nf-core_modules/software/bowtie/align/meta.yml
2020-12-17 07:33:44 +01:00

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2.1 KiB
YAML

name: bowtie_align
description: Align reads to a reference genome using bowtie
keywords:
- align
- fasta
- genome
- reference
tools:
- bowtie:
description: |
bowtie is a software package for mapping DNA sequences against
a large reference genome, such as the human genome.
homepage: http://bowtie-bio.sourceforge.net/index.shtml
documentation: http://bowtie-bio.sourceforge.net/manual.shtml
arxiv: arXiv:1303.3997
params:
- outdir:
type: string
description: |
The pipeline's output directory. By default, the module will
output files into `$params.outdir/<SOFTWARE>`
- publish_dir_mode:
type: string
description: |
Value for the Nextflow `publishDir` mode parameter.
Available: symlink, rellink, link, copy, copyNoFollow, move.
- enable_conda:
type: boolean
description: |
Run the module with Conda using the software specified
via the `conda` directive
- singularity_pull_docker_container:
type: boolean
description: |
Instead of directly downloading Singularity images for use with Singularity,
force the workflow to pull and convert Docker containers instead.
- save_unaligned:
type: boolean
description: Save unaligned reads
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.
- index:
type: file
description: Bowtie genome index files
pattern: "*.ebwt"
output:
- sam:
type: file
description: Output SAM file containing read alignments
pattern: "*.{sam}"
- version:
type: file
description: File containing software version
pattern: "*.{version.txt}"
authors:
- "@kevinmenden"