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https://github.com/MillironX/nf-core_modules.git
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978087354e
* Update main.nf * Update meta.yml * Re-add logos as not staged in a way that works with MultiQC config files * Fix MeaPhlAn3 module name * Fix metayaml * Fix meta.yml
66 lines
2.4 KiB
Text
66 lines
2.4 KiB
Text
#!/usr/bin/env nextflow
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nextflow.enable.dsl = 2
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include { UNTAR } from '../../../../modules/untar/main.nf'
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include { METAPHLAN3_METAPHLAN3 } from '../../../../modules/metaphlan3/metaphlan3/main.nf'
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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 = [ [], file('https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/delete_me/metaphlan_database.tar.gz', checkIfExists: true) ]
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UNTAR ( db )
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METAPHLAN3_METAPHLAN3 ( input, UNTAR.out.untar.map{ it[1] } )
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}
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workflow test_metaphlan3_single_end_nodb {
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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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UNTAR ( db )
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METAPHLAN3_METAPHLAN3 ( input, [] )
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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 = [ [], file('https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/delete_me/metaphlan_database.tar.gz', checkIfExists: true) ]
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UNTAR ( db )
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METAPHLAN3_METAPHLAN3 ( input, UNTAR.out.untar.map{ it[1] } )
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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 = [ [], file('https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/delete_me/metaphlan_database.tar.gz', checkIfExists: true) ]
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UNTAR ( db )
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SAMTOOLS_VIEW ( input, [] )
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METAPHLAN3_METAPHLAN3 ( SAMTOOLS_VIEW.out.bam, UNTAR.out.untar.map{ it[1] } )
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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 = [ [], file('https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/delete_me/metaphlan_database.tar.gz', checkIfExists: true) ]
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UNTAR ( db )
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METAPHLAN3_METAPHLAN3 ( input, UNTAR.out.untar.map{ it[1] } )
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}
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