nf-core_modules/modules/gatk4/calculatecontamination/meta.yml
GCJMackenzie aa32a8a72e
new module: gatk4/calculatecontamination (#778)
* initiated files for calculate contamination

* pushing local repo to remote

* created script, filled in meta yml, created tests and test yml. local checks passing, needs repo side test data

* added option and tests for outputting optional segmentation file

* saving for test push

* versions updated, test data added

* Update main.nf

* fixed versions info, should report correctly now

* small update to main.nf outputs formatting

* Apply suggestions from code review

* Update test_data.config

* Apply suggestions from code review

Co-authored-by: GCJMackenzie <gavin.mackenzie@nibsc.org>
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-10-05 22:52:00 +01:00

53 lines
1.9 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
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"