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rebase 326#330

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carynwillis merged 39 commits intoissue_326NCI-CGR/GwasQcPipeline:issue_326from defaultNCI-CGR/GwasQcPipeline:defaultCopy head branch name to clipboardSep 26, 2024

+1,387-247

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Commits on Sep 25, 2024

• Update submodule data (GwasQcPipeline-test-data)

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• makes illumina_manifest_file optional in the config

  

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• Uses snps_array name instead of bpm to name *.abf.txt

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• Adds a new idat_intensity workflow

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• Adds vcf2abf.py and vcf2adpc.py as prep scripts for contamination checks with vcf entry

  

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• Creates a BCF entry point.

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• Removes IDAT intensity checks from contamination.smk

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• Adds rules contamination.smk to do contamination checks with bcf input.

  

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• Enables contamiantion check with bcf input in cluster mode.

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• Adds capability to infer median intensity directly from input BCF/VCF.

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• Adds the distinction of contamination and intensity checks in the snakefile and sample_qc subworkflow

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• Correcting conditions such with BCF input intensity and contamination check is default

  

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• Renames variable vcf_file to bcf_file when bcf file is refered.

  

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• Removes the duplicated subworkflow file for intensity checks.

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• Updates the docstring in contamination.smk to indicate when BCF file is used.

  

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• Renames input variable to bcf_file.

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• Imports snakemake params all at once in grouped_contamination.py

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• Removes typo duplicated header in entry_points

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• Shifts to using IGC score instead of gentrain score in vcf2adpc.py for contamination checks.

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• Adds a config suffix validator for bcf_file.

  

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• Removes some debugging lines from vcf2abf.py

  

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• Shifts to using IGC as genotype score for preparing abf using vcf2abf.

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• Removes commented lines from vcf2adpc.py and vcf2abf.py

  

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• fixes a black syntax issue in importing snakemake params in grouped_contamatination.py

  

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• Modifies vcf2abf to not use gentrain score in preparing abf.

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• Includes a None case in the BCF config validator to work with unit testing.

  

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• Adds the app mode in median_intensity_from_vcf to work directly as stand-alone.

  

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• Adds the new unit test scripts relevent to BCF entry

  

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• docs: updates docstring to show bcf as a user_file in config

  

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• docs: Updates the entry_point documentation to show BCF as an entry_point.

  

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• docs: Updates contamination subworkflow documentation to show processing with BCF input.

  

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• docs: Adds the documentation for new intensity subworkflow and shows processing for both IDAT and BCF input.

  

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• docs: Updates index to include intensity_check subworkflow.

  

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• docs: corrects spellings in documentation

  

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• Removes jupyter comment lines from scripts.

  

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• docs: updates the docstring for user_files in config section to include BCF.

  

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• docs: redo updates the user_files docstring to include BCF.

  

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• Merge pull request #314 from NCI-CGR/data_catalog

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Commits on Sep 26, 2024

• docs: Fix typo in subject_qc docs

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