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54 lines
2.6 KiB
Text
54 lines
2.6 KiB
Text
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#!/usr/bin/env nextflow
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nextflow.enable.dsl = 2
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include { BWAMETH_ALIGN as BWAMETH_ALIGN_SE } from '../../../../software/bwameth/align/main.nf' addParams( options: [ publish_dir:'test_single_end' ] )
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include { BWAMETH_ALIGN as BWAMETH_ALIGN_PE } from '../../../../software/bwameth/align/main.nf' addParams( options: [ publish_dir:'test_paired_end' ] )
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/*
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* Test with single-end data
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*/
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workflow test_bwameth_align_single_end {
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def input = []
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def index = []
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input = [ [ id:'test', single_end:true ], // meta map
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[ file("${launchDir}/tests/data/fastq/methylated_dna/Ecoli_10K_methylated_R1.fastq.gz", checkIfExists: true) ] ]
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index = [ file("${launchDir}/tests/data/index/E_coli/bwameth/NC_010473.fa.bwameth.c2t", checkIfExists: true),
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file("${launchDir}/tests/data/index/E_coli/bwameth/NC_010473.fa.bwameth.c2t.amb", checkIfExists: true),
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file("${launchDir}/tests/data/index/E_coli/bwameth/NC_010473.fa.bwameth.c2t.ann", checkIfExists: true),
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file("${launchDir}/tests/data/index/E_coli/bwameth/NC_010473.fa.bwameth.c2t.bwt", checkIfExists: true),
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file("${launchDir}/tests/data/index/E_coli/bwameth/NC_010473.fa.bwameth.c2t.sa", checkIfExists: true),
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file("${launchDir}/tests/data/index/E_coli/bwameth/NC_010473.fa.bwameth.c2t.pac", checkIfExists: true) ]
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BWAMETH_ALIGN_SE (
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input,
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index
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)
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}
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/*
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* Test with paired-end data
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*/
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workflow test_bwameth_align_paired_end {
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def input = []
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def index = []
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input = [ [ id:'test', single_end:false ], // meta map
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[ file("${launchDir}/tests/data/fastq/methylated_dna/Ecoli_10K_methylated_R1.fastq.gz", checkIfExists: true),
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file("${launchDir}/tests/data/fastq/methylated_dna/Ecoli_10K_methylated_R2.fastq.gz", checkIfExists: true) ] ]
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index = [ file("${launchDir}/tests/data/index/E_coli/bwameth/NC_010473.fa.bwameth.c2t", checkIfExists: true),
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file("${launchDir}/tests/data/index/E_coli/bwameth/NC_010473.fa.bwameth.c2t.amb", checkIfExists: true),
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file("${launchDir}/tests/data/index/E_coli/bwameth/NC_010473.fa.bwameth.c2t.ann", checkIfExists: true),
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file("${launchDir}/tests/data/index/E_coli/bwameth/NC_010473.fa.bwameth.c2t.bwt", checkIfExists: true),
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file("${launchDir}/tests/data/index/E_coli/bwameth/NC_010473.fa.bwameth.c2t.sa", checkIfExists: true),
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file("${launchDir}/tests/data/index/E_coli/bwameth/NC_010473.fa.bwameth.c2t.pac", checkIfExists: true) ]
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BWAMETH_ALIGN_PE (
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input,
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index
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)
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}
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