mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-11-14 05:43:08 +00:00
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
21 lines
1 KiB
Text
21 lines
1 KiB
Text
#!/usr/bin/env nextflow
|
|
|
|
nextflow.enable.dsl = 2
|
|
|
|
include { RSEM_PREPAREREFERENCE } from '../../../../modules/rsem/preparereference/main.nf' addParams(options: [args: "--star"])
|
|
include { RSEM_CALCULATEEXPRESSION } from '../../../../modules/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 )
|
|
}
|