55be39c46549a0cec4a1c5b73db3ae0d5'),
OFile(name='cases_cnaseq.txt', size=684, hash='ead904e8ab6753499f2980b09a0187ef3a55d0cc'),
OFile(name='cases_cna.txt', size=616, hash='8d3dc67168382830a270feec6a0efddf52cc5dd4'),
OFile(name='cases_sequenced.txt', size=629, hash='188bde59b913c82b9a783d19c37b81c959b4696d')], dir=output_dir),
'portal_clinical_patient_meta_file': OFile(
Expand Down Expand Up @@ -155,6 +155,118 @@ def test_run_worflow_one_maf(self):
self.assertEqual(lines[0], ['Hugo_Symbol', 'Sample1'])
self.assertEqual(len(lines), 587)

def test_run_worflow_one_maf_extra_ids(self):
"""
Test that the workflow works correctly when run with a single maf and extra sample IDs
"""
data_clinical_file = os.path.join(DATA_SETS['Proj_1']['INPUTS_DIR'], "Proj_1_sample_data_clinical.txt")
sample_summary_file = os.path.join(DATA_SETS['Proj_1']['QC_DIR'], "Proj_1_SampleSummary.txt")
self.input = {
"project_id": "Proj_1",
"project_name": "Proj_1",
"project_short_name": "Proj_1",
"project_description": "project",
"project_pi": "Dr. Jones",
"request_pi": "Dr. Franklin",
"is_impact": True,
"argos_version_string": "2.x",
"cancer_type": "MEL",
"cancer_study_identifier": 'Proj_1',
"cbio_meta_cna_segments_filename": "Proj_1_meta_cna_hg19_seg.txt",
"cbio_segment_data_filename": "Proj_1_data_cna_hg19.seg",
"helix_filter_version": "20.06.1",
"extra_sample_ids": ["Sample100", "Sample101"],
"data_clinical_file": {
"path": data_clinical_file,
"class": "File"
},
"sample_summary_file": {
"path": sample_summary_file,
"class": "File"
},
"targets_list": {
"path": DATA_SETS['Proj_1']["targets_list"],
"class": "File"
},
"known_fusions_file": {
"path": KNOWN_FUSIONS_FILE,
"class": "File"
},
"mutation_maf_files": [
{
"path": os.path.join(DATA_SETS['Proj_1']['MAF_DIR'], "Sample1.Sample2.muts.maf"),
"class": "File"
}
],
"mutation_svs_txt_files": [
{
"path": os.path.join(DATA_SETS['Proj_1']['MAF_DIR'], "Sample1.Sample2.svs.pass.vep.portal.txt"),
"class": "File"
}
],
"facets_hisens_cncf_files": [
{
"path": os.path.join(DATA_SETS['Proj_1']['FACETS_DIR'], "Sample2.rg.md.abra.printreads__Sample1.rg.md.abra.printreads_hisens.cncf.txt"),
"class": "File"
}
],
"facets_hisens_seg_files": [
{
"path": os.path.join(DATA_SETS['Proj_1']['FACETS_DIR'], "Sample2.rg.md.abra.printreads__Sample1.rg.md.abra.printreads_hisens.seg"),
"class": "File"
}
],
}

output_json, output_dir = self.run_cwl()

expected_output = {
'portal_case_list_dir': ODir(name='case_lists', items=[
OFile(name='cases_all.txt', size=604, hash='a7bad4f55be39c46549a0cec4a1c5b73db3ae0d5'),
OFile(name='cases_cnaseq.txt', size=684, hash='ead904e8ab6753499f2980b09a0187ef3a55d0cc'),
OFile(name='cases_cna.txt', size=616, hash='8d3dc67168382830a270feec6a0efddf52cc5dd4'),
OFile(name='cases_sequenced.txt', size=629, hash='188bde59b913c82b9a783d19c37b81c959b4696d')], dir=output_dir),
'portal_clinical_patient_meta_file': OFile(
name='meta_clinical_patient.txt', size=136, hash='bbfd617bded72d6e9f2071285ac5a7867b0ec6fb', dir=output_dir),
'portal_cna_ascna_file': OFile(
name='data_CNA.ascna.txt', size=6154, hash='e06f41b3ad538740519cec581bcbd5cd812e5f00', dir=output_dir),

