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30 lines
1.7 KiB
Text
30 lines
1.7 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 } from '../../../../software/bismark/align/main.nf' addParams( options: [:] )
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include { BISMARK_DEDUPLICATE } from '../../../../software/bismark/deduplicate/main.nf' addParams( options: [:] )
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include { BISMARK_METHYLATIONEXTRACTOR } from '../../../../software/bismark/methylationextractor/main.nf' addParams( options: [:] )
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include { BISMARK_SUMMARY } from '../../../../software/bismark/summary/main.nf' addParams( options: [:] )
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workflow test_bismark_summary {
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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 ( input, BISMARK_GENOMEPREPARATION.out.index )
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BISMARK_DEDUPLICATE ( BISMARK_ALIGN.out.bam )
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BISMARK_METHYLATIONEXTRACTOR ( BISMARK_DEDUPLICATE.out.bam, BISMARK_GENOMEPREPARATION.out.index )
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BISMARK_SUMMARY (
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BISMARK_ALIGN.out.bam.collect{ meta, bam -> bam },
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BISMARK_ALIGN.out.report.collect{ meta, report -> report },
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BISMARK_DEDUPLICATE.out.report.collect{ meta, bam -> bam },
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BISMARK_METHYLATIONEXTRACTOR.out.report.collect{ meta, report -> report },
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BISMARK_METHYLATIONEXTRACTOR.out.mbias.collect{ meta, mbias -> mbias }
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)
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}
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