nf-core_modules/tests/modules/last/postmask/main.nf

#!/usr/bin/env nextflow

nextflow.enable.dsl = 2

include { LAST_POSTMASK } from '../../../../modules/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 )
}
New module last/postmask to filter alignment files (#526) 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. 2021-06-08 05:14:08 -04:00			`#!/usr/bin/env nextflow`

			`nextflow.enable.dsl = 2`

Rename software/ directory to modules/ to re-organise module structure (#567) * Update README * Rename pytest_software.yml to pytest_modules.yml * Rename main software directory to modules * Remove deprecated modules * Rename tests software to modules * Replace paths for tests in pytest_modules.yml * Replace software with modules in Github Actions * Replace software with modules in main.nf tests * Rename software to modules in test.yml 2021-07-07 05:10:18 -04:00			`include { LAST_POSTMASK } from '../../../../modules/last/postmask/main.nf' addParams( options: [suffix:'.postmask'] )`
New module last/postmask to filter alignment files (#526) 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. 2021-06-08 05:14:08 -04:00
			`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 )`
			`}`