mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-11-10 20:23:10 +00:00
f479d4fb8d
* files for learnreadorientationmodel initialised for first commit * finished scripts and yml files. test working locally but needs an f1r2 test data on nf-core before it can be submitted * updated test data location * versions file updated, test data added * updated versions file, edited test file * small formatting update to main.nf * Update main.nf * Update test_data.config * updated tests main.nf * Update test_data.config * Apply suggestions from code review * Update modules/gatk4/learnreadorientationmodel/main.nf * Update modules/gatk4/learnreadorientationmodel/meta.yml * fixed tests failing Co-authored-by: GCJMackenzie <gavin.mackenzie@nibsc.org> Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
41 lines
1.3 KiB
YAML
41 lines
1.3 KiB
YAML
name: gatk4_learnreadorientationmodel
|
|
description: |
|
|
Uses f1r2 counts collected during mutect2 to Learn the prior probability of read orientation artifacts
|
|
keywords:
|
|
- gatk4
|
|
- learnreadorientationmodel
|
|
- readorientationartifacts
|
|
- mutect2
|
|
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' ]
|
|
- f1r2:
|
|
type: list
|
|
description: list of f1r2 files to be used as input.
|
|
pattern: "*.f1r2.tar.gz"
|
|
|
|
output:
|
|
- artifactprior:
|
|
type: file
|
|
description: file containing artifact-priors to be used by filtermutectcalls
|
|
pattern: "*.tar.gz"
|
|
- versions:
|
|
type: file
|
|
description: File containing software versions
|
|
pattern: "versions.yml"
|
|
|
|
authors:
|
|
- "@GCJMackenzie"
|