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292e8eceb9
* Specify more guidelines on input channels * Linting * Updates based on code review * Update README.md * Fix broken sentence * Add MALT with incomplete tests * Parameter typo fix * Clean up test yaml * Finish MALT module prior UNZIP and MALT_BUILD modiules * Add required modules for tests * Sync test out with malt-build * Fix input parameters in tests based on final build module * Update modules/malt/run/meta.yml Co-authored-by: Gregor Sturm <mail@gregor-sturm.de> Co-authored-by: Gregor Sturm <mail@gregor-sturm.de>
21 lines
951 B
Text
21 lines
951 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' addParams( options: [:] )
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include { MALT_BUILD } from '../../../../modules/malt/build/main.nf' addParams( options: [:] )
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include { MALT_RUN } from '../../../../modules/malt/run/main.nf' addParams( options: [:] )
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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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gff = file(params.test_data['sarscov2']['genome']['genome_gff3'], checkIfExists: true)
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seq_type = "DNA"
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map_db = file("https://software-ab.informatik.uni-tuebingen.de/download/megan6/megan-nucl-Jan2021.db.zip", checkIfExists: true)
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input = file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true)
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mode = "BlastN"
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UNZIP ( map_db )
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MALT_BUILD ( fastas, seq_type, gff, UNZIP.out.unzipped_archive )
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MALT_RUN ( input, mode, MALT_BUILD.out.index )
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}
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