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ca321ce69d
The `last-postmask` tool distributed with [LAST](https://gitlab.com/mcfrith/last) filters alignments in a MAF file to remove those with too many masked (lower-case) positions compared with their score. As other filter modules like `last/split`, its output file risks to overwrite its input file as their names are constructed from the sample ID when multiple filters are chained in the pipeline. I added a check that gives a clearer error message in this case. Please let me know what you think about; I can add this test to the existing LAST modules as well. This new module is part of the work discribed in Issue #464. During this development, we fix the version of LAST to 1219 to ensure consistency. We will upgrade it later.
13 lines
390 B
Text
13 lines
390 B
Text
#!/usr/bin/env nextflow
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nextflow.enable.dsl = 2
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include { LAST_POSTMASK } from '../../../../software/last/postmask/main.nf' addParams( options: [suffix:'.postmask'] )
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workflow test_last_postmask {
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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_POSTMASK ( input )
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}
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