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e937c7950a
* Update README * Rename pytest_software.yml to pytest_modules.yml * Rename main software directory to modules * Remove deprecated modules * Rename tests software to modules * Replace paths for tests in pytest_modules.yml * Replace software with modules in Github Actions * Replace software with modules in main.nf tests * Rename software to modules in test.yml
29 lines
1.5 KiB
Text
29 lines
1.5 KiB
Text
#!/usr/bin/env nextflow
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nextflow.enable.dsl = 2
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include { STAR_GENOMEGENERATE } from '../../../../modules/star/genomegenerate/main.nf' addParams( options: [args: '--genomeSAindexNbases 9'] )
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include { STAR_ALIGN } from '../../../../modules/star/align/main.nf' addParams( options: [args: '--readFilesCommand zcat'] )
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workflow test_star_alignment_single_end {
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input = [ [ id:'test', single_end:true ], // meta map
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[ file("${launchDir}/tests/data/generic/fastq/test_single_end.fastq.gz", checkIfExists: true) ]
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]
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fasta = file("${launchDir}/tests/data/generic/fasta/GCF_000019425.1_ASM1942v1_genomic.fna", checkIfExists: true)
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gtf = file("${launchDir}/tests/data/generic/gtf/GCF_000019425.1_ASM1942v1_genomic.gtf", checkIfExists: true)
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STAR_GENOMEGENERATE ( fasta, gtf )
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STAR_ALIGN ( input, STAR_GENOMEGENERATE.out.index, gtf )
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}
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workflow test_star_alignment_paired_end {
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input = [ [ id:'test', single_end:false ], // meta map
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[ file("${launchDir}/tests/data/generic/fastq/test_R1.fastq.gz", checkIfExists: true),
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file("${launchDir}/tests/data/generic/fastq/test_R2.fastq.gz", checkIfExists: true) ]
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]
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fasta = file("${launchDir}/tests/data/generic/fasta/GCF_000019425.1_ASM1942v1_genomic.fna", checkIfExists: true)
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gtf = file("${launchDir}/tests/data/generic/gtf/GCF_000019425.1_ASM1942v1_genomic.gtf", checkIfExists: true)
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STAR_GENOMEGENERATE ( fasta, gtf )
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STAR_ALIGN ( input, STAR_GENOMEGENERATE.out.index, gtf )
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}
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