mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-12-22 11:08:17 +00:00
3c8ca3fec4
* files created for createsompon, script written, meta written, still needs tests * updated to 2.0.0 method input, however this requires a genomicsDB input now * script finished, meta yaml updated. Tests working locally, test yaml made, needs genomicsdb example on nf-core to run repository tests * versions updated, issue with test data not able to download directory * updated tests to include repo-side data * Apply suggestions from code review * Update modules/gatk4/createsomaticpanelofnormals/main.nf Co-authored-by: GCJMackenzie <gavin.mackenzie@nibsc.org> Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
55 lines
1.7 KiB
YAML
55 lines
1.7 KiB
YAML
name: gatk4_createsomaticpanelofnormals
|
|
description: Create a panel of normals contraining germline and artifactual sites for use with mutect2.
|
|
keywords:
|
|
- gatk4
|
|
- createsomaticpanelofnormals
|
|
- panelofnormals
|
|
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']
|
|
- genoomicsdb:
|
|
type: directory
|
|
description: genomicsDB workspace that contains the samples to create the somatic panel of normals with.
|
|
pattern: "*_genomicsDBworkspace"
|
|
- fasta:
|
|
type: file
|
|
description: The reference fasta file
|
|
pattern: "*.fasta"
|
|
- fastaidx:
|
|
type: file
|
|
description: Index of reference fasta file
|
|
pattern: "fasta.fai"
|
|
- dict:
|
|
type: file
|
|
description: GATK sequence dictionary
|
|
pattern: "*.dict"
|
|
|
|
output:
|
|
- vcf:
|
|
type: file
|
|
description: panel of normal as compressed vcf file
|
|
pattern: "*.vcf.gz"
|
|
- tbi:
|
|
type: file
|
|
description: Index of vcf file
|
|
pattern: "*vcf.gz.tbi"
|
|
- versions:
|
|
type: file
|
|
description: File containing software versions
|
|
pattern: "versions.yml"
|
|
|
|
authors:
|
|
- "@GCJMackenzie"
|