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https://github.com/MillironX/nf-core_modules.git
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53109d53c0
* Inital nf-core create * remove TODO comments, input and output files defined * add get version in script * added flow control for single/paired end data * added script main commands * removed completed TODO messages * removed completed TODO messages * added software info * added input reads description * added output description * added description and keywords * added single end test * added paired end test * fixed sample name flag * fixed reverse read variable * added test yaml * update for pytest_software * order in pytest_software was different * replaced functions.nf with copy from another module * simplify read command line Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> Co-authored-by: Nicholas TODA <nicholas.toda@mnhn.fr> Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
24 lines
809 B
Text
24 lines
809 B
Text
#!/usr/bin/env nextflow
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nextflow.enable.dsl = 2
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include { GATK4_FASTQTOSAM } from '../../../../software/gatk4/fastqtosam/main.nf' addParams( options: [:] )
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workflow test_gatk4_fastqtosam_single_end {
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def input = []
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input = [ [ id:'test', single_end:true ], // meta map
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file("${launchDir}/tests/data/genomics/sarscov2/fastq/test_1.fastq.gz", checkIfExists: true) ]
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GATK4_FASTQTOSAM ( input )
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}
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workflow test_gatk4_fastqtosam_paired_end {
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def input = []
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input = [ [ id:'test', single_end:false ], // meta map
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file("${launchDir}/tests/data/genomics/sarscov2/fastq/test_1.fastq.gz", checkIfExists: true),
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file("${launchDir}/tests/data/genomics/sarscov2/fastq/test_2.fastq.gz", checkIfExists: true) ]
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GATK4_FASTQTOSAM ( input )
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}
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