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1f465a63d0
* bbmap/bbduk module created * created bbmap/bbduk module * updated main.nf * changed test.yml tags * removed whitespaces * Adjusted main.nf spacing * whitespace, tags * fix optional files, tags, tidy code * fix suffix * Apply suggestions from code review Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
45 lines
1.7 KiB
Text
45 lines
1.7 KiB
Text
#!/usr/bin/env nextflow
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nextflow.enable.dsl = 2
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include { BBMAP_BBDUK } from '../../../../software/bbmap/bbduk/main.nf' addParams( options: [ 'args' : 'trimq=10 qtrim=r', 'suffix' : '.trim' ] )
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workflow test_bbmap_bbduk_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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BBMAP_BBDUK ( input, [] )
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}
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workflow test_bbmap_bbduk_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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BBMAP_BBDUK ( input, [] )
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}
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workflow test_bbmap_bbduk_se_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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contaminants = [file(params.test_data['sarscov2']['genome']['transcriptome_fasta'], checkIfExists: true) ] // transciptome file - remove contaminants (*trim.fastq files empty)
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BBMAP_BBDUK ( input, contaminants )
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}
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workflow test_bbmap_bbduk_pe_ref {
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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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contaminants = [file(params.test_data['sarscov2']['genome']['transcriptome_fasta'], checkIfExists: true) ]
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BBMAP_BBDUK ( input, contaminants )
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}
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