nf-core_modules/modules/gatk4/baserecalibrator/meta.yml
Harshil Patel e937c7950a
Rename software/ directory to modules/ to re-organise module structure (#567)
* 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
2021-07-07 10:10:18 +01:00

58 lines
1.7 KiB
YAML

name: gatk4_baserecalibrator
description: Generate recalibration table for Base Quality Score Recalibration (BQSR)
keywords:
- sort
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', single_end:false ]
- bam:
type: file
description: BAM file from alignment
pattern: "*.{bam}"
- fasta:
type: file
description: The reference fasta file
- fastaidx:
type: file
description: Index of reference fasta file
- dict:
type: file
description: GATK sequence dictionary
- intervalsBed:
type: file
description: Bed file with the genomic regions included in the library (optional)
- knownSites:
type: file
description: Bed file with the genomic regions included in the library (optional)
output:
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- version:
type: file
description: File containing software version
pattern: "*.{version.txt}"
- table:
type: file
description: Recalibration table from BaseRecalibrator
pattern: "*.{table}"
authors:
- "@yocra3"