nf-core_modules/tests/modules/mosdepth/main.nf

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#!/usr/bin/env nextflow
nextflow.enable.dsl = 2
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include { MOSDEPTH } from '../../../modules/mosdepth/main.nf'
include { MOSDEPTH as MOSDEPTH_FAIL } from '../../../modules/mosdepth/main.nf'
include { MOSDEPTH as MOSDEPTH_WINDOW } from '../../../modules/mosdepth/main.nf'
include { MOSDEPTH as MOSDEPTH_THRESHOLD } from '../../../modules/mosdepth/main.nf'
include { MOSDEPTH as MOSDEPTH_QUANTIZED } from '../../../modules/mosdepth/main.nf'
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workflow test_mosdepth {
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input = [
[ id:'test', single_end:true ],
file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true),
file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true)
]
MOSDEPTH ( input, [], [] )
}
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workflow test_mosdepth_bed {
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input = [
[ id:'test', single_end:true ],
file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true),
file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true)
]
bed = file(params.test_data['homo_sapiens']['genome']['genome_bed'], checkIfExists: true)
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MOSDEPTH ( input, bed, [] )
}
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workflow test_mosdepth_cram {
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input = [
[ id:'test', single_end:true ],
file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram'], checkIfExists: true),
file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram_crai'], checkIfExists: true)
]
fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
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MOSDEPTH ( input, [], fasta )
}
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workflow test_mosdepth_cram_bed {
input = [
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[ id:'test', single_end:true ],
file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram'], checkIfExists: true),
file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram_crai'], checkIfExists: true)
]
bed = file(params.test_data['homo_sapiens']['genome']['genome_bed'], checkIfExists: true)
fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
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MOSDEPTH ( input, bed, fasta )
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}
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workflow test_mosdepth_window {
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input = [
[ id:'test', single_end:true ],
file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true),
file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true)
]
bed = file(params.test_data['homo_sapiens']['genome']['genome_bed'], checkIfExists: true)
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MOSDEPTH_WINDOW ( input, [], [] )
}
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workflow test_mosdepth_quantized {
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input = [
[ id:'test', single_end:true ],
file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true),
file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true)
]
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MOSDEPTH_QUANTIZED ( input, [], [] )
}
workflow test_mosdepth_thresholds {
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input = [
[ id:'test', single_end:true ],
file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true),
file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true)
]
bed = file(params.test_data['homo_sapiens']['genome']['genome_bed'], checkIfExists: true)
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MOSDEPTH_THRESHOLD ( input, bed, [] )
}
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workflow test_mosdepth_fail {
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input = [
[ id:'test', single_end:true ],
file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true),
file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true)
]
bed = file(params.test_data['homo_sapiens']['genome']['genome_bed'], checkIfExists: true)
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MOSDEPTH_FAIL ( input, bed, [] )
}