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c8168bc351
* Update LAST to version 1238. * Update functions.nf to the latest devel version. * Update test MD5sums after updating software version. * Make portable on MacOS * Allow input alignments to be uncompressed. While the strategy in this family of modules is to make all inputs and outputs compressed, this change might be useful to some users. As of LAST 2138, `last/split` does not allow its input to be compressed. * Search for .des file, that is guaranteed to be unique. Some LAST indexes have more than one .bck file and it makes the name detection crash. In this commit, I also standardise how the names are detected. * Use value input channel and optional output channels to handle formats. As discussed on Slack, it is preferred to use a value input channel instead of sneaking options through `params.args2` or `params.format` as we did. Likewise, optional output channels with clearly labeled format are preferred to 'catch-all' wildcards.
79 lines
2.3 KiB
YAML
79 lines
2.3 KiB
YAML
name: last_mafconvert
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description: Converts MAF alignments in another format.
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keywords:
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- LAST
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- convert
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- alignment
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- MAF
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tools:
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- last:
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description: LAST finds & aligns related regions of sequences.
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homepage: https://gitlab.com/mcfrith/last
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documentation: https://gitlab.com/mcfrith/last/-/blob/main/doc/
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tool_dev_url: https://gitlab.com/mcfrith/last
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doi: ""
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licence: ['GPL v3-or-later']
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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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- maf:
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type: file
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description: Multiple Aligment Format (MAF) file, optionally compressed with gzip
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pattern: "*.{maf.gz,maf}"
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- format:
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type: value
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description: Output format (one of axt, blast, blasttab, chain, gff, html, psl, sam, or tab)
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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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- 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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- axt_gz:
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type: file
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description: Gzipped pairwise alignment in Axt (Blastz) format (optional)
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pattern: "*.axt.gz"
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- blast_gz:
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type: file
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description: Gzipped pairwise alignment in blast format (optional)
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pattern: "*.blast.gz"
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- blasttab_gz:
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type: file
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description: Gzipped pairwise alignment in blasttab format (optional)
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pattern: "*.blasttab.gz"
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- chain_gz:
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type: file
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description: Gzipped pairwise alignment in UCSC chain format (optional)
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pattern: "*.chain.gz"
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- gff_gz:
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type: file
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description: Gzipped pairwise alignment in GFF format (optional)
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pattern: "*.gff.gz"
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- html_gz:
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type: file
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description: Gzipped pairwise alignment in HTML format (optional)
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pattern: "*.html.gz"
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- psl_gz:
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type: file
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description: Gzipped pairwise alignment in PSL (BLAT) format (optional)
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pattern: "*.psl.gz"
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- SAM:
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type: file
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description: Gzipped pairwise alignment in SAM format (optional)
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pattern: "*.sam.gz"
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- tab:
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type: file
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description: Gzipped pairwise alignment in TAB format (optional)
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pattern: "*.tab.gz"
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authors:
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- "@aleksandrabliznina"
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