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b592cea30b
* New last/train module to train alignment parameters. The last-train command creates a parameter file that will be used by last/lastal module for sequence alignment. It takes indexed sequences and query sequences as input and we use the metadata of both to create an id of the parameter output file. Submission of the LAST modules is discussed in more details in the issue #464. For consistancy, we use LAST version 1219 for this whole development and will upgrade later. * Corrected files according to the nf-core v1.14 standards. * Fixed function.nf file for the last-train module. * Apply suggestions from code review Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Find index name. * Correct after the input channels were changed. * Use double underscore as a name separator. Single underscores can happen in ids, therefore, we would like to keep two underscores. * Remove extra spaces. * Fixed the passing of the "score matrix" line. * Apply suggestions from code review Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update software/last/train/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
48 lines
1.2 KiB
YAML
48 lines
1.2 KiB
YAML
name: last_train
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description: Find suitable score parameters for sequence alignment
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keywords:
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- LAST
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- train
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- fastq
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- fasta
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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/last-train.rst
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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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- 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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- 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: FASTA/FASTQ file
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pattern: "*.{fasta,fastq}"
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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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- param_file:
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type: file
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description: Trained parameter file
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pattern: "*.par"
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authors:
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- "@aleksandrabliznina"
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