mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-11-14 05:43:08 +00:00
e745e167c1
* fix yml formatting * allow fastq.gz and fq.gz as file input, add meta.yml and test * fix yaml files * Revert "allow fastq.gz and fq.gz as file input, add meta.yml and test" This reverts commit 34002d7a7a8c7f7bb4600c3377f35c87849f71a4. * prettier magic! * fix comments for yamllint * remove node version number * fix linting errors Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
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"
|