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Pay attention to optional files when generating NGS analysis templates #466

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merged 1 commit into from Jun 3, 2021
Merged

Pay attention to optional files when generating NGS analysis templates #466

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2 changes: 1 addition & 1 deletion cidc_schemas/__init__.py
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Expand Up @@ -2,4 +2,4 @@

__author__ = """James Lindsay"""
__email__ = "jlindsay@jimmy.harvard.edu"
__version__ = "0.24.35"
__version__ = "0.24.36"
6 changes: 4 additions & 2 deletions cidc_schemas/schemas/templates/analyses/wes_analysis_template.json
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Expand Up @@ -134,14 +134,16 @@
"merge_pointer": "/rna/haplotyper",
"gcs_uri_format": "{protocol identifier}/wes/{run id}/analysis/haplotyper.vcf.gz",
"type_ref": "assays/components/local_file.json#properties/file_path",
"is_artifact": 1
"is_artifact": 1,
"allow_empty": true
},
{
"parse_through": "lambda run: f'{folder or \"\"}analysis/rna/{run}/{run}_tnscope.filter.neoantigen.vep.rna.vcf'",
"merge_pointer": "/rna/vcf_tnscope_filter_neoantigen",
"gcs_uri_format": "{protocol identifier}/wes/{run id}/analysis/vcf_tnscope_filter_neoantigen.vcf",
"type_ref": "assays/components/local_file.json#properties/file_path",
"is_artifact": 1
"is_artifact": 1,
"allow_empty": true
},
{
"parse_through": "lambda run: f'{folder or \"\"}analysis/report.tar.gz'",
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2 changes: 2 additions & 0 deletions cidc_schemas/template.py
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Expand Up @@ -525,6 +525,8 @@ def _convert_api_to_template(name: str, schema: dict, assay_schema: dict):
"type_ref": "assays/components/local_file.json#properties/file_path",
"is_artifact": 1,
}
if entry.get("optional", False):
subsubtemplate["allow_empty"] = True

subtemplate[long_key]["process_as"].append(subsubtemplate)
used_merge_pointers.append(merge_pointer)
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