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01cc326c23
* Specify more guidelines on input channels * Linting * Updates based on code review * Update README.md * Fix broken sentence * Start work, continue once on non-mobile internet * finished and working on conda * Update modules/amps/main.nf Co-authored-by: Jose Espinosa-Carrasco <kadomu@gmail.com> * Apply suggestions from code review Co-authored-by: Jose Espinosa-Carrasco <kadomu@gmail.com> Co-authored-by: Jose Espinosa-Carrasco <kadomu@gmail.com>
32 lines
1.6 KiB
Text
32 lines
1.6 KiB
Text
#!/usr/bin/env nextflow
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nextflow.enable.dsl = 2
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include { UNZIP as UNZIP_MALT } from '../../../modules/unzip/main.nf' addParams( options: [:] )
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include { UNZIP as UNZIP_MALTEXTRACT } 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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include { MALTEXTRACT } from '../../../modules/maltextract/main.nf' addParams( options: [args: "-f def_anc"] )
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include { AMPS } from '../../../modules/amps/main.nf' addParams( options: [:] )
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workflow test_amps {
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fastas = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
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gff = []
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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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taxon_list = file(params.test_data['sarscov2']['genome']['taxon_list_txt'], checkIfExists: true)
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ncbi_dir = file(params.test_data['sarscov2']['genome']['ncbi_taxmap_zip'], checkIfExists: true)
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filter = "def_anc"
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UNZIP_MALT ( map_db )
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UNZIP_MALTEXTRACT ( ncbi_dir )
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MALT_BUILD ( fastas, seq_type, gff, UNZIP_MALT.out.unzipped_archive )
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MALT_RUN ( input, mode, MALT_BUILD.out.index )
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MALTEXTRACT ( MALT_RUN.out.rma6, taxon_list, UNZIP_MALTEXTRACT.out.unzipped_archive)
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AMPS ( MALTEXTRACT.out.results, taxon_list, filter )
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}
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