nf-core_modules/modules/samtools/fastq/meta.yml

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name: samtools_fastq
description: Converts a SAM/BAM/CRAM file to FASTQ
keywords:
- bam
- sam
- cram
- fastq
tools:
- samtools:
description: |
SAMtools is a set of utilities for interacting with and post-processing
short DNA sequence read alignments in the SAM, BAM and CRAM formats, written by Heng Li.
These files are generated as output by short read aligners like BWA.
homepage: http://www.htslib.org/
documentation: hhttp://www.htslib.org/doc/samtools.html
doi: 10.1093/bioinformatics/btp352
input:
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- bam:
type: file
description: BAM/CRAM/SAM file
pattern: "*.{bam,cram,sam}"
output:
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- fasta:
type: file
description: compressed FASTQ file
pattern: "*.fastq.gz"
- versions:
type: file
description: File containing software versions
pattern: "versions.yml"
authors:
- "@suzannejin"