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* add atlas/pmd * update atlas/pmd tests * Add atlas/PMD module * Remove comment * Run Prettier * Incorporate Review by @jfy133 Co-authored-by: maxibor <maxime.borry@gmail.com> Co-authored-by: Maxime Borry <maxibor@users.noreply.github.com> Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
19 lines
694 B
Text
19 lines
694 B
Text
#!/usr/bin/env nextflow
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nextflow.enable.dsl = 2
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include { ATLAS_PMD } from '../../../../modules/atlas/pmd/main.nf'
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workflow test_atlas_pmd {
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input = [
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[ id:'test', single_end:false ], // meta map
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file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true),
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file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true),
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[]
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]
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fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
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fai = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)
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ATLAS_PMD ( input, fasta, fai )
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}
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