[Clair3_Variants] Clair3_Variants_ONT_PHB workflow#708

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Michal-Babins wants to merge 22 commits intomainfrom mb-clair3-variant-dev

+359-3

Commits on Dec 24, 2024

Add Clair3 variant calling workflow and related tasks; enhance minimap2 with additional options
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Add Clair3 variant calling workflow for ONT data; rename and update descriptor
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Rename Clair3 variant calling workflow for ONT data for consistency
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Commits on Dec 26, 2024

Refactor Clair3 variant calling workflow and Minimap2 task parameters for clarity and consistency
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Add Clair3 Variants workflow documentation for ONT data and update navigation
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Update samtools_faidx task to copy reference file and adjust output; modify Clair3 workflow to use indexed FASTA
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Refactor samtools_faidx task to directly index FASTA file and update Clair3 workflow to use the correct reference genome file
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Clean up whitespace and reduce CPU allocation in Clair3 variant detection and FASTA utility tasks
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Refactor Clair3 variant detection task to create local copies of BAM and reference files with expected names for compatibility
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Add haploid calling options to Clair3 variant detection task and workflow
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Refactor Clair3 variant detection tasks to improve parameter naming and streamline file handling
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Update Clair3 variant detection task to create local FASTA and FAI copies with correct names for compatibility
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Update Clair3 variant detection task to use Docker image with extra models
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Commits on Dec 31, 2024

Commits on Jan 7, 2025

Update Clair3 variants documentation and workflow outputs for ONT data processing
Michal-Babins
committed