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Add XY filtration workflow#191

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Faizal-Eeman wants to merge 67 commits intomainuclahs-cds/pipeline-call-gSNP:mainfrom mmootor-add-xy-filtrationuclahs-cds/pipeline-call-gSNP:mmootor-add-xy-filtrationCopy head branch name to clipboard

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Commits

Commits on Nov 26, 2024

• add patient_sex to template

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  73e1e03

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• add XY filter script from project-method-AlgorithmEvaluation-BNCH-000122-GIABGermlineVariant

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Commits on Dec 7, 2024

• add par_bed parameter to template.config

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• add genome build to template

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Commits on Dec 19, 2024

• add user input sample id

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• add sample sex; remove redundant code; exremove het calls for XY

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• fix variables

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• extract autosomes

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• merge autosomes and XY filtered calls

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• change vcf header extraction location

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• Add workflow steps to script note

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• clean up script

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Commits on Dec 20, 2024

• add skeleton code for vcf header temp file

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Commits on Dec 21, 2024

• write VCF source to temp file and parameterize it

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• add arg for variant caller

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• set variant caller source

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• improve documentation

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• add hail v0.2.133 and docker image to default config

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• add filter-xy NF script

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• add NF skeleton

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• add script dir var in main

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• add xy filtration command

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• rename XY script

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Commits on Dec 28, 2024

• change arg variant_caller to vcf_source_file

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• add VCF source extraction code to script section in nextflow module

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• revert script output to bgz

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• set publishDir

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• add channel for xy filter and call process

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• include filter XY module in main

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Commits on Dec 30, 2024

• simplify xy filter channel

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• add script dir ch

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• add script dir input to NF module

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• fix docker tag

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Commits on Jan 7, 2025

• update script command to take vcf file source

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• update sample sex parameter in template

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• update template config

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• add parameters to schema

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• add genome build arg to script command

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• parameterize genome build in script

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• temporarily add hail dev tag

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• add params.par_bed as input

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• add par_bed as process input

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• fix output vcf dataset at export in script

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Commits on Jan 8, 2025

• fix pylint

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• update docker hail version

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• remove cat command

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• fix log output dir

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• standardize process name with tool name at the end

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• standardize process name with tool name at the end

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• update sample_sex comment in template

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• add default and choices for genome_build

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• add choices for sample_sex in schema

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• add resource allocation to filter_XY_Hail

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• emit xy filtered output

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• generate checksum for xy filtered vqsr VCF

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Commits on Jan 9, 2025

• add system command to VCF header

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• Add XY filtration step to README

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• fix process name

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• add XY filteration params to README

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• Update script description

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• add xy_filtration_workflow.md

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• add GRCh38 PAR to README

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• fix pylint

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• fix publishDir rules

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• Update outputs in README

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• Upddate CHANGELOG

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Commits on Jan 10, 2025

• update output filename

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