# NOTE: same as the merged_cna_file file in this case
'portal_cna_data_file': OFile(
name='data_CNA.txt', size=5355, hash='c1682f09406478fc404e40758b0c5e9c47dce5cb', dir=output_dir),

'portal_data_clinical_patient_file': OFile(
name='data_clinical_patient.txt', size=643, hash='9417dcabddd6ab2cbe98167bccd9b9e4fa182562', dir=output_dir),
'portal_data_clinical_sample_file': OFile(
name='data_clinical_sample.txt', size=7592, hash='2a0c59593fa7726743b2fe46db9d955dbc625453', dir=output_dir),
'portal_fusions_data_file': OFile(
name='data_fusions.txt', size=99, hash='c16f763b248813fcdde76f7486f1ddc4e9856038', dir=output_dir),
'portal_hisens_segs': OFile(
name='Proj_1_data_cna_hg19.seg', size=1322, hash='cae32a187d973441dd6e554e07ae81bebecb8980', dir=output_dir),
'portal_meta_clinical_sample_file': OFile(
name='meta_clinical_sample.txt', size=134, hash='29d7eda8ae439aaaa531b2d10fa5c03f943edf11', dir=output_dir),
'portal_meta_cna_file': OFile(
name='meta_CNA.txt', size=264, hash='1123609f24529c407b04b5dbd22efd6a453b3965', dir=output_dir),
'portal_meta_cna_segments_file': OFile(
name='Proj_1_meta_cna_hg19_seg.txt', size=188, hash='c100c7c6cfb7f67f991d356725abea6204e99d6b', dir=output_dir),
'portal_meta_fusions_file': OFile(
name='meta_fusions.txt', size=221, hash='5417138de92de1c35aa123c1e8800d710bb1f7cb', dir=output_dir),
'portal_meta_mutations_extended_file': OFile(
name='meta_mutations_extended.txt', size=264, hash='c1e0524b9ee612710b1921053bdb3f32120831ec', dir=output_dir),
'portal_meta_study_file': OFile(
name='meta_study.txt', size=134, hash='182c7c39315d7ce91cbb8d96f98134d676324cf6', dir=output_dir),
'portal_muts_file': OFile(
name='data_mutations_extended.txt', size=4766, hash='5c92b50bdd1d7c45af8fd180448a68926b8248e6', dir=output_dir),
'portal_report': OFile(
name='report.html', size=1016472, hash='4be1f9395bb83330dcffaecf76def4456db99a62', dir=output_dir)
}

self.maxDiff = None
strip_related_keys = [
('basename', 'report.html', ['size', 'checksum'])
]
self.assertCWLDictEqual(output_json, expected_output, related_keys = strip_related_keys)


def test_run_worflow_two_mafs(self):
"""
Expand Down Expand Up @@ -238,8 +350,8 @@ def test_run_worflow_two_mafs(self):

