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38 lines
1.2 KiB
Text
38 lines
1.2 KiB
Text
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#!/usr/bin/env nextflow
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nextflow.enable.dsl = 2
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include { MINIMAP2_ALIGN } from '../../../../software/minimap2/align/main.nf' addParams( options: [:] )
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workflow test_minimap2_align_single_end {
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def fasta = file("${launchDir}/tests/data/fasta/E_coli/NC_010473.fa", checkIfExists: true)
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def input = []
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input = [ [ id:'test', single_end:true ], // meta map
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[ file("${launchDir}/tests/data/fastq/rna/test_R1.fastq.gz", checkIfExists: true) ] ]
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MINIMAP2_ALIGN ( input, fasta )
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}
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workflow test_minimap2_align_paired_end {
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def fasta = file("${launchDir}/tests/data/fasta/E_coli/NC_010473.fa", checkIfExists: true)
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def input = []
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input = [ [ id:'test', single_end:false ], // meta map
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[ file("${launchDir}/tests/data/fastq/rna/test_R1.fastq.gz", checkIfExists: true),
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file("${launchDir}/tests/data/fastq/rna/test_R2.fastq.gz", checkIfExists: true) ] ]
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MINIMAP2_ALIGN ( input, fasta )
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}
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workflow test_minimap2_align_pairwise {
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def fasta = file("${launchDir}/tests/data/fasta/E_coli/NC_010473.fa", checkIfExists: true)
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def input = []
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input = [ [ id:'test', single_end:false ], // meta map
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[ fasta ] ]
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MINIMAP2_ALIGN ( input, fasta )
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}
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