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

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name: gatk4_getpileupsummaries
description: |
Summarizes counts of reads that support reference, alternate and other alleles for given sites. Results can be used with CalculateContamination. Requires a common germline variant sites file, such as from gnomAD.
keywords:
- gatk4
- getpileupsumaries
- readcountssummary
- germlinevariantsites
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: file
description: BAM/CRAM file to be summarised.
pattern: "*.{bam,cram}"
- input_index:
type: file
description: BAM/CRAM file index.
pattern: "*.{bai,crai}"
- intervals:
type: file
description: File containing specified sites to be used for the summary. If this option is not specified, variants file is used instead automatically.
pattern: "*.interval_list"
- fasta:
type: file
description: The reference fasta file
pattern: "*.fasta"
- fai:
type: file
description: Index of reference fasta file
pattern: "*.fasta.fai"
- dict:
type: file
description: GATK sequence dictionary
pattern: "*.dict"
- variants:
type: file
description: Population vcf of germline sequencing, containing allele fractions. Is also used as sites file if no separate sites file is specified.
pattern: "*.vcf.gz"
- variants_tbi:
type: file
description: Index file for the germline resource.
pattern: "*.vcf.gz.tbi"
output:
- pileup:
type: file
description: File containing the pileup summary table.
pattern: "*.pileups.table"
- versions:
type: file
description: File containing software versions
pattern: "versions.yml"
authors:
- "@GCJMackenzie"