expected_output = {
'portal_case_list_dir': ODir(name='case_lists', items=[
OFile(name='cases_all.txt', size=604, hash='b8abebd686a5a4e3897af9546ee3e9e5fee8cf25'),
OFile(name='cases_cnaseq.txt', size=684, hash='3bc39070fa15b305c9b1f4a041b75c6a0ddbba9a'),
OFile(name='cases_all.txt', size=604, hash='a7bad4f55be39c46549a0cec4a1c5b73db3ae0d5'),
OFile(name='cases_cnaseq.txt', size=684, hash='ead904e8ab6753499f2980b09a0187ef3a55d0cc'),
OFile(name='cases_cna.txt', size=616, hash='8d3dc67168382830a270feec6a0efddf52cc5dd4'),
OFile(name='cases_sequenced.txt', size=629, hash='188bde59b913c82b9a783d19c37b81c959b4696d')], dir=output_dir),
'portal_clinical_patient_meta_file': OFile(
Expand Down Expand Up @@ -395,9 +507,9 @@ def test_with_facets_txt(self):
expected_output = {
'portal_case_list_dir':
ODir(name='case_lists', items=[
OFile(name='cases_all.txt', size=194, hash='744b6aca3004f89bdb3f437ea87d4e3991394eaa'),
OFile(name='cases_cnaseq.txt', size=274, hash='9f7b03a5d0a9b8911c5c76ed0e6fe7712ee2a21f'),
OFile(name='cases_cna.txt', size=206, hash='cc34a33f2103c0a8f6630799fbc72508fd40aee4'),
OFile(name='cases_all.txt', size=194, hash='12639bb3d01e7e4aa0f94f53a3b8d757e3e6d98f'),
OFile(name='cases_cnaseq.txt', size=274, hash='8f9e091b826c682d6ab3dbf5577ac8af10e52ed8'),
OFile(name='cases_cna.txt', size=206, hash='6a7ad5b8c570f5e0c8d38ce5ad222ea945ad0066'),
OFile(name='cases_sequenced.txt', size=219, hash='738b2c81d52fd202df1afda31d2750affd09b3f1')], dir=output_dir),
'portal_clinical_patient_meta_file': OFile(
name='meta_clinical_patient.txt', size=136, hash='bbfd617bded72d6e9f2071285ac5a7867b0ec6fb', dir=output_dir),
Expand Down Expand Up @@ -580,9 +692,9 @@ def test_with_facets_txt_and_facets_mafs(self):

expected_output = {
'portal_case_list_dir': ODir(name='case_lists', items=[
OFile(name='cases_all.txt', size=194, hash='744b6aca3004f89bdb3f437ea87d4e3991394eaa'),
OFile(name='cases_cnaseq.txt', size=274, hash='9f7b03a5d0a9b8911c5c76ed0e6fe7712ee2a21f'),
OFile(name='cases_cna.txt', size=206, hash='cc34a33f2103c0a8f6630799fbc72508fd40aee4'),
OFile(name='cases_all.txt', size=194, hash='12639bb3d01e7e4aa0f94f53a3b8d757e3e6d98f'),
OFile(name='cases_cnaseq.txt', size=274, hash='8f9e091b826c682d6ab3dbf5577ac8af10e52ed8'),
OFile(name='cases_cna.txt', size=206, hash='6a7ad5b8c570f5e0c8d38ce5ad222ea945ad0066'),
OFile(name='cases_sequenced.txt', size=219, hash='738b2c81d52fd202df1afda31d2750affd09b3f1')], dir=output_dir),
'portal_clinical_patient_meta_file': OFile(
name='meta_clinical_patient.txt', size=136, hash='bbfd617bded72d6e9f2071285ac5a7867b0ec6fb', dir=output_dir),
Expand Down Expand Up @@ -751,9 +863,9 @@ def test_with_mixed_mafs(self):

expected_output = {
'portal_case_list_dir': ODir(name='case_lists', items=[
OFile(name='cases_all.txt', size=194, hash='744b6aca3004f89bdb3f437ea87d4e3991394eaa'),
OFile(name='cases_cnaseq.txt', size=274, hash='9f7b03a5d0a9b8911c5c76ed0e6fe7712ee2a21f'),
OFile(name='cases_cna.txt', size=206, hash='cc34a33f2103c0a8f6630799fbc72508fd40aee4'),
OFile(name='cases_all.txt', size=194, hash='12639bb3d01e7e4aa0f94f53a3b8d757e3e6d98f'),
OFile(name='cases_cnaseq.txt', size=274, hash='8f9e091b826c682d6ab3dbf5577ac8af10e52ed8'),
OFile(name='cases_cna.txt', size=206, hash='6a7ad5b8c570f5e0c8d38ce5ad222ea945ad0066'),
OFile(name='cases_sequenced.txt', size=219, hash='738b2c81d52fd202df1afda31d2750affd09b3f1')], dir=output_dir),
'portal_clinical_patient_meta_file': OFile(
name='meta_clinical_patient.txt', size=136, hash='bbfd617bded72d6e9f2071285ac5a7867b0ec6fb', dir=output_dir),
Expand Down

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