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https://github.com/MillironX/nf-core_modules.git
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e080f4c8ac
* fix: remove left-over unnecessary code * Adds support for meta lists for unzip and untar * Fix test inputs * Update all modules to support extraction of decompressed file from untar/unzip new meta + file tuple * Update all modules to support extraction of decompressed file from untar/unzip new meta + file tuple * Fix MALTEXTRACT/AMPS * Fix further modules * Fix cellranger * Apply suggestions from code review Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
31 lines
1.5 KiB
Text
31 lines
1.5 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'
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include { UNZIP as UNZIP_MALTEXTRACT } 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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include { MALTEXTRACT } from '../../../modules/maltextract/main.nf'
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workflow test_maltextract {
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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 = [
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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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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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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.map{ it[1] } )
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MALT_RUN ( input, mode, MALT_BUILD.out.index )
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ch_input_to_maltextract = MALT_RUN.out.rma6.map{ it[1] }
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MALTEXTRACT ( ch_input_to_maltextract, taxon_list, UNZIP_MALTEXTRACT.out.unzipped_archive.map{ it[1] })
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}
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