nf-core_modules/modules/gatk4/fastqtosam/meta.yml
Edmund Miller f080015754
Prettier (#1405)
* 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>
2022-03-18 14:27:50 +01:00

47 lines
1.4 KiB
YAML

name: gatk4_fastqtosam
description: Converts FastQ file to SAM/BAM format
keywords:
- bam
- fastq
- convert
tools:
- gatk4:
description: Genome Analysis Toolkit (GATK4)
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
tool_dev_url: https://github.com/broadinstitute/gatk
doi: "10.1158/1538-7445.AM2017-3590"
licence: ["MIT"]
input:
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- reads:
type: file
description: List of input FastQ files of size 1 and 2 for single-end and paired-end data,
respectively.
pattern: "*.fastq.gz"
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"
- bam:
type: file
description: Converted BAM file
pattern: "*.bam"
authors:
- "@ntoda03"