name: last_mafconvert description: Converts MAF alignments in another format. keywords: - LAST - convert - alignment - MAF tools: - last: description: LAST finds & aligns related regions of sequences. homepage: https://gitlab.com/mcfrith/last documentation: https://gitlab.com/mcfrith/last/-/blob/main/doc/ tool_dev_url: https://gitlab.com/mcfrith/last doi: "" licence: ['GPL v3-or-later'] input: - meta: type: map description: | Groovy Map containing sample information e.g. [ id:'test', single_end:false ] - maf: type: file description: Multiple Aligment Format (MAF) file, optionally compressed with gzip pattern: "*.{maf.gz,maf}" - format: type: value description: Output format (one of axt, blast, blasttab, chain, gff, html, psl, sam, or tab) output: - meta: type: map description: | Groovy Map containing sample information e.g. [ id:'test', single_end:false ] - version: type: file description: File containing software version pattern: "versions.yml" - axt_gz: type: file description: Gzipped pairwise alignment in Axt (Blastz) format (optional) pattern: "*.axt.gz" - blast_gz: type: file description: Gzipped pairwise alignment in blast format (optional) pattern: "*.blast.gz" - blasttab_gz: type: file description: Gzipped pairwise alignment in blasttab format (optional) pattern: "*.blasttab.gz" - chain_gz: type: file description: Gzipped pairwise alignment in UCSC chain format (optional) pattern: "*.chain.gz" - gff_gz: type: file description: Gzipped pairwise alignment in GFF format (optional) pattern: "*.gff.gz" - html_gz: type: file description: Gzipped pairwise alignment in HTML format (optional) pattern: "*.html.gz" - psl_gz: type: file description: Gzipped pairwise alignment in PSL (BLAT) format (optional) pattern: "*.psl.gz" - SAM: type: file description: Gzipped pairwise alignment in SAM format (optional) pattern: "*.sam.gz" - tab: type: file description: Gzipped pairwise alignment in TAB format (optional) pattern: "*.tab.gz" authors: - "@aleksandrabliznina"