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30 lines
1.1 KiB
Text
30 lines
1.1 KiB
Text
#!/usr/bin/env nextflow
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nextflow.enable.dsl = 2
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include { MINIMAP2_ALIGN } from '../../../../modules/minimap2/align/main.nf'
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workflow test_minimap2_align_single_end {
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input = [ [ id:'test', single_end:true ], // meta map
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[ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true)]
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]
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fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
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bam_format = true
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cigar_paf_format = false
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cigar_bam = false
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MINIMAP2_ALIGN ( input, fasta, bam_format, cigar_paf_format, cigar_bam)
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}
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workflow test_minimap2_align_paired_end {
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input = [ [ id:'test', single_end:false ], // meta map
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[ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
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file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true) ]
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]
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fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
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bam_format = true
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cigar_paf_format = false
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cigar_bam = false
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MINIMAP2_ALIGN ( input, fasta, bam_format, cigar_paf_format, cigar_bam )
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}
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