mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-11-10 20:23:10 +00:00
e745e167c1
* fix yml formatting * allow fastq.gz and fq.gz as file input, add meta.yml and test * fix yaml files * Revert "allow fastq.gz and fq.gz as file input, add meta.yml and test" This reverts commit 34002d7a7a8c7f7bb4600c3377f35c87849f71a4. * prettier magic! * fix comments for yamllint * remove node version number * fix linting errors Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
67 lines
1.9 KiB
YAML
67 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
|
|
- intervals:
|
|
type: file
|
|
description: Bed file with the genomic regions included in the library (optional)
|
|
- fasta:
|
|
type: file
|
|
description: The reference fasta file
|
|
pattern: "*.fasta"
|
|
- fai:
|
|
type: file
|
|
description: Index of reference fasta file
|
|
pattern: "*.fasta.fai"
|
|
- dict:
|
|
type: file
|
|
description: GATK sequence dictionary
|
|
pattern: "*.dict"
|
|
|
|
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"
|