mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-09-22 16:12:04 +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
32 lines
1.6 KiB
Text
32 lines
1.6 KiB
Text
#!/usr/bin/env nextflow
|
|
|
|
nextflow.enable.dsl = 2
|
|
|
|
include { HISAT2_EXTRACTSPLICESITES } from '../../../../modules/hisat2/extractsplicesites/main.nf' addParams( options: [:] )
|
|
include { HISAT2_BUILD } from '../../../../modules/hisat2/build/main.nf' addParams( options: [:] )
|
|
include { HISAT2_ALIGN } from '../../../../modules/hisat2/align/main.nf' addParams( options: [:] )
|
|
|
|
workflow test_hisat2_align_single_end {
|
|
input = [ [ id:'test', single_end:true ], // meta map
|
|
[ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true) ]
|
|
]
|
|
fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
|
|
gtf = file(params.test_data['sarscov2']['genome']['genome_gtf'], checkIfExists: true)
|
|
|
|
HISAT2_EXTRACTSPLICESITES ( gtf )
|
|
HISAT2_BUILD ( fasta, gtf, HISAT2_EXTRACTSPLICESITES.out.txt )
|
|
HISAT2_ALIGN ( input, HISAT2_BUILD.out.index, HISAT2_EXTRACTSPLICESITES.out.txt )
|
|
}
|
|
|
|
workflow test_hisat2_align_paired_end {
|
|
input = [ [ id:'test', single_end:false ], // meta map
|
|
[ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
|
|
file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true)]
|
|
]
|
|
fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
|
|
gtf = file(params.test_data['sarscov2']['genome']['genome_gtf'], checkIfExists: true)
|
|
|
|
HISAT2_EXTRACTSPLICESITES ( gtf )
|
|
HISAT2_BUILD ( fasta, gtf, HISAT2_EXTRACTSPLICESITES.out.txt )
|
|
HISAT2_ALIGN ( input, HISAT2_BUILD.out.index, HISAT2_EXTRACTSPLICESITES.out.txt )
|
|
}
|