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e621f78757
* Update salmon/quant to provide '--libType A' option * Modify lib_type description to be a string * Update tests * lyb_type can be explicitly overwrite * Update main.nf * Update main.nf * Update main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
50 lines
2.4 KiB
Text
50 lines
2.4 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(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true)
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]
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genome_fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
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transcript_fasta = file(params.test_data['sarscov2']['genome']['transcriptome_fasta'], checkIfExists: true)
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gtf = file(params.test_data['sarscov2']['genome']['genome_gtf'], 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_paired_end {
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input = [ [ id:'test', single_end:false ], // meta map
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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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genome_fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
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transcript_fasta = file(params.test_data['sarscov2']['genome']['transcriptome_fasta'], checkIfExists: true)
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gtf = file(params.test_data['sarscov2']['genome']['genome_gtf'], 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_single_end_lib_type_A {
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input = [ [ id:'test', single_end:true ], // meta map
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file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true)
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]
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genome_fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
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transcript_fasta = file(params.test_data['sarscov2']['genome']['transcriptome_fasta'], checkIfExists: true)
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gtf = file(params.test_data['sarscov2']['genome']['genome_gtf'], 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, 'A' )
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}
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