nf-core_modules/tests/software/bwameth/align/main.nf

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#!/usr/bin/env nextflow
nextflow.enable.dsl = 2
include { BWAMETH_ALIGN as BWAMETH_ALIGN_SE } from '../../../../software/bwameth/align/main.nf' addParams( options: [ publish_dir:'test_single_end' ] )
include { BWAMETH_ALIGN as BWAMETH_ALIGN_PE } from '../../../../software/bwameth/align/main.nf' addParams( options: [ publish_dir:'test_paired_end' ] )
/*
* Test with single-end data
*/
workflow test_bwameth_align_single_end {
def input = []
input = [ [ id:'test', single_end:true ], // meta map
[ file("${launchDir}/tests/data/fastq/methylated_dna/Ecoli_10K_methylated_R1.fastq.gz", checkIfExists: true) ] ]
BWAMETH_ALIGN_SE (
input,
file("${launchDir}/tests/data/index/E_coli/bwameth", checkIfExists: true)
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)
}
/*
* Test with paired-end data
*/
workflow test_bwameth_align_paired_end {
def input = []
input = [ [ id:'test', single_end:false ], // meta map
[ file("${launchDir}/tests/data/fastq/methylated_dna/Ecoli_10K_methylated_R1.fastq.gz", checkIfExists: true),
file("${launchDir}/tests/data/fastq/methylated_dna/Ecoli_10K_methylated_R2.fastq.gz", checkIfExists: true) ] ]
BWAMETH_ALIGN_PE (
input,
file("${launchDir}/tests/data/index/E_coli/bwameth", checkIfExists: true)
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)
}