mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-11-11 04:33:10 +00:00
409af2f27c
* feat: code polishing * Apply suggestions from code review Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de> * code polishing * more code polishing * code polishing * tests for applybqsrspark * fix typo * no need to check md5sum for versions.yml * fix: use correct syntax * code polishing again * add tests for markduplicatesspark * simplify mergevcfs tests * add tests for baserecalibratorspark * fix: path to entry * code polishing * fix linting * simplify module * update meta.yml * fix pair mode * fix: MITO mode * more tests * fix command * bad copy paste * fix typos * fix tests * fix test * update meta.yml * correct versions.yml in all test.yml * code polishing * code polishing * more code polishing * fix args * add tmpdir for all Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de>
52 lines
1.9 KiB
YAML
52 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
|
|
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"
|
|
|
|
output:
|
|
- contamination:
|
|
type: file
|
|
description: File containing the contamination table.
|
|
pattern: "*.contamination.table"
|
|
- segmentation:
|
|
type: file
|
|
description: output table containing segmentation of tumor minor allele fractions (optional)
|
|
pattern: "*.segmentation.table"
|
|
- versions:
|
|
type: file
|
|
description: File containing software versions
|
|
pattern: "versions.yml"
|
|
|
|
authors:
|
|
- "@GCJMackenzie"
|
|
- "@maxulysse"
|