nf-core/sarek

Enable Mutect2 force-calling using --alleles flag

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#1,883 opened on May 2, 2025

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enhancementgood first issue

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Description

Description of feature

Would it be possible to expose the --alleles flag for gatk mutect2 force-calling. This would allow the user to provide a reference vcf of variants on which to force call mutations in the sample of interest.

Contributor guide

Research direction
Locate the Mutect2 process definition in the pipeline, add the alleles parameter to the command, and update any related configuration files.
Tech stack
None
Domain
data
Issue type
Feature
DifficultyEstimated implementation difficulty for a new contributor, from 1 for very small changes to 5 for expert-level work.
2
Estimated timeA rough time range for an experienced contributor to investigate, implement, test, and prepare a pull request.
1-3 hours
Activity statusHow available the issue appears right now: fresh, active, stale, blocked, or waiting on maintainer input.
Fresh
ClarityHow clearly the issue explains the expected change, acceptance criteria, and next step.
Clear
Prerequisites
Nextflow
Newbie friendlinessA 1-100 score estimating how approachable this issue is for first-time contributors.
70