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35 lines
2.1 KiB
Text
35 lines
2.1 KiB
Text
#!/usr/bin/env nextflow
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nextflow.enable.dsl = 2
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def quant_options = [args: '--minAssignedFrags 1']
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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: quant_options )
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workflow test_salmon_index {
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genome_fasta = file("${launchDir}/tests/data/fasta/covid/GCA_011545545.1_ASM1154554v1_genomic.fna", checkIfExists: true)
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transcript_fasta = file("${launchDir}/tests/data/fasta/covid/GCA_011545545.1_ASM1154554v1_cds_from_genomic.fna", checkIfExists: true)
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SALMON_INDEX ( genome_fasta, transcript_fasta )
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}
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workflow test_salmon_quant_pe {
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genome_fasta = file("${launchDir}/tests/data/fasta/covid/GCA_011545545.1_ASM1154554v1_genomic.fna", checkIfExists: true)
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transcript_fasta = file("${launchDir}/tests/data/fasta/covid/GCA_011545545.1_ASM1154554v1_cds_from_genomic.fna", checkIfExists: true)
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gtf = file("${launchDir}/tests/data/gff/covid/GCA_011545545.1_ASM1154554v1_genomic.gtf", checkIfExists: true)
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input = [ [ id:'test', single_end:false ], // meta map
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[ file("${launchDir}/tests/data/fastq/rna/covid/EPI_ISL_486436_1.fastq.gz", checkIfExists: true),
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file("${launchDir}/tests/data/fastq/rna/covid/EPI_ISL_486436_2.fastq.gz", checkIfExists: true) ] ]
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SALMON_INDEX ( genome_fasta, transcript_fasta )
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SALMON_QUANT( input, SALMON_INDEX.out.index, gtf, transcript_fasta, false)
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}
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workflow test_salmon_quant_se {
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genome_fasta = file("${launchDir}/tests/data/fasta/covid/GCA_011545545.1_ASM1154554v1_genomic.fna", checkIfExists: true)
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transcript_fasta = file("${launchDir}/tests/data/fasta/covid/GCA_011545545.1_ASM1154554v1_cds_from_genomic.fna", checkIfExists: true)
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gtf = file("${launchDir}/tests/data/gff/covid/GCA_011545545.1_ASM1154554v1_genomic.gtf", checkIfExists: true)
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input = [ [ id:'test', single_end:true ], // meta map
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file("${launchDir}/tests/data/fastq/rna/covid/EPI_ISL_486436_1.fastq.gz", checkIfExists: true) ]
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SALMON_INDEX ( genome_fasta, transcript_fasta )
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SALMON_QUANT( input, SALMON_INDEX.out.index, gtf, transcript_fasta, false)
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}
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