nf-core_modules/tests/software/rsem/calculateexpression/main.nf
Kevin Menden fce4e60864
Fix rsem (#555)
* bump bcftools filter

* fix bcftools

* rsem/preparereference

* added calculateexpression

* meta.yml and pytest_software

* paired end

* add test.yml
2021-07-02 13:09:48 +02:00

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#!/usr/bin/env nextflow
nextflow.enable.dsl = 2
include { RSEM_PREPAREREFERENCE } from '../../../../software/rsem/preparereference/main.nf' addParams(options: [args: "--star"])
include { RSEM_CALCULATEEXPRESSION } from '../../../../software/rsem/calculateexpression/main.nf' addParams(options: [args: "--star --star-gzipped-read-file"])
workflow test_rsem_calculateexpression {
fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
gtf = file(params.test_data['homo_sapiens']['genome']['genome_gtf'], checkIfExists: true)
input = [ [ id:'test', single_end:false, strandedness: 'forward' ], // meta map
[file(params.test_data['homo_sapiens']['illumina']['test_rnaseq_1_fastq_gz'], checkIfExists: true),
file(params.test_data['homo_sapiens']['illumina']['test_rnaseq_2_fastq_gz'], checkIfExists: true)]
]
RSEM_PREPAREREFERENCE ( fasta, gtf )
RSEM_CALCULATEEXPRESSION( input, RSEM_PREPAREREFERENCE.out.index )
}