mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-09-21 15:52:05 +00:00
316aedaaa6
* saving changes to checkout * saving to sort out other branch * removed yml tracking of files that cant be tracked due to directory name changing between runs * test data added, ready for pr * fix eol linting error * Update modules/gatk4/genomicsdbimport/main.nf Co-authored-by: Francesco L <53608000+lescai@users.noreply.github.com> * merging with master * update push to show progress * tests now working untar able to pass data to genomicsdbimport * commit to checkout * tests updated, module reworked to simplify and emit updated gendb * Apply suggestions from code review Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * update meta.yml Priority of input options changed, updated to reflect this * Update test.yml name prefix changed in main script, test.yml updated to reflect this * fix tests due to review changes * bug fixes, multicalling samples and gendb emissions now fixed * Update pytest_modules.yml * Update meta.yml Co-authored-by: GCJMackenzie <gavin.mackenzie@nibsc.org> Co-authored-by: Francesco L <53608000+lescai@users.noreply.github.com> Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> Co-authored-by: Gregor Sturm <mail@gregor-sturm.de>
84 lines
3.2 KiB
YAML
84 lines
3.2 KiB
YAML
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"
|