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 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 GFA 1.0 format pattern: "*.{gfa}" - versions: type: file description: File containing software versions pattern: "versions.yml" authors: - "@heuermh"