mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-12-22 11:08:17 +00:00
3aacd46da2
* backfilled modules with meta.yml that had no license identifier * harmonized BSD license names * whitespace linting at modules/unzip/meta.yml:12 * harmonized software from US NIH-NCBI/NIST to 'US-Government-Work' * Update modules/bcftools/index/meta.yml `bcftools` is dual-licensed, use associative array to allow for multiple licenses Co-authored-by: Michael L Heuer <heuermh@acm.org> Co-authored-by: Michael L Heuer <heuermh@acm.org>
54 lines
2 KiB
YAML
54 lines
2 KiB
YAML
name: gatk4_calculatecontamination
|
|
description: |
|
|
Calculates the fraction of reads from cross-sample contamination based on summary tables from getpileupsummaries. Output to be used with filtermutectcalls.
|
|
keywords:
|
|
- gatk4
|
|
- calculatecontamination
|
|
- cross-samplecontamination
|
|
- getpileupsummaries
|
|
- filtermutectcalls
|
|
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' ]
|
|
- pileup:
|
|
type: file
|
|
description: File containing the pileups summary table of a tumor sample to be used to calculate contamination.
|
|
pattern: "*.pileups.table"
|
|
- matched:
|
|
type: file
|
|
description: File containing the pileups summary table of a normal sample that matches with the tumor sample specified in pileup argument. This is an optional input.
|
|
pattern: "*.pileups.table"
|
|
- segmentout:
|
|
type: boolean
|
|
description: specifies whether to output the segmentation table.
|
|
|
|
output:
|
|
- contamination:
|
|
type: file
|
|
description: File containing the contamination table.
|
|
pattern: "*.contamination.table"
|
|
- segmentation:
|
|
type: file
|
|
description: optional output table containing segmentation of tumor minor allele fractions.
|
|
pattern: "*.segmentation.table"
|
|
- versions:
|
|
type: file
|
|
description: File containing software versions
|
|
pattern: "versions.yml"
|
|
|
|
authors:
|
|
- "@GCJMackenzie"
|