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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>
23 lines
599 B
Text
23 lines
599 B
Text
#!/usr/bin/env nextflow
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nextflow.enable.dsl = 2
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include { LAST_LASTDB } from '../../../../software/last/lastdb/main.nf' addParams( options: ['args': '-Q0'] )
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workflow test_last_lastdb {
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input = [ [ id:'test' ], // meta map
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file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
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]
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LAST_LASTDB ( input )
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}
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workflow test_last_lastdb_gzipped_input {
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input = [ [ id:'test' ], // meta map
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file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true)
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]
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LAST_LASTDB ( input )
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}
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