nf-core_modules/modules/gatk4/mutect2/meta.yml

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name: gatk4_mutect2
description: Call somatic SNVs and indels via local assembly of haplotypes.
keywords:
- gatk4
- mutect2
- haplotype
- somatic
tools:
- gatk4:
description: |
Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools
with a primary focus on variant discovery and genotyping. Its powerful processing engine
and high-performance computing features make it capable of taking on projects of any size.
homepage: https://gatk.broadinstitute.org/hc/en-us
documentation: https://gatk.broadinstitute.org/hc/en-us/categories/360002369672s
doi: 10.1158/1538-7445.AM2017-3590
licence: ['Apache-2.0']
input:
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test']
- input:
type: list
description: list of BAM files, also able to take CRAM as an input
pattern: "*.{bam/cram}"
- input_index:
type: list
description: list of BAM file indexes, also able to take CRAM indexes as an input
pattern: "*.{bam.bai/cram.crai}"
- which_norm:
type: list
description: optional list of sample headers contained in the normal sample bam files (these are required for tumor_normal_pair mode)
pattern: "testN"
- run_single:
type: boolean
description: Specify whether or not to run in tumor_single mode instead of tumor_normal_pair mode (will be ignored if run_pon is also true)
pattern: "true/false"
- run_pon:
type: boolean
description: Specify whether or not to run in panel_of_normal mode instead of tumor_normal_pair mode
pattern: "true/false"
- run_mito:
type: boolean
description: Specify whether or not to run in mitochondria-mode instead of tumor_normal_pair mode
pattern: "true/false"
- interval_label:
type: string
description: Specify the label used for mitochondrial chromosome when mutect2 is run in mitochondria mode.
pattern: "chrM"
- fasta:
type: file
description: The reference fasta file
pattern: "*.fasta"
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- fai:
type: file
description: Index of reference fasta file
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pattern: "*.fasta.fai"
- dict:
type: file
description: GATK sequence dictionary
pattern: "*.dict"
- germline_resource:
type: file
description: Population vcf of germline sequencing, containing allele fractions.
pattern: "*.vcf.gz"
- germline_resource_tbi:
type: file
description: Index file for the germline resource.
pattern: "*.vcf.gz.tbi"
- panel_of_normals:
type: file
description: vcf file to be used as a panel of normals.
pattern: "*.vcf.gz"
- panel_of_normals_tbi:
type: file
description: Index for the panel of normals.
pattern: "*.vcf.gz.tbi"
output:
- vcf:
type: file
description: compressed vcf file
pattern: "*.vcf.gz"
- tbi:
type: file
description: Index of vcf file
pattern: "*vcf.gz.tbi"
- stats:
type: file
description: Stats file that pairs with output vcf file
pattern: "*vcf.gz.stats"
- f1r2:
type: file
description: file containing information to be passed to LearnReadOrientationModel (only outputted when tumor_normal_pair mode is run)
pattern: "*.f1r2.tar.gz"
- versions:
type: file
description: File containing software versions
pattern: "versions.yml"
authors:
- "@GCJMackenzie"