nf-core_modules/tests/software/bowtie/main.nf

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#!/usr/bin/env nextflow
nextflow.enable.dsl = 2
include { BOWTIE_INDEX } from '../../../software/bowtie/index/main.nf' addParams( options: [:] )
include { BOWTIE_ALIGN } from '../../../software/bowtie/align/main.nf' addParams( options: [:] )
workflow test_bowtie_index {
fasta = file("${launchDir}/tests/data/fasta/E_coli/NC_010473.fa", checkIfExists: true)
BOWTIE_INDEX ( fasta )
}
workflow test_bowtie_alignment_single_end {
fasta = file("${launchDir}/tests/data/fasta/E_coli/NC_010473.fa", checkIfExists: true)
BOWTIE_INDEX ( fasta )
def input = []
input = [ [ id:'test', single_end:true ], // meta map
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[ file("${launchDir}/tests/data/fastq/rna/test_R1.fastq.gz", checkIfExists: true) ] ]
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BOWTIE_ALIGN ( input, BOWTIE_INDEX.out.index )
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}
workflow test_bowtie_alignment_paired_end {
fasta = file("${launchDir}/tests/data/fasta/E_coli/NC_010473.fa", checkIfExists: true)
BOWTIE_INDEX ( fasta )
def input = []
input = [ [ id:'test', single_end:false ], // meta map
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[ file("${launchDir}/tests/data/fastq/rna/test_R1.fastq.gz", checkIfExists: true),
file("${launchDir}/tests/data/fastq/rna/test_R2.fastq.gz", checkIfExists: true) ] ]
BOWTIE_ALIGN ( input, BOWTIE_INDEX.out.index )
}