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67 lines
2.1 KiB
YAML
67 lines
2.1 KiB
YAML
name: seqwish_induce
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description: Induce a variation graph in GFA format from alignments in PAF format
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keywords:
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- induce
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- paf
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- gfa
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- graph
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- variation graph
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tools:
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- seqwish:
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description: |
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seqwish implements a lossless conversion from pairwise alignments between
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sequences to a variation graph encoding the sequences and their alignments.
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homepage: https://github.com/ekg/seqwish
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documentation: https://github.com/ekg/seqwish
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params:
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- outdir:
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type: string
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description: |
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The pipeline's output directory. By default, the module will
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output files into `$params.outdir/<SOFTWARE>`
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- publish_dir_mode:
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type: string
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description: |
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Value for the Nextflow `publishDir` mode parameter.
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Available: symlink, rellink, link, copy, copyNoFollow, move.
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- enable_conda:
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type: boolean
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description: |
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Run the module with Conda using the software specified
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via the `conda` directive
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- singularity_pull_docker_container:
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type: boolean
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description: |
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Instead of directly downloading Singularity images for use with Singularity,
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force the workflow to pull and convert Docker containers instead.
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input:
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- meta:
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type: map
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description: |
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Groovy Map containing sample information
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e.g. [ id:'test', single_end:false ]
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- paf:
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type: file
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description: PAF file of alignments
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pattern: "*.{paf,paf.gz}"
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- fasta:
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type: file
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description: FASTA file used to generate alignments
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pattern: "*.{fa,fa.gz,fasta,fasta.gz}"
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output:
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- meta:
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type: map
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description: |
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Groovy Map containing sample information
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e.g. [ id:'test', single_end:false ]
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- gfa:
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type: file
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description: Variation graph in GFA1 format
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pattern: "*.{gfa}"
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- version:
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type: file
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description: File containing software version
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pattern: "*.{version.txt}"
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authors:
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- "@heuermh"
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