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0745213729
* 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.
13 lines
398 B
Text
13 lines
398 B
Text
#!/usr/bin/env nextflow
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nextflow.enable.dsl = 2
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include { LAST_MAFCONVERT } from '../../../../software/last/mafconvert/main.nf' addParams( options: ['format':'psl'] )
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workflow test_last_mafconvert {
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input = [ [ id:'contigs.genome' ], // meta map
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file(params.test_data['sarscov2']['genome']['contigs_genome_maf_gz'], checkIfExists: true) ]
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LAST_MAFCONVERT ( input )
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}
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