mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-11-13 05:13:09 +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
20 lines
784 B
Text
Executable file
20 lines
784 B
Text
Executable file
#!/usr/bin/env nextflow
|
|
|
|
nextflow.enable.dsl = 2
|
|
|
|
include { SEQUENZAUTILS_BAM2SEQZ } from '../../../../modules/sequenzautils/bam2seqz/main.nf' addParams( options: [:] )
|
|
|
|
workflow test_sequenzautils_bam2seqz {
|
|
|
|
tumourbam = file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true)
|
|
normalbam = file(params.test_data['sarscov2']['illumina']['test_single_end_sorted_bam'], checkIfExists: true)
|
|
|
|
input = [ [ id:'test' ], // meta map
|
|
tumourbam,
|
|
normalbam
|
|
]
|
|
fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
|
|
wig = file(params.test_data['sarscov2']['illumina']['test_wig_gz'], checkIfExists: true)
|
|
|
|
SEQUENZAUTILS_BAM2SEQZ ( input, fasta, wig )
|
|
}
|