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https://github.com/MillironX/nf-core_modules.git
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e751e5040a
* Bump software versions for viralrecon modules * Remove custom params.save_unaligned from bowtie2_align * Unify samtools modules and error if input and output names are the same * Fix ALL the tests
35 lines
1.2 KiB
Text
35 lines
1.2 KiB
Text
#!/usr/bin/env nextflow
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nextflow.enable.dsl = 2
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include { BOWTIE2_BUILD } from '../../../../modules/bowtie2/build/main.nf'
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include { BOWTIE2_ALIGN } from '../../../../modules/bowtie2/align/main.nf'
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workflow test_bowtie2_align_single_end {
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input = [
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[ id:'test', single_end:true ], // meta map
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[
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file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true)
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]
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]
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fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
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save_unaligned = false
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BOWTIE2_BUILD ( fasta )
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BOWTIE2_ALIGN ( input, BOWTIE2_BUILD.out.index, save_unaligned )
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}
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workflow test_bowtie2_align_paired_end {
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input = [
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[ id:'test', single_end:false ], // meta map
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[
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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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]
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fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
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save_unaligned = false
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BOWTIE2_BUILD ( fasta )
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BOWTIE2_ALIGN ( input, BOWTIE2_BUILD.out.index, save_unaligned )
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}
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