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16d20a7cc4
* New last/lastdb module to index sequences before alignment. The `lastdb` command creates a sequence index for the LAST aligner (https://gitlab.com/mcfrith/last). Input can be in FASTA or FASTQ format, and compression is handled automagically. DNA or protein sequences can be indexed. The sequence index is a collection of files sharing the same basename. This module sets the basename to the sample identifier (`$meta.id`) and creates the index in a directory always called `lastdb`. The module's output channel then conveys a copy of the metadata and the path to the `lastdb` directory. Other modules will follow (see Issue #464). The LAST aligner can align proteins to proteins, DNA to DNA and can translate DNA align to proteins. * Remove trailing whitespace. * Apply suggestions from code review Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update as suggested in PR. * Attempt to pass linting. Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
41 lines
1.1 KiB
YAML
41 lines
1.1 KiB
YAML
name: last_lastdb
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description: Prepare sequences for subsequent alignment with lastal.
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keywords:
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- LAST
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- index
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- fasta
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- fastq
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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/lastdb.rst
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tool_dev_url: https://gitlab.com/mcfrith/last
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doi: ""
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licence: ['GPL-3.0-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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- fastx:
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type: file
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description: >
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Sequence file in FASTA or FASTQ format.
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May be compressed with gzip.
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pattern: "*.{fasta,fasta.gz,fastq,fastq.gz}"
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output:
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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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- index:
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type: directory
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description: directory containing the files of the LAST index
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pattern: "lastdb/"
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authors:
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- "@charles-plessy"
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