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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>
22 lines
1.1 KiB
Text
22 lines
1.1 KiB
Text
#!/usr/bin/env nextflow
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nextflow.enable.dsl = 2
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include { UNTAR } from '../../../../modules/untar/main.nf'
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include { ARTIC_MINION } from '../../../../modules/artic/minion/main.nf'
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workflow test_artic_minion {
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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']['nanopore']['test_fastq_gz'], checkIfExists: true)
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]
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fast5_tar = [ [], file(params.test_data['sarscov2']['nanopore']['fast5_tar_gz'], checkIfExists: true) ]
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sequencing_summary = file(params.test_data['sarscov2']['nanopore']['test_sequencing_summary'], checkIfExists: true)
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fasta = file('https://github.com/artic-network/primer-schemes/raw/master/nCoV-2019/V3/nCoV-2019.reference.fasta', checkIfExists: true)
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bed = file('https://github.com/artic-network/primer-schemes/raw/master/nCoV-2019/V3/nCoV-2019.primer.bed', checkIfExists: true)
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fast5_dir = UNTAR ( fast5_tar ).untar.map{ it[1] }
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ARTIC_MINION ( input, fast5_dir, sequencing_summary, fasta, bed, [], '', 'nCoV-2019', '3')
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}
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