mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-11-14 13:43:09 +00:00
e937c7950a
* Update README * Rename pytest_software.yml to pytest_modules.yml * Rename main software directory to modules * Remove deprecated modules * Rename tests software to modules * Replace paths for tests in pytest_modules.yml * Replace software with modules in Github Actions * Replace software with modules in main.nf tests * Rename software to modules in test.yml
45 lines
1.3 KiB
YAML
45 lines
1.3 KiB
YAML
name: gatk4_mergebamalignment
|
|
description: Merge unmapped with mapped BAM files
|
|
keywords:
|
|
- bam
|
|
- merge
|
|
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']
|
|
- aligned:
|
|
type: file
|
|
description: The aligned bam file
|
|
pattern: "*.{bam}"
|
|
- unaligned:
|
|
type: file
|
|
description: The unmaped bam file
|
|
pattern: "*.{bam}"
|
|
- fasta:
|
|
type: file
|
|
description: The reference fasta file
|
|
- dict:
|
|
type: file
|
|
description: GATK sequence dictionary
|
|
output:
|
|
- bam:
|
|
type: file
|
|
description: The merged bam file
|
|
pattern: "*.bam"
|
|
- version:
|
|
type: file
|
|
description: File containing software version
|
|
pattern: "*.version.txt"
|
|
authors:
|
|
- "@kevinmenden"
|