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nf-core_modules/modules/last/mafconvert/meta.yml

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New last/mafconvert module to convert MAF alignments. (#527) * New last/mafconvert module to convert MAF alignments. The `maf-convert` tool distributed with [LAST](https://gitlab.com/mcfrith/last) reads alignmnts in [MAF](https://genome-asia.ucsc.edu/FAQ/FAQformat.html#format5) format and converts them in another format (axt, blast, blasttab, chain, gff, html, psl, sam, tab). This new module is part of the work described in Issue #464. During this development, we fix the versiob of LAST to 1219 to ensure consistency. We will upgrade it later. * Delete white space. * Update the function.nf file to the dev version.
2021-06-09 06:38:57 +00:00
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
Update last module (#533) * 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.
2021-06-14 11:27:27 +00:00
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)
New last/mafconvert module to convert MAF alignments. (#527) * New last/mafconvert module to convert MAF alignments. The `maf-convert` tool distributed with [LAST](https://gitlab.com/mcfrith/last) reads alignmnts in [MAF](https://genome-asia.ucsc.edu/FAQ/FAQformat.html#format5) format and converts them in another format (axt, blast, blasttab, chain, gff, html, psl, sam, tab). This new module is part of the work described in Issue #464. During this development, we fix the versiob of LAST to 1219 to ensure consistency. We will upgrade it later. * Delete white space. * Update the function.nf file to the dev version.
2021-06-09 06:38:57 +00:00
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
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 08:41:24 +00:00
pattern: "versions.yml"
Update last module (#533) * 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.
2021-06-14 11:27:27 +00:00
- axt_gz:
New last/mafconvert module to convert MAF alignments. (#527) * New last/mafconvert module to convert MAF alignments. The `maf-convert` tool distributed with [LAST](https://gitlab.com/mcfrith/last) reads alignmnts in [MAF](https://genome-asia.ucsc.edu/FAQ/FAQformat.html#format5) format and converts them in another format (axt, blast, blasttab, chain, gff, html, psl, sam, tab). This new module is part of the work described in Issue #464. During this development, we fix the versiob of LAST to 1219 to ensure consistency. We will upgrade it later. * Delete white space. * Update the function.nf file to the dev version.
2021-06-09 06:38:57 +00:00
type: file
Update last module (#533) * 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.
2021-06-14 11:27:27 +00:00
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"
New last/mafconvert module to convert MAF alignments. (#527) * New last/mafconvert module to convert MAF alignments. The `maf-convert` tool distributed with [LAST](https://gitlab.com/mcfrith/last) reads alignmnts in [MAF](https://genome-asia.ucsc.edu/FAQ/FAQformat.html#format5) format and converts them in another format (axt, blast, blasttab, chain, gff, html, psl, sam, tab). This new module is part of the work described in Issue #464. During this development, we fix the versiob of LAST to 1219 to ensure consistency. We will upgrade it later. * Delete white space. * Update the function.nf file to the dev version.
2021-06-09 06:38:57 +00:00
authors:
- "@aleksandrabliznina"
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