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1d668eefa2
* Update seqwish to version 0.7.2 * seqwish can work with a comma-separated list of PAFs * level with nf-core/modules master branch * update seqwish/induce to v0.7.6 * add pangenome test data * test seqwish/induce v0.7.6 with pangenomics test data * we already have pointed to the pangenomics test data sets * update paths to test data * add path to bgzipped fa, gzi, fai * remove one tab * remove one tab * actually execute the 2nd test * try to fix versions.yml * pangenomic tests can be run in their own subworkflow * maybe the csv input is the problem * remove space as suggested by Rike * csv input was not the problem * update test.yml * typo * enable pangenome tests * add md5sum for pangenomic test * Update tests/modules/seqwish/induce/test.yml Co-authored-by: Gisela Gabernet <gisela.gabernet@gmail.com> * PAF input is a list of files * beautify comment Co-authored-by: Michael L Heuer <heuermh@acm.org> Co-authored-by: Gisela Gabernet <gisela.gabernet@gmail.com> Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com>
47 lines
1.3 KiB
YAML
47 lines
1.3 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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licence: ["MIT"]
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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: list
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description: comma-separated PAF file(s) of alignments, single entry allowed
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pattern: "[*.{paf,paf.gz},*.{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 GFA 1.0 format
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pattern: "*.{gfa}"
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- versions:
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type: file
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description: File containing software versions
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pattern: "versions.yml"
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authors:
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- "@heuermh"
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