nf-core_modules/tests/software/bismark/align/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 as BISMARK_ALIGN_SE } from '../../../../software/bismark/align/main.nf' addParams( options: [ publish_dir:'test_single_end' ] )
include { BISMARK_ALIGN as BISMARK_ALIGN_PE } from '../../../../software/bismark/align/main.nf' addParams( options: [ publish_dir:'test_paired_end' ] )
//
// Test with single-end data
//
workflow test_bismark_align_single_end {
input = [ [ id:'test', single_end:true ], // meta map
[ file(params.test_data['sarscov2']['illumina']['test_methylated_1_fastq_gz'], checkIfExists: true) ]
]
fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
BISMARK_GENOMEPREPARATION ( fasta )
BISMARK_ALIGN_SE ( input, BISMARK_GENOMEPREPARATION.out.index )
}
//
// Test with paired-end data
//
workflow test_bismark_align_paired_end {
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_PE ( input, BISMARK_GENOMEPREPARATION.out.index )
}