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1765225042
* feat: view is now in args2 so we can use sort * forgot one split_cpus * feat: update with new logic * fix: add more info * fix: remove split_cpus logic
73 lines
2.2 KiB
Text
73 lines
2.2 KiB
Text
#!/usr/bin/env nextflow
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nextflow.enable.dsl = 2
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include { BWAMEM2_INDEX } from '../../../../modules/bwamem2/index/main.nf'
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include { BWAMEM2_MEM } from '../../../../modules/bwamem2/mem/main.nf'
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//
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// Test with single-end data
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//
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workflow test_bwamem2_mem_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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BWAMEM2_INDEX ( fasta )
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BWAMEM2_MEM ( input, BWAMEM2_INDEX.out.index, false )
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}
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//
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// Test with single-end data and sort
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//
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workflow test_bwamem2_mem_single_end_sort {
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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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BWAMEM2_INDEX ( fasta )
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BWAMEM2_MEM ( input, BWAMEM2_INDEX.out.index, true )
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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_bwamem2_mem_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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BWAMEM2_INDEX ( fasta )
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BWAMEM2_MEM ( input, BWAMEM2_INDEX.out.index, false )
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}
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//
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// Test with paired-end data and sort
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//
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workflow test_bwamem2_mem_paired_end_sort {
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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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BWAMEM2_INDEX ( fasta )
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BWAMEM2_MEM ( input, BWAMEM2_INDEX.out.index, true )
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}
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