mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-11-11 04:33:10 +00:00
1765225042
* feat: view is now in args2 so we can use sort * forgot one split_cpus * feat: update with new logic * fix: add more info * fix: remove split_cpus logic
73 lines
2.2 KiB
Text
73 lines
2.2 KiB
Text
#!/usr/bin/env nextflow
|
|
|
|
nextflow.enable.dsl = 2
|
|
|
|
include { BWAMEM2_INDEX } from '../../../../modules/bwamem2/index/main.nf'
|
|
include { BWAMEM2_MEM } from '../../../../modules/bwamem2/mem/main.nf'
|
|
|
|
//
|
|
// Test with single-end data
|
|
//
|
|
workflow test_bwamem2_mem_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)
|
|
|
|
BWAMEM2_INDEX ( fasta )
|
|
BWAMEM2_MEM ( input, BWAMEM2_INDEX.out.index, false )
|
|
}
|
|
|
|
//
|
|
// Test with single-end data and sort
|
|
//
|
|
workflow test_bwamem2_mem_single_end_sort {
|
|
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)
|
|
|
|
BWAMEM2_INDEX ( fasta )
|
|
BWAMEM2_MEM ( input, BWAMEM2_INDEX.out.index, true )
|
|
}
|
|
|
|
|
|
//
|
|
// Test with paired-end data
|
|
//
|
|
workflow test_bwamem2_mem_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)
|
|
|
|
BWAMEM2_INDEX ( fasta )
|
|
BWAMEM2_MEM ( input, BWAMEM2_INDEX.out.index, false )
|
|
}
|
|
|
|
//
|
|
// Test with paired-end data and sort
|
|
//
|
|
workflow test_bwamem2_mem_paired_end_sort {
|
|
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)
|
|
|
|
BWAMEM2_INDEX ( fasta )
|
|
BWAMEM2_MEM ( input, BWAMEM2_INDEX.out.index, true )
|
|
}
|