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44 lines
1.6 KiB
Text
44 lines
1.6 KiB
Text
#!/usr/bin/env nextflow
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nextflow.enable.dsl = 2
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include { BWA_INDEX } from '../../../software/bwa/index/main.nf' addParams( options: [:] )
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include { BWA_MEM as BWA_MEM_SE } from '../../../software/bwa/mem/main.nf' addParams( options: [ publish_dir:'test_single_end' ] )
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include { BWA_MEM as BWA_MEM_PE } from '../../../software/bwa/mem/main.nf' addParams( options: [ publish_dir:'test_paired_end' ] )
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workflow test_bwa_index {
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BWA_INDEX ( file("${launchDir}/tests/data/fasta/E_coli/NC_010473.fa", checkIfExists: true) )
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}
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/*
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* Test with single-end data
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*/
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workflow test_bwa_mem_single_end {
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def input = []
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input = [ [ id:'test', single_end:true ], // meta map
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[ file("${launchDir}/tests/data/fastq/dna/Ecoli_DNA_R1.fastq.gz", checkIfExists: true) ] ]
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BWA_MEM_SE (
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input,
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file("${launchDir}/tests/data/index/E_coli/bwa/NC_010473.fa.{amb,ann,bwt,pac,sa}", checkIfExists: true),
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file("${launchDir}/tests/data/fasta/E_coli/NC_010473.fa", checkIfExists: true)
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)
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}
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/*
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* Test with paired-end data
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*/
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workflow test_bwa_mem_paired_end {
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def input = []
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input = [ [ id:'test', single_end:false ], // meta map
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[ file("${launchDir}/tests/data/fastq/dna/Ecoli_DNA_R1.fastq.gz", checkIfExists: true),
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file("${launchDir}/tests/data/fastq/dna/Ecoli_DNA_R2.fastq.gz", checkIfExists: true) ] ]
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BWA_MEM_PE (
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input,
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file("${launchDir}/tests/data/index/E_coli/bwa/NC_010473.fa.{amb,ann,bwt,pac,sa}", checkIfExists: true),
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file("${launchDir}/tests/data/fasta/E_coli/NC_010473.fa", checkIfExists: true)
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)
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}
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