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e937c7950a
* Update README * Rename pytest_software.yml to pytest_modules.yml * Rename main software directory to modules * Remove deprecated modules * Rename tests software to modules * Replace paths for tests in pytest_modules.yml * Replace software with modules in Github Actions * Replace software with modules in main.nf tests * Rename software to modules in test.yml
29 lines
624 B
Text
29 lines
624 B
Text
#!/usr/bin/env nextflow
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nextflow.enable.dsl = 2
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include { ARTIC_GUPPYPLEX } from '../../../../modules/artic/guppyplex/main.nf' addParams( options: [:] )
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process STAGE_FASTQ_DIR {
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input:
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tuple val(meta), path(fastq_file)
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output:
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tuple val(meta), path('fastq'), emit: fastq_dir
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script:
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"""
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mkdir fastq
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mv ${fastq_file} fastq
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"""
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}
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workflow test_artic_guppyplex {
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input = [ [ id:'test' ],
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file(params.test_data['sarscov2']['nanopore']['test_fastq_gz'], checkIfExists: true) ]
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STAGE_FASTQ_DIR ( input )
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ARTIC_GUPPYPLEX ( STAGE_FASTQ_DIR.out.fastq_dir )
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}
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