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99 lines
3.3 KiB
Text
99 lines
3.3 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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sort = false
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BOWTIE2_BUILD ( fasta )
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BOWTIE2_ALIGN ( input, BOWTIE2_BUILD.out.index, save_unaligned, sort )
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}
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workflow test_bowtie2_align_single_end_sorted {
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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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sort = true
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BOWTIE2_BUILD ( fasta )
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BOWTIE2_ALIGN ( input, BOWTIE2_BUILD.out.index, save_unaligned, sort )
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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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sort = false
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BOWTIE2_BUILD ( fasta )
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BOWTIE2_ALIGN ( input, BOWTIE2_BUILD.out.index, save_unaligned, sort )
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}
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workflow test_bowtie2_align_paired_end_sorted {
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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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sort = true
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BOWTIE2_BUILD ( fasta )
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BOWTIE2_ALIGN ( input, BOWTIE2_BUILD.out.index, save_unaligned, sort )
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}
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workflow test_bowtie2_align_single_end_large_index {
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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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sort = false
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BOWTIE2_BUILD ( fasta )
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BOWTIE2_ALIGN ( input, BOWTIE2_BUILD.out.index, save_unaligned, sort )
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}
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workflow test_bowtie2_align_paired_end_large_index {
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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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sort = false
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BOWTIE2_BUILD ( fasta )
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BOWTIE2_ALIGN ( input, BOWTIE2_BUILD.out.index, save_unaligned, sort )
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}
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