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https://github.com/MillironX/nf-core_modules.git
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daab0a77dd
* Update main.nf * Update meta.yml * Re-add logos as not staged in a way that works with MultiQC config files * Update main.nf * Remove now unnecessary input channel * Remove unused channel from tests * Update hAMRonization to 1.1.1 and add hAMRonization farGene * Fix hamronizatio ntests * Prettier * Fix fargene linting * Correct file * Fix fargene output * Apply suggestions from code review Co-authored-by: Jasmin F <73216762+jasmezz@users.noreply.github.com> * Fix summarise tests * Prettier Co-authored-by: Jasmin F <73216762+jasmezz@users.noreply.github.com>
19 lines
669 B
Text
19 lines
669 B
Text
#!/usr/bin/env nextflow
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nextflow.enable.dsl = 2
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include { GUNZIP } from '../../../modules/gunzip/main.nf'
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include { FARGENE } from '../../../modules/fargene/main.nf'
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include { HAMRONIZATION_FARGENE } from '../../../../modules/hamronization/fargene/main.nf'
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workflow test_hamronization_fargene {
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input = [ [ id:'test', single_end:false ], // meta map
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file(params.test_data['bacteroides_fragilis']['illumina']['test1_contigs_fa_gz'], checkIfExists: true) ]
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hmm_model = 'class_a'
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GUNZIP ( input )
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FARGENE ( GUNZIP.out.gunzip, hmm_model )
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HAMRONIZATION_FARGENE ( FARGENE.out.hmm, 'tsv', '0.1', '0.1' )
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}
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