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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>
28 lines
1.1 KiB
Text
28 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 { LAST_LASTAL } from '../../../../modules/last/lastal/main.nf'
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workflow test_last_lastal_with_dummy_param_file {
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input = [ [ id:'contigs', single_end:false ], // meta map
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file(params.test_data['sarscov2']['illumina']['contigs_fasta'], checkIfExists: true),
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[] ]
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db = [ [], file(params.test_data['sarscov2']['genome']['lastdb_tar_gz'], checkIfExists: true) ]
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UNTAR ( db )
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LAST_LASTAL ( input, UNTAR.out.untar.map{ it[1] })
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}
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workflow test_last_lastal_with_real_param_file {
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input = [ [ id:'contigs', single_end:false ], // meta map
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file(params.test_data['sarscov2']['illumina']['contigs_fasta'], checkIfExists: true),
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file(params.test_data['sarscov2']['genome']['contigs_genome_par'], checkIfExists: true) ]
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db = [ [], file(params.test_data['sarscov2']['genome']['lastdb_tar_gz'], checkIfExists: true) ]
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UNTAR ( db )
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LAST_LASTAL ( input, UNTAR.out.untar.map{ it[1] })
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}
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