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 {
def input = []
input = [ [ id:'test', single_end:false ], // meta map
[ file("${launchDir}/tests/data/genomics/sarscov2/fastq/test_methylated_1.fastq.gz", checkIfExists: true),
file("${launchDir}/tests/data/genomics/sarscov2/fastq/test_methylated_2.fastq.gz", checkIfExists: true) ] ]
BISMARK_GENOMEPREPARATION ( file("${launchDir}/tests/data/genomics/sarscov2/fasta/test_genome.fasta", checkIfExists: true) )
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 }
)
}