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

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2021-09-20 09:27:34 +00:00
#!/usr/bin/env nextflow
nextflow.enable.dsl = 2
include { BBMAP_INDEX } from '../../../../modules/bbmap/index/main.nf' addParams( options: [:] )
include { BBMAP_ALIGN } from '../../../../modules/bbmap/align/main.nf' addParams( options: [:] )
include { BBMAP_ALIGN as BBMAP_ALIGN_PIGZ } from '../../../../modules/bbmap/align/main.nf' addParams( options: [args: "unpigz=t" ] )
workflow test_bbmap_align_paired_end_fasta_ref {
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)
BBMAP_ALIGN ( input, fasta )
}
workflow test_bbmap_align_paired_end_index_ref {
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)
BBMAP_INDEX ( fasta )
BBMAP_ALIGN ( input, BBMAP_INDEX.out.index )
}
workflow test_bbmap_align_single_end_index_ref {
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)
BBMAP_INDEX ( fasta )
BBMAP_ALIGN ( input, BBMAP_INDEX.out.index )
}
workflow test_bbmap_align_paired_end_index_ref_pigz {
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)
BBMAP_INDEX ( fasta )
BBMAP_ALIGN_PIGZ ( input, BBMAP_INDEX.out.index )
}