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nf-core_modules/software/last/mafswap/meta.yml

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New module last/mafswap to reorder sequences in alignments (#500) * New module last/mafswap to reorder sequences in alignments The `maf-swap` tool distributed with [LAST](https://gitlab.com/mcfrith/last) reorders sequences in alignment files in Multiple Alignment Format. When run without command-line arguments, it will swap the target and the query sequences. This is useful when turning a many-to-many alignment into a many-to-one and then a one-to-one alignment in conjunction with the `last-split` command (split, swap, split and swap again). The LAST aligner outputs MAF files, but other tools also use this format. As MAF files can be very large (up to hundreds of gigabytes), the module expects its input to be compressed with gzip and will compress its output. This new module is part of the work described in Issue #464. During this development, we fix the version of LAST to 1219 to ensure consistency (hence ignore lint's version warning). * Update MD5 sum. Actually, 7029066c27ac6f5ef18d660d5741979a is the MD5 sum of an empty file compressed with `gzip --no-name`… This happened because I forgot to update the config file after correcting the module… sorry ! * Apply suggestions from code review Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Change name as suggested in pull request. Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-05-19 07:59:23 +00:00
name: last_mafswap
description: Reorder alignments in a MAF file
keywords:
- LAST
- reorder
- 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-3.0-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}"
New module last/mafswap to reorder sequences in alignments (#500) * New module last/mafswap to reorder sequences in alignments The `maf-swap` tool distributed with [LAST](https://gitlab.com/mcfrith/last) reorders sequences in alignment files in Multiple Alignment Format. When run without command-line arguments, it will swap the target and the query sequences. This is useful when turning a many-to-many alignment into a many-to-one and then a one-to-one alignment in conjunction with the `last-split` command (split, swap, split and swap again). The LAST aligner outputs MAF files, but other tools also use this format. As MAF files can be very large (up to hundreds of gigabytes), the module expects its input to be compressed with gzip and will compress its output. This new module is part of the work described in Issue #464. During this development, we fix the version of LAST to 1219 to ensure consistency (hence ignore lint's version warning). * Update MD5 sum. Actually, 7029066c27ac6f5ef18d660d5741979a is the MD5 sum of an empty file compressed with `gzip --no-name`… This happened because I forgot to update the config file after correcting the module… sorry ! * Apply suggestions from code review Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Change name as suggested in pull request. Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-05-19 07:59:23 +00:00
output:
- maf:
type: file
description: Multiple Aligment Format (MAF) file, compressed with gzip
pattern: "*.{maf.gz}"
- version:
type: file
description: File containing software version
pattern: "*.{version.txt}"
authors:
- "@charles-plessy"
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