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acb1a12a56
* Re-organise all test data * Fix ECLint * Fix ECLint agaaainn * Now is not the time EClint
31 lines
1.7 KiB
Text
31 lines
1.7 KiB
Text
#!/usr/bin/env nextflow
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nextflow.enable.dsl = 2
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include { SALMON_INDEX } from '../../../../software/salmon/index/main.nf' addParams( options: [:] )
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include { SALMON_QUANT } from '../../../../software/salmon/quant/main.nf' addParams( options: [args: '--minAssignedFrags 1'] )
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workflow test_salmon_quant_single_end {
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input = [ [ id:'test', single_end:true ], // meta map
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file("${launchDir}/tests/data/genomics/sarscov2/illumina/fastq/test_1.fastq.gz", checkIfExists: true)
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]
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genome = file("${launchDir}/tests/data/genomics/sarscov2/genome/genome.fasta", checkIfExists: true)
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transcriptome = file("${launchDir}/tests/data/genomics/sarscov2/genome/transcriptome.fasta", checkIfExists: true)
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gtf = file("${launchDir}/tests/data/genomics/sarscov2/genome/genome.gtf", checkIfExists: true)
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SALMON_INDEX ( genome, transcriptome )
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SALMON_QUANT ( input, SALMON_INDEX.out.index, gtf, transcriptome, false )
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}
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workflow test_salmon_quant_paired_end {
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input = [ [ id:'test', single_end:false ], // meta map
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[ file("${launchDir}/tests/data/genomics/sarscov2/illumina/fastq/test_1.fastq.gz", checkIfExists: true),
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file("${launchDir}/tests/data/genomics/sarscov2/illumina/fastq/test_2.fastq.gz", checkIfExists: true) ]
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]
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genome = file("${launchDir}/tests/data/genomics/sarscov2/genome/genome.fasta", checkIfExists: true)
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transcriptome = file("${launchDir}/tests/data/genomics/sarscov2/genome/transcriptome.fasta", checkIfExists: true)
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gtf = file("${launchDir}/tests/data/genomics/sarscov2/genome/genome.gtf", checkIfExists: true)
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SALMON_INDEX ( genome, transcriptome )
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SALMON_QUANT ( input, SALMON_INDEX.out.index, gtf, transcriptome, false )
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}
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