nf-core_modules/tests/software/bismark/summary/main.nf

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#!/usr/bin/env nextflow
nextflow.enable.dsl = 2
include { BISMARK_GENOMEPREPARATION } from '../../../../software/bismark/genomepreparation/main.nf' addParams( options: [:] )
include { BISMARK_ALIGN } from '../../../../software/bismark/align/main.nf' addParams( options: [:] )
include { BISMARK_DEDUPLICATE } from '../../../../software/bismark/deduplicate/main.nf' addParams( options: [:] )
include { BISMARK_METHYLATIONEXTRACTOR } from '../../../../software/bismark/methylationextractor/main.nf' addParams( options: [:] )
include { BISMARK_SUMMARY } from '../../../../software/bismark/summary/main.nf' addParams( options: [:] )
workflow test_bismark_summary {
input = [ [ id:'test', single_end:false ], // meta map
[ file(params.test_data['sarscov2']['illumina']['test_methylated_1_fastq_gz'], checkIfExists: true),
file(params.test_data['sarscov2']['illumina']['test_methylated_2_fastq_gz'], checkIfExists: true) ]
]
fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
BISMARK_GENOMEPREPARATION ( fasta )
BISMARK_ALIGN ( input, BISMARK_GENOMEPREPARATION.out.index )
BISMARK_DEDUPLICATE ( BISMARK_ALIGN.out.bam )
BISMARK_METHYLATIONEXTRACTOR ( BISMARK_DEDUPLICATE.out.bam, BISMARK_GENOMEPREPARATION.out.index )
BISMARK_SUMMARY (
BISMARK_ALIGN.out.bam.collect{ meta, bam -> bam },
BISMARK_ALIGN.out.report.collect{ meta, report -> report },
BISMARK_DEDUPLICATE.out.report.collect{ meta, bam -> bam },
BISMARK_METHYLATIONEXTRACTOR.out.report.collect{ meta, report -> report },
BISMARK_METHYLATIONEXTRACTOR.out.mbias.collect{ meta, mbias -> mbias }
)
}