feat: Add Pharmcat and Pangu #44
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- added to inputs - still needs filepaths - updated README - still needs descriptions for output - added pharmcat_positions to ReferenceData - updated main and sample_analysis Validates with womtool and miniwdl
README.md
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| | Array[File] | hificnv_copynum_bedgraphs | Copy number values calculated for each region | | | ||
| | Array[File] | hificnv_depth_bws | Bigwig file containing the depth measurements from HiFiCNV | | | ||
| | Array[File] | hificnv_maf_bws | Bigwig file containing the minor allele frequency measurements from DeepVariant, generated by HiFiCNV | | | ||
| | Array[File] | pangu_jsons | | | | ||
| | Array[File] | pangu_tsvs | | | | ||
| | Array[File] | fixed_pangu_tsvs | | | | ||
| | Array[File?] | pharmcat_missing_pgx_vcfs | | | | ||
| | Array[File] | pharmcat_preprocessed_filtered_vcfs | | | | ||
| | Array[File] | pharmcat_match_jsons | | | | ||
| | Array[File] | pharmcat_phenotype_jsons | | | | ||
| | Array[File] | pharmcat_report_htmls | | | | ||
| | Array[File] | pharmcat_report_jsons | | | |
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Ask @jrharting to provide brief documentation for each Pharmcat output file.
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for pharmcat, is it ok to refer to the tool website? or do you need a short blurb here too?
https://pharmcat.org/examples/#output
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The pangu_tsvs are intermediates for passing pangu outputs to pharmcat. these could be deleted after running and not returned.
The pangu json is a detailed description of the CYP2D6 star allele call. More info here : https://github.com/PacificBiosciences/pangu/tree/main#caller-outputs
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We'll link out to pangu and pharmcat documentation the first time they're mentioned in the outputs, but we do want to have a brief description. It could be as simple as "PGx report from Pharmcat, html format".
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| Array[File] | pangu_jsons | Detailed CYP2D6 calling report containing calls and coverage| |
| Array[File] | pangu_tsvs | CYP2D6 call for input to pharmCAT reports | |
| Array[File] | fixed_pangu_tsvs | (fixed) CYP2D6 call for input to pharmCAT reports | |
| Array[File?] | pharmcat_missing_pgx_vcfs | PGx-cataloged variants not found in sample vcf | |
| Array[File] | pharmcat_preprocessed_filtered_vcfs | VCF with filled reference calls at all PGx variants with sample coverage above minimum | |
| Array[File] | pharmcat_match_jsons | JSON files with detailed information about how data in the sample VCF matches up with haplotype definitions| |
| Array[File] | pharmcat_phenotype_jsons | Match data and combined with outside call data with assigned function and metabolizer values| |
| Array[File] | pharmcat_report_htmls | HTML file with matched phenotype to information found in CPIC guideline data| |
| Array[File] | pharmcat_report_jsons | JSON file with matched phenotype to information found in CPIC guideline data| |
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i can fill in a different template if it would be easier ...
backends/hpc/inputs.hpc.json
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| "data": "<local_path_prefix>/dataset/GRCh38/pharmcat/#TODO", | ||
| "data_index": "<local_path_prefix>/dataset/GRCh38/pharmcat/#TODO" |
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Update all backend templates with paths to pharmcat_positions VCF/index.
wdl-ci.config.json
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| "workflows/wdl-common/wdl/tasks/pharmcat.wdl": { | ||
| "key": "workflows/wdl-common/wdl/tasks/pharmcat.wdl", | ||
| "name": "", | ||
| "description": "", | ||
| "tasks": { | ||
| "pharmcat_preprocess": { | ||
| "key": "pharmcat_preprocess", | ||
| "digest": "", | ||
| "tests": [] | ||
| }, | ||
| "filter_preprocessed_vcf": { | ||
| "key": "filter_preprocessed_vcf", | ||
| "digest": "", | ||
| "tests": [] | ||
| }, | ||
| "pangu_cyp2d6": { | ||
| "key": "pangu_cyp2d6", | ||
| "digest": "", | ||
| "tests": [] | ||
| }, | ||
| "run_pharmcat": { | ||
| "key": "run_pharmcat", | ||
| "digest": "", | ||
| "tests": [] | ||
| } | ||
| } | ||
| }, |
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Add Pharmcat tests.
williamrowell
requested changes
May 24, 2023
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Remaining changes:
- remove pangu_tsvs and fixed_pangu_tsvs from sample_analysis.wdl and main.wdl outputs, as recommended by JH; also remove from README.md
- update output documentation in README.md using notes from JH; link out to Pangu/Pharmcat documentation when necessary; we should cut/paste these updates into wdl-targetenrichment README.md as well
- add entry for Pharmcat in "Tool versions and Docker images" table in README.md
- add pharmcat_positions to data bundle, sync to Azure/AWS/GCP/Zenodo; update backend inputs.json templates with paths
- run on HPC using HG005/6/7 Sequel II trio and HG002/3/4 Revio trio datasets
- create minimal test dataset to be used in wdl-ci, upload to where test data lives in CoA blob; update wdl-ci.config.json with real tests
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- moved Pharcat subworkflow from tasks to workflows - removed the internal scatter, so Pharmcat workflow runs once per sample - broke out the pharmcat inputs and removed some inputs that were no longer used - updated parameter_meta
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I think we're good to go except for:
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Uses this image now: PacificBiosciences/wdl-dockerfiles#32 |
williamrowell
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Add Pharmcat & pangu to humanWGS workflow