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meta.yml
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meta.yml
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name: fgbio_fastqtobam
description: |
Using the fgbio tools, converts FASTQ files sequenced into unaligned BAM or CRAM files possibly moving the UMI barcode into the RX field of the reads
keywords:
- unaligned
- bam
- cram
tools:
- fgbio:
description: A set of tools for working with genomic and high throughput sequencing data, including UMIs
homepage: http://fulcrumgenomics.github.io/fgbio/
documentation: http://fulcrumgenomics.github.io/fgbio/tools/latest/
tool_dev_url: https://github.com/fulcrumgenomics/fgbio
licence: ["MIT"]
input:
- reads:
type: file
description: pair of reads to be converted into BAM file
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.yml}"
- bam:
type: file
description: Unaligned, unsorted BAM file
pattern: "*.{bam}"
- cram:
type: file
description: Unaligned, unsorted CRAM file
pattern: "*.{cram}"
authors:
- "@lescai"
- "@matthdsm"
- "@nvnieuwk"
maintainers:
- "@lescai"
- "@matthdsm"
- "@nvnieuwk"