nf-core_modules/modules/gatk4/applybqsr/meta.yml
FriederikeHanssen 3df4fe6085
add freebayes/somatic and update freebayes/germline (#990)
* add freebayes/somatic and update freebayes/germline to new syntax and cram

* add pytest

* update with new freebayes/germline path
2021-10-29 17:05:06 +02:00

64 lines
1.9 KiB
YAML

name: gatk4_applybqsr
description: Apply base quality score recalibration (BQSR) to a bam file
keywords:
- bqsr
- bam
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', single_end:false ]
- input:
type: file
description: BAM/CRAM file from alignment
pattern: "*.{bam,cram}"
- input_index:
type: file
description: BAI/CRAI file from alignment
pattern: "*.{bai,crai}"
- bqsr_table:
type: file
description: Recalibration table from gatk4_baserecalibrator
- 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)
output:
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- versions:
type: file
description: File containing software versions
pattern: "versions.yml"
- bam:
type: file
description: Recalibrated BAM file
pattern: "*.{bam}"
authors:
- "@yocra3"
- "@FriederikeHanssen"