nf-core_modules/tests/modules/bamcmp/main.nf

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#!/usr/bin/env nextflow
nextflow.enable.dsl = 2
include { BWA_INDEX } from '../../../modules/bwa/index/main.nf'
include { BWA_MEM } from '../../../modules/bwa/mem/main.nf'
include { BWA_INDEX as BWA_INDEX_COV2 } from '../../../modules/bwa/index/main.nf'
include { BWA_MEM as BWA_MEM_COV2 } from '../../../modules/bwa/mem/main.nf'
include { SAMTOOLS_SORT } from '../../../modules/samtools/sort/main.nf'
include { SAMTOOLS_SORT as SAMTOOLS_SORT_COV2 } from '../../../modules/samtools/sort/main.nf'
include { BAMCMP } from '../../../modules/bamcmp/main.nf'
workflow test_bamcmp {
input = [
[ id:'test'], // meta map
[ file(params.test_data['homo_sapiens']['illumina']['test_1_fastq_gz'], checkIfExists: true) ]
]
fasta1 = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
fasta2 = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
BWA_INDEX ( fasta1 )
BWA_MEM ( input, BWA_INDEX.out.index, false )
SAMTOOLS_SORT (BWA_MEM.out.bam)
BWA_INDEX_COV2 ( fasta2 )
BWA_MEM_COV2 ( input, BWA_INDEX_COV2.out.index, false )
SAMTOOLS_SORT_COV2 (BWA_MEM_COV2.out.bam)
BAMCMP (SAMTOOLS_SORT.out.bam.join(SAMTOOLS_SORT_COV2.out.bam, by: [0]))
}