mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-11-11 12:43:09 +00:00
043a7d1e3c
* remove deprecated test tags * fix bowtie, gatk4/applybsqr * fix gatk4 baserecalibrator * fixed shovill * fixed yara/mapper * fixed kallistobustools/ref paths
27 lines
1.1 KiB
Text
27 lines
1.1 KiB
Text
#!/usr/bin/env nextflow
|
|
|
|
nextflow.enable.dsl = 2
|
|
|
|
include { BOWTIE_BUILD } from '../../../../software/bowtie/build/main.nf' addParams( options: [:] )
|
|
include { BOWTIE_ALIGN } from '../../../../software/bowtie/align/main.nf' addParams( options: [:] )
|
|
|
|
workflow test_bowtie_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)
|
|
|
|
BOWTIE_BUILD ( fasta )
|
|
BOWTIE_ALIGN ( input, BOWTIE_BUILD.out.index )
|
|
}
|
|
|
|
workflow test_bowtie_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)
|
|
|
|
BOWTIE_BUILD ( fasta )
|
|
BOWTIE_ALIGN ( input, BOWTIE_BUILD.out.index )
|
|
}
|