nf-core_modules/tests/modules/samtools/view/main.nf
2022-05-06 15:34:18 +02:00

33 lines
1.1 KiB
Text

#!/usr/bin/env nextflow
nextflow.enable.dsl = 2
include { SAMTOOLS_VIEW } from '../../../../modules/samtools/view/main.nf'
workflow test_samtools_view {
input = [ [ id:'test', single_end:false ], // meta map
file(params.test_data['sarscov2']['illumina']['test_paired_end_bam'], checkIfExists: true),
[]
]
SAMTOOLS_VIEW ( input, [] )
}
workflow test_samtools_view_cram {
input = [ [ id: 'test' ], // meta map
file(params.test_data['homo_sapiens']['illumina']['test_paired_end_recalibrated_sorted_cram'], checkIfExists: true),
file(params.test_data['homo_sapiens']['illumina']['test_paired_end_recalibrated_sorted_cram_crai'], checkIfExists: true)
]
fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
SAMTOOLS_VIEW ( input, fasta )
}
workflow test_samtools_view_stubs {
input = [ [ id:'test', single_end:false ], // meta map
file(params.test_data['sarscov2']['illumina']['test_paired_end_bam'], checkIfExists: true),
[]
]
SAMTOOLS_VIEW ( input, [] )
}