nf-core_modules/tests/modules/samtools/ampliconclip/main.nf

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#!/usr/bin/env nextflow
nextflow.enable.dsl = 2
include { SAMTOOLS_AMPLICONCLIP } from '../../../../modules/samtools/ampliconclip/main.nf' addParams([:])
workflow test_samtools_ampliconclip_no_stats_no_rejects {
input = [
[ id:'test', single_end:false ],
file(params.test_data['sarscov2']['illumina']['test_paired_end_bam'], checkIfExists: true)
]
bed = file(params.test_data['sarscov2']['genome']['test_bed'], checkIfExists: true)
save_cliprejects = false
save_clipstats = false
SAMTOOLS_AMPLICONCLIP ( input, bed, save_cliprejects, save_clipstats )
}
workflow test_samtools_ampliconclip_no_stats_with_rejects {
input = [
[ id:'test', single_end:false ],
file(params.test_data['sarscov2']['illumina']['test_paired_end_bam'], checkIfExists: true)
]
bed = file(params.test_data['sarscov2']['genome']['test_bed'], checkIfExists: true)
save_cliprejects = true
save_clipstats = false
SAMTOOLS_AMPLICONCLIP ( input, bed, save_cliprejects, save_clipstats )
}
workflow test_samtools_ampliconclip_with_stats_with_rejects {
input = [
[ id:'test', single_end:false ],
file(params.test_data['sarscov2']['illumina']['test_paired_end_bam'], checkIfExists: true)
]
bed = file(params.test_data['sarscov2']['genome']['test_bed'], checkIfExists: true)
save_cliprejects = true
save_clipstats = true
SAMTOOLS_AMPLICONCLIP ( input, bed, save_cliprejects, save_clipstats )
}