nf-core_modules/tests/modules/dragmap/align/main.nf

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#!/usr/bin/env nextflow
nextflow.enable.dsl = 2
include { DRAGMAP_HASHTABLE } from '../../../../modules/dragmap/hashtable/main.nf'
include { DRAGMAP_ALIGN } from '../../../../modules/dragmap/align/main.nf'
workflow test_dragmap_align_single_end {
input = [
[ id:'test', single_end:true ], // meta map
[
file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true)
]
]
fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
DRAGMAP_HASHTABLE ( fasta )
DRAGMAP_ALIGN ( input, DRAGMAP_HASHTABLE.out.hashmap, false )
}
workflow test_dragmap_align_single_end_sort {
input = [
[ id:'test', single_end:true ], // meta map
[
file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true)
]
]
fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
DRAGMAP_HASHTABLE ( fasta )
DRAGMAP_ALIGN ( input, DRAGMAP_HASHTABLE.out.hashmap, true )
}
workflow test_dragmap_align_paired_end {
input = [
[ id:'test', single_end:false ], // meta map
[
file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true)
]
]
fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
DRAGMAP_HASHTABLE ( fasta )
DRAGMAP_ALIGN ( input, DRAGMAP_HASHTABLE.out.hashmap, false )
}
workflow test_dragmap_align_paired_end_sort {
input = [
[ id:'test', single_end:false ], // meta map
[
file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true)
]
]
fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
DRAGMAP_HASHTABLE ( fasta )
DRAGMAP_ALIGN ( input, DRAGMAP_HASHTABLE.out.hashmap, true )
}