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7afb962f0b
* 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 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>
80 lines
3 KiB
YAML
80 lines
3 KiB
YAML
name: gatk4_genomicsdbimport
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description: merge GVCFs from multiple samples. For use in joint genotyping or somatic panel of normal creation.
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keywords:
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- gatk4
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- genomicsdbimport
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- genomicsdb
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- panelofnormalscreation
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- jointgenotyping
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tools:
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- gatk4:
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description: |
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Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools
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with a primary focus on variant discovery and genotyping. Its powerful processing engine
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and high-performance computing features make it capable of taking on projects of any size.
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homepage: https://gatk.broadinstitute.org/hc/en-us
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documentation: https://gatk.broadinstitute.org/hc/en-us/categories/360002369672s
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doi: 10.1158/1538-7445.AM2017-3590
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input:
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- meta:
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type: map
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description: |
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Groovy Map containing sample information
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e.g. [ id:'test']
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- vcf:
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type: list
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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.
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pattern: "*.vcf.gz"
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- tbi:
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type: list
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description: list of tbi files that match with the input vcf files
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pattern: "*.vcf.gz_tbi"
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- wspace:
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type: path
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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.
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pattern: "/path/to/existing/gendb"
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- intervalfile:
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type: file
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description: file containing the intervals to be used when creating the genomicsdb
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pattern: "*.interval_list"
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- intervalval:
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type: string
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description: if an intervals file has not been spcified, the value enetered here will be used as an interval via the "-L" argument
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pattern: "example: chr1:1000-10000"
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- run_intlist:
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type: boolean
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description: Specify whether to run get interval list mode, this option cannot be specified at the same time as run_updatewspace.
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pattern: "true/false"
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- run_updatewspace:
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type: boolean
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description: Specify whether to run update genomicsdb mode, this option takes priority over run_intlist.
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pattern: "true/false"
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- input_map:
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type: boolean
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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.
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pattern: "*.sample_map"
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output:
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- genomicsdb:
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type: directory
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description: Directory containing the files that compose the genomicsdb workspace, this is only output for create mode, as update changes an existing db
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pattern: "*_genomicsdb"
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- intervallist:
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type: file
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description: File containing the intervals used to generate the genomicsdb, only created by get intervals mode.
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pattern: "*.interval_list"
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- versions:
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type: file
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description: File containing software versions
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pattern: "versions.yml"
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authors:
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- "@GCJMackenzie"
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