mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-12-26 15:38:17 -05:00
e937c7950a
* Update README * Rename pytest_software.yml to pytest_modules.yml * Rename main software directory to modules * Remove deprecated modules * Rename tests software to modules * Replace paths for tests in pytest_modules.yml * Replace software with modules in Github Actions * Replace software with modules in main.nf tests * Rename software to modules in test.yml
29 lines
1.7 KiB
Text
29 lines
1.7 KiB
Text
#!/usr/bin/env nextflow
|
|
|
|
nextflow.enable.dsl = 2
|
|
|
|
include { BISMARK_GENOMEPREPARATION } from '../../../../modules/bismark/genomepreparation/main.nf' addParams( options: [:] )
|
|
include { BISMARK_ALIGN } from '../../../../modules/bismark/align/main.nf' addParams( options: [:] )
|
|
include { BISMARK_DEDUPLICATE } from '../../../../modules/bismark/deduplicate/main.nf' addParams( options: [:] )
|
|
include { BISMARK_METHYLATIONEXTRACTOR } from '../../../../modules/bismark/methylationextractor/main.nf' addParams( options: [:] )
|
|
include { BISMARK_SUMMARY } from '../../../../modules/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 }
|
|
)
|
|
}
|