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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
17 lines
643 B
Text
17 lines
643 B
Text
#!/usr/bin/env nextflow
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nextflow.enable.dsl = 2
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include { GRAPHMAP2_INDEX } from '../../../../modules/graphmap2/index/main.nf' addParams( options: [:] )
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include { GRAPHMAP2_ALIGN } from '../../../../modules/graphmap2/align/main.nf' addParams( options: [:] )
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workflow test_graphmap2_align {
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input = [ [ id:'test' ], // meta map
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[ file(params.test_data['sarscov2']['nanopore']['test_fastq_gz'], checkIfExists: true) ]
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]
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fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
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GRAPHMAP2_INDEX ( fasta )
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GRAPHMAP2_ALIGN ( input, fasta, GRAPHMAP2_INDEX.out.index )
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}
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