nf-core_modules/modules/gatk4/genomicsdbimport/meta.yml

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name: gatk4_genomicsdbimport
description: merge GVCFs from multiple samples. For use in joint genotyping or somatic panel of normal creation.
keywords:
- gatk4
- genomicsdbimport
- genomicsdb
- panelofnormalscreation
- jointgenotyping
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']
- vcf:
type: list
description: either a list of vcf files to be used to create or update a genomicsdb, or a file that contains a map to vcf files to be used.
pattern: "*.vcf.gz"
- tbi:
type: list
description: list of tbi files that match with the input vcf files
pattern: "*.vcf.gz_tbi"
- wspace:
type: path
description: path to an existing genomicsdb to be used in update db mode or get intervals mode. This WILL NOT specify name of a new genomicsdb in create db mode.
pattern: "/path/to/existing/gendb"
- intervalfile:
type: file
description: file containing the intervals to be used when creating the genomicsdb
pattern: "*.interval_list"
- intervalval:
type: string
description: if an intervals file has not been spcified, the value enetered here will be used as an interval via the "-L" argument
pattern: "example: chr1:1000-10000"
- run_intlist:
type: boolean
description: Specify whether to run get interval list mode, this option cannot be specified at the same time as run_updatewspace.
pattern: "true/false"
- run_updatewspace:
type: boolean
description: Specify whether to run update genomicsdb mode, this option takes priority over run_intlist.
pattern: "true/false"
- input_map:
type: boolean
description: Specify whether the vcf input is providing a list of vcf file(s) or a single file containing a map of paths to vcf files to be used to create or update a genomicsdb.
pattern: "*.sample_map"
output:
- genomicsdb:
type: directory
description: Directory containing the files that compose the genomicsdb workspace, this is only output for create mode, as update changes an existing db
pattern: "*/$prefix"
- updatedb:
type: directory
description: Directory containing the files that compose the updated genomicsdb workspace, this is only output for update mode, and should be the same path as the input wspace.
pattern: "same/path/as/wspace"
- intervallist:
type: file
description: File containing the intervals used to generate the genomicsdb, only created by get intervals mode.
pattern: "*.interval_list"
- versions:
type: file
description: File containing software versions
pattern: "versions.yml"
authors:
- "@GCJMackenzie"