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be8d7b3293
* Rollback version * Start work rollback to 0.4.1 * Further changes * Re do dynamic flag creation * Prettier.
26 lines
981 B
Text
26 lines
981 B
Text
#!/usr/bin/env nextflow
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nextflow.enable.dsl = 2
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include { UNZIP } from '../../../../modules/unzip/main.nf'
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include { MALT_BUILD } from '../../../../modules/malt/build/main.nf'
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include { MALT_RUN } from '../../../../modules/malt/run/main.nf'
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workflow test_malt_run {
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fastas = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
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seq_type = "DNA"
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map_accession = [ [], file("https://software-ab.informatik.uni-tuebingen.de/download/megan6/nucl_acc2tax-Jul2019.abin.zip", checkIfExists: true) ]
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mapping_type = 'ref'
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mapping_db = 'taxonomy'
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input = [
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[ 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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]
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mode = "BlastN"
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UNZIP ( map_accession )
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MALT_BUILD ( fastas, seq_type, UNZIP.out.unzipped_archive.map{ it[1] }, "ref", "taxonomy" )
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MALT_RUN ( input, mode, MALT_BUILD.out.index )
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}
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