nf-core_modules/tests/modules/bwamem2/mem/main.nf
Maxime U. Garcia 1765225042
Add new boolean sort_bam as input to be able to chose between sort and view in bwamem and bwamem2mem (#1125)
* 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
2021-12-08 14:31:27 +00:00

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 )
}