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60 lines
2.4 KiB
Text
60 lines
2.4 KiB
Text
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#!/usr/bin/env nextflow
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nextflow.enable.dsl = 2
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include { BBMAP_INDEX } from '../../../../modules/bbmap/index/main.nf' addParams( options: [:] )
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include { BBMAP_ALIGN } from '../../../../modules/bbmap/align/main.nf' addParams( options: [:] )
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include { BBMAP_ALIGN as BBMAP_ALIGN_PIGZ } from '../../../../modules/bbmap/align/main.nf' addParams( options: [args: "unpigz=t" ] )
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workflow test_bbmap_align_paired_end_fasta_ref {
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input = [ [ 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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BBMAP_ALIGN ( input, fasta )
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}
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workflow test_bbmap_align_paired_end_index_ref {
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input = [ [ 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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BBMAP_INDEX ( fasta )
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BBMAP_ALIGN ( input, BBMAP_INDEX.out.index )
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}
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workflow test_bbmap_align_single_end_index_ref {
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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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BBMAP_INDEX ( fasta )
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BBMAP_ALIGN ( input, BBMAP_INDEX.out.index )
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}
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workflow test_bbmap_align_paired_end_index_ref_pigz {
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input = [ [ 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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BBMAP_INDEX ( fasta )
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BBMAP_ALIGN_PIGZ ( input, BBMAP_INDEX.out.index )
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}
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