nf-core_modules/software/seqwish/induce/meta.yml

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2021-02-17 17:19:47 +00:00
name: seqwish_induce
description: Induce a variation graph in GFA format from alignments in PAF format
keywords:
- induce
- paf
- gfa
- graph
- variation graph
tools:
- seqwish:
description: |
seqwish implements a lossless conversion from pairwise alignments between
sequences to a variation graph encoding the sequences and their alignments.
homepage: https://github.com/ekg/seqwish
documentation: https://github.com/ekg/seqwish
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.
input:
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- paf:
type: file
description: PAF file of alignments
pattern: "*.{paf,paf.gz}"
- fasta:
type: file
description: FASTA file used to generate alignments
pattern: "*.{fa,fa.gz,fasta,fasta.gz}"
output:
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- gfa:
type: file
description: Variation graph in GFA1 format
pattern: "*.{gfa}"
- version:
type: file
description: File containing software version
pattern: "*.{version.txt}"
authors:
- "@heuermh"