mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-12-23 11:38:17 +00:00
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
|
|
|
|
nextflow.enable.dsl = 2
|
|
|
|
include { LAST_POSTMASK } from '../../../../software/last/postmask/main.nf' addParams( options: [suffix:'.postmask'] )
|
|
|
|
workflow test_last_postmask {
|
|
|
|
input = [ [ id:'contigs.genome' ], // meta map
|
|
file(params.test_data['sarscov2']['genome']['contigs_genome_maf_gz'], checkIfExists: true) ]
|
|
|
|
LAST_POSTMASK ( input )
|
|
}
|