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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
21 lines
1.2 KiB
Text
21 lines
1.2 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 { ARTIC_MINION } from '../../../../modules/artic/minion/main.nf' addParams( fast5_dir: true, sequencing_summary: true, artic_minion_medaka_model:false )
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workflow test_artic_minion {
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input = [ [ id:'test', single_end:false ], // meta map
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file(params.test_data['sarscov2']['nanopore']['test_fastq_gz'], checkIfExists: true) ]
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fast5_tar = [ file(params.test_data['sarscov2']['nanopore']['fast5_tar_gz'], checkIfExists: true) ]
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sequencing_summary = [ file(params.test_data['sarscov2']['nanopore']['test_sequencing_summary'], checkIfExists: true) ]
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fasta = [ file('https://github.com/artic-network/primer-schemes/raw/master/nCoV-2019/V3/nCoV-2019.reference.fasta', checkIfExists: true) ]
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bed = [ file('https://github.com/artic-network/primer-schemes/raw/master/nCoV-2019/V3/nCoV-2019.primer.bed', checkIfExists: true) ]
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dummy_file = [ ]
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fast5_dir = UNTAR ( fast5_tar ).untar
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ARTIC_MINION ( input, fast5_dir, sequencing_summary, fasta, bed, dummy_file, 'nCoV-2019', '3')
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}
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