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https://github.com/MillironX/nf-core_modules.git
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e080f4c8ac
* fix: remove left-over unnecessary code * Adds support for meta lists for unzip and untar * Fix test inputs * Update all modules to support extraction of decompressed file from untar/unzip new meta + file tuple * Update all modules to support extraction of decompressed file from untar/unzip new meta + file tuple * Fix MALTEXTRACT/AMPS * Fix further modules * Fix cellranger * Apply suggestions from code review Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
57 lines
2.1 KiB
Text
57 lines
2.1 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 { SAMTOOLS_VIEW } from '../../../modules/samtools/view/main.nf'
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include { METAPHLAN3 } from '../../../modules/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 ( input, UNTAR.out.untar.map{ it[1] } )
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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 ( 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 ( 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 ( input, UNTAR.out.untar.map{ it[1] } )
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}
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