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894349b9b5
* Update test data names. Closes: #459 Thanks: @FriederikeHanssen (`samtools` tests are already fixed by another commit) * Fix file names in tests. The update of test data name required changes in the test yml files. I also updated the `bismark/summary/main.nf` file to get its data from the `params.test_data` map.
29 lines
1.7 KiB
Text
29 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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input = [ [ id:'test', single_end:false ], // meta map
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[ file(params.test_data['sarscov2']['illumina']['test_methylated_1_fastq_gz'], checkIfExists: true),
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file(params.test_data['sarscov2']['illumina']['test_methylated_2_fastq_gz'], checkIfExists: true) ]
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]
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fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
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BISMARK_GENOMEPREPARATION ( fasta )
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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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