nf-core_modules/modules/last/mafconvert/meta.yml
Gregor Sturm 906577873b
Bulk update modules to use versions.yml (#739)
* New functions.nf

* Convert code to create versions.yml

* Update meta.yml

* update output channel

* Fix more meta.yml

* Manually update remaining modules

* remove superflous echo

* Fix misformatted meta.yml files

* Fix yaml, was list instead of dict

* fix version for bcftools

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-09-27 09:41:24 +01:00

79 lines
2.3 KiB
YAML

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"