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42 lines
1.6 KiB
Text
42 lines
1.6 KiB
Text
#!/usr/bin/env nextflow
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nextflow.enable.dsl = 2
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include { BISMARK_GENOMEPREPARATION } from '../../../../software/bismark/genomepreparation/main.nf' addParams( options: [:] )
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include { BISMARK_ALIGN as BISMARK_ALIGN_SE } from '../../../../software/bismark/align/main.nf' addParams( options: [ publish_dir:'test_single_end' ] )
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include { BISMARK_ALIGN as BISMARK_ALIGN_PE } from '../../../../software/bismark/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_bismark_align_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("${launchDir}/tests/data/genomics/sarscov2/fastq/test_methylated_1.fastq.gz", checkIfExists: true) ] ]
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BISMARK_GENOMEPREPARATION ( file("${launchDir}/tests/data/genomics/sarscov2/fasta/test_genome.fasta", checkIfExists: true) )
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BISMARK_ALIGN_SE (
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input,
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BISMARK_GENOMEPREPARATION.out.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_bismark_align_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("${launchDir}/tests/data/genomics/sarscov2/fastq/test_methylated_1.fastq.gz", checkIfExists: true),
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file("${launchDir}/tests/data/genomics/sarscov2/fastq/test_methylated_2.fastq.gz", checkIfExists: true) ] ]
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BISMARK_GENOMEPREPARATION ( file("${launchDir}/tests/data/genomics/sarscov2/fasta/test_genome.fasta", checkIfExists: true) )
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BISMARK_ALIGN_PE (
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input,
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BISMARK_GENOMEPREPARATION.out.index
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)
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}
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