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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>
41 lines
1.5 KiB
Text
41 lines
1.5 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 { VCFANNO } from '../../../modules/vcfanno/main.nf'
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workflow test_vcfanno {
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input = [
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[ id:'test_compressed', single_end:false ], // meta map
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file(params.test_data['sarscov2']['illumina']['test_vcf_gz'], checkIfExists: true),
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file(params.test_data['sarscov2']['illumina']['test_vcf_gz_tbi'], checkIfExists: true)
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]
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input_2 = [ [ id:'test_compressed', single_end:false ], // meta map
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[] ]
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toml = file(params.test_data['homo_sapiens']['genome']['vcfanno_toml'], checkIfExists: true)
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resource_dir = [[], file(params.test_data['homo_sapiens']['genome']['vcfanno_tar_gz'], checkIfExists: true) ]
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UNTAR ( resource_dir )
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VCFANNO ( input, input_2, toml, UNTAR.out.untar.map{ it[1] } )
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}
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workflow test_vcfanno_uncompressed {
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input = [ [ id:'test_uncompressed', single_end:false ], // meta map
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[] ,[] ]
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input_2 = [
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[ id:'test_uncompressed', single_end:false ], // meta map
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file(params.test_data['sarscov2']['illumina']['test_vcf'], checkIfExists: true)
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]
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toml = file(params.test_data['homo_sapiens']['genome']['vcfanno_toml'], checkIfExists: true)
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resource_dir = [[], file(params.test_data['homo_sapiens']['genome']['vcfanno_tar_gz'], checkIfExists: true) ]
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UNTAR ( resource_dir )
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VCFANNO ( input, input_2, toml, UNTAR.out.untar.map{ it[1] } )
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}
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