mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-12-23 19:48:16 +00:00
f080015754
* style: Add prettier config files * build: Add prettier vscode extension * ci: Replace markdownlint and yamllint with prettier * style: Run prettier * style: Use indent of 2 for markdown as well https://github.com/nf-core/tools/pull/1470#issuecomment-1071028358 * style: Fix indent * style: Let editorconfig take over tab widths * style: yaml => yml * ci: Run prettier once Co-authored-by: Phil Ewels <phil.ewels@scilifelab.se> Co-authored-by: Phil Ewels <phil.ewels@scilifelab.se>
70 lines
2.3 KiB
YAML
70 lines
2.3 KiB
YAML
name: gatk4_getpileupsummaries
|
|
description: |
|
|
Summarizes counts of reads that support reference, alternate and other alleles for given sites. Results can be used with CalculateContamination. Requires a common germline variant sites file, such as from gnomAD.
|
|
keywords:
|
|
- gatk4
|
|
- getpileupsumaries
|
|
- readcountssummary
|
|
- germlinevariantsites
|
|
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' ]
|
|
- input:
|
|
type: file
|
|
description: BAM/CRAM file to be summarised.
|
|
pattern: "*.{bam,cram}"
|
|
- input_index:
|
|
type: file
|
|
description: BAM/CRAM file index.
|
|
pattern: "*.{bai,crai}"
|
|
- intervals:
|
|
type: file
|
|
description: File containing specified sites to be used for the summary. If this option is not specified, variants file is used instead automatically.
|
|
pattern: "*.interval_list"
|
|
- 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"
|
|
- variants:
|
|
type: file
|
|
description: Population vcf of germline sequencing, containing allele fractions. Is also used as sites file if no separate sites file is specified.
|
|
pattern: "*.vcf.gz"
|
|
- variants_tbi:
|
|
type: file
|
|
description: Index file for the germline resource.
|
|
pattern: "*.vcf.gz.tbi"
|
|
|
|
output:
|
|
- pileup:
|
|
type: file
|
|
description: File containing the pileup summary table.
|
|
pattern: "*.pileups.table"
|
|
- versions:
|
|
type: file
|
|
description: File containing software versions
|
|
pattern: "versions.yml"
|
|
|
|
authors:
|
|
- "@GCJMackenzie"
|