nf-core_modules/tests/software/minimap2/align/main.nf

25 lines
1,000 B
Text
Raw Normal View History

2021-02-04 19:42:08 +00:00
#!/usr/bin/env nextflow
nextflow.enable.dsl = 2
include { MINIMAP2_ALIGN } from '../../../../software/minimap2/align/main.nf' addParams( options: [:] )
workflow test_minimap2_align_single_end {
input = [ [ id:'test', single_end:true ], // meta map
[ file("${launchDir}/tests/data/genomics/sarscov2/illumina/fastq/test_1.fastq.gz", checkIfExists: true) ]
]
fasta = file("${launchDir}/tests/data/genomics/sarscov2/genome/genome.fasta", checkIfExists: true)
2021-02-04 19:42:08 +00:00
MINIMAP2_ALIGN ( input, fasta )
}
workflow test_minimap2_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("${launchDir}/tests/data/genomics/sarscov2/genome/genome.fasta", checkIfExists: true)
2021-02-04 19:42:08 +00:00
MINIMAP2_ALIGN ( input, fasta )
}