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