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59 lines
2.3 KiB
Text
59 lines
2.3 KiB
Text
#!/usr/bin/env nextflow
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nextflow.enable.dsl = 2
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include { UNTAR } from '../../../software/untar/main.nf' addParams( options: [:] )
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include { SAMTOOLS_VIEW } from '../../../software/samtools/view/main.nf' addParams( options: ['suffix': '.sam'] )
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include { METAPHLAN3 } from '../../../software/metaphlan3/main.nf' addParams( options: [ 'args':'--index mpa_v30_CHOCOPhlAn_201901 --add_viruses --bt2_ps very-sensitive-local' ] )
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workflow test_metaphlan3_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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db = channel.fromPath('https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/delete_me/metaphlan_database.tar.gz', type: 'dir', checkIfExists: true)
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UNTAR ( db )
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METAPHLAN3 ( input, UNTAR.out.untar )
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}
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workflow test_metaphlan3_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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db = channel.fromPath('https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/delete_me/metaphlan_database.tar.gz', type: 'dir', checkIfExists: true)
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UNTAR ( db )
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METAPHLAN3 ( input, UNTAR.out.untar )
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}
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workflow test_metaphlan3_sam {
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input = [ [ id:'test'], // meta map
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[ file(params.test_data['sarscov2']['illumina']['test_single_end_bam'], checkIfExists: true) ]
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]
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db = channel.fromPath('https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/delete_me/metaphlan_database.tar.gz', type: 'dir', checkIfExists: true)
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UNTAR ( db )
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SAMTOOLS_VIEW ( input )
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METAPHLAN3 ( SAMTOOLS_VIEW.out.bam, UNTAR.out.untar )
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}
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workflow test_metaphlan3_fasta {
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input = [ [ id:'test', single_end:true], // meta map
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[ file(params.test_data['sarscov2']['genome']['transcriptome_fasta'], checkIfExists: true) ]
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]
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db = channel.fromPath('https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/delete_me/metaphlan_database.tar.gz', type: 'dir', checkIfExists: true)
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UNTAR ( db )
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METAPHLAN3 ( input, UNTAR.out.untar )
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}
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