mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-09-21 07:42:05 +00:00
ac1e6df076
* Make samtools/merge cram compliant * samtools/stats cram compliance * update yml file * samtools/view to deal with crams * Update tests to make sure cram works * also fix tmp dir and min mem in one go * basequalityrecal test for cram + min mem + tmpdir * update haplotypecaller for sarek * update haplotype yml * update markdup to allow multiple bams, take out params to be passed with options.args * remove TODO statement * Remove variable md5sum * add emtpy input to stats module in subworkflows * subworkflows seem to work now on my side * Apply code review Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se> * replace bam with input to be more inclusive * rename everywhere * rename input * remove variable checksum Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se>
64 lines
1.9 KiB
YAML
64 lines
1.9 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
|
|
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}"
|
|
- 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 ]
|
|
- versions:
|
|
type: file
|
|
description: File containing software versions
|
|
pattern: "versions.yml"
|
|
- table:
|
|
type: file
|
|
description: Recalibration table from BaseRecalibrator
|
|
pattern: "*.{table}"
|
|
|
|
authors:
|
|
- "@yocra3"
|
|
- "@FriederikeHanssen"
|