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https://github.com/MillironX/nf-core_modules.git
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555f1710e0
* Update test paths in bwa mappers * Fix indentation * indices pass lcoally now * no idea how they could ever pass before, Tests pass locally no * Update samtools and bwamem2 versions * Correct mulled containers + md5
33 lines
1.1 KiB
Text
33 lines
1.1 KiB
Text
#!/usr/bin/env nextflow
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nextflow.enable.dsl = 2
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include { BWA_INDEX } from '../../../../software/bwa/index/main.nf' addParams( options: [:] )
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include { BWA_MEM } from '../../../../software/bwa/mem/main.nf' addParams( options: [:] )
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/*
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* Test with single-end data
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*/
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workflow test_bwa_mem_single_end {
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input = [ [ id:'test', single_end:true ], // meta map
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[ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true) ]
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]
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fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
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BWA_INDEX ( fasta )
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BWA_MEM ( input, BWA_INDEX.out.index )
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}
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/*
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* Test with paired-end data
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*/
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workflow test_bwa_mem_paired_end {
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input = [ [ id:'test', single_end:false ], // meta map
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[ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
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file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true) ]
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]
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fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
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BWA_INDEX ( fasta )
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BWA_MEM ( input, BWA_INDEX.out.index )
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}
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