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https://github.com/MillironX/nf-core_modules.git
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043a7d1e3c
* remove deprecated test tags * fix bowtie, gatk4/applybsqr * fix gatk4 baserecalibrator * fixed shovill * fixed yara/mapper * fixed kallistobustools/ref paths
27 lines
1.1 KiB
Text
27 lines
1.1 KiB
Text
#!/usr/bin/env nextflow
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nextflow.enable.dsl = 2
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include { BOWTIE_BUILD } from '../../../../software/bowtie/build/main.nf' addParams( options: [:] )
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include { BOWTIE_ALIGN } from '../../../../software/bowtie/align/main.nf' addParams( options: [:] )
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workflow test_bowtie_align_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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BOWTIE_BUILD ( fasta )
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BOWTIE_ALIGN ( input, BOWTIE_BUILD.out.index )
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}
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workflow test_bowtie_align_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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BOWTIE_BUILD ( fasta )
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BOWTIE_ALIGN ( input, BOWTIE_BUILD.out.index )
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}
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