nf-core_modules/software/gatk4/fastqtosam/meta.yml

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name: gatk4_fastqtosam
description: Converts FastQ file to 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: ['BSD-3-clause']
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 ]
- version:
type: file
description: File containing software version
pattern: "*.{version.txt}"
- bam:
type: file
description: Converted BAM file
pattern: "*.bam"
authors:
- "@ntoda03"