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ee46c19d03
* add Picard FastqToSam * Update test.yml * update tests * possible fix? * fixed! * Update modules/picard/fastqtosam/main.nf Co-authored-by: Moritz E. Beber <midnighter@posteo.net> * Update modules/picard/fastqtosam/main.nf Co-authored-by: Moritz E. Beber <midnighter@posteo.net> * simplify tests * fix tests * revert version check Co-authored-by: CMGG ICT Team <ict@cmgg.be> Co-authored-by: Moritz E. Beber <midnighter@posteo.net>
43 lines
1.1 KiB
Text
43 lines
1.1 KiB
Text
#!/usr/bin/env nextflow
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nextflow.enable.dsl = 2
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include { PICARD_FASTQTOSAM } from '../../../../modules/picard/fastqtosam/main.nf'
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workflow test_picard_fastqtosam_single {
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input = [
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[ id:'test', single_end:true ], // meta map
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[
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file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true)
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]
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]
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PICARD_FASTQTOSAM ( input )
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}
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workflow test_picard_fastqtosam_paired {
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input = [
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[ id:'test', single_end:false ], // meta map
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[
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file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
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file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true)
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]
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]
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PICARD_FASTQTOSAM ( input )
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}
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workflow test_picard_fastqtosam_paired_custom_samplename {
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input = [
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[ id:'test', single_end:false ], // meta map
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[
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file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
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file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true)
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]
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]
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PICARD_FASTQTOSAM ( input )
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}
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