mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-09-21 15:52:05 +00:00
99 lines
3.3 KiB
Text
99 lines
3.3 KiB
Text
#!/usr/bin/env nextflow
|
|
|
|
nextflow.enable.dsl = 2
|
|
|
|
include { BOWTIE2_BUILD } from '../../../../modules/bowtie2/build/main.nf'
|
|
include { BOWTIE2_ALIGN } from '../../../../modules/bowtie2/align/main.nf'
|
|
|
|
workflow test_bowtie2_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)
|
|
save_unaligned = false
|
|
sort = false
|
|
|
|
BOWTIE2_BUILD ( fasta )
|
|
BOWTIE2_ALIGN ( input, BOWTIE2_BUILD.out.index, save_unaligned, sort )
|
|
}
|
|
|
|
workflow test_bowtie2_align_single_end_sorted {
|
|
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)
|
|
save_unaligned = false
|
|
sort = true
|
|
|
|
BOWTIE2_BUILD ( fasta )
|
|
BOWTIE2_ALIGN ( input, BOWTIE2_BUILD.out.index, save_unaligned, sort )
|
|
}
|
|
|
|
workflow test_bowtie2_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)
|
|
save_unaligned = false
|
|
sort = false
|
|
|
|
BOWTIE2_BUILD ( fasta )
|
|
BOWTIE2_ALIGN ( input, BOWTIE2_BUILD.out.index, save_unaligned, sort )
|
|
}
|
|
|
|
workflow test_bowtie2_align_paired_end_sorted {
|
|
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)
|
|
save_unaligned = false
|
|
sort = true
|
|
|
|
BOWTIE2_BUILD ( fasta )
|
|
BOWTIE2_ALIGN ( input, BOWTIE2_BUILD.out.index, save_unaligned, sort )
|
|
}
|
|
|
|
workflow test_bowtie2_align_single_end_large_index {
|
|
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)
|
|
save_unaligned = false
|
|
sort = false
|
|
|
|
BOWTIE2_BUILD ( fasta )
|
|
BOWTIE2_ALIGN ( input, BOWTIE2_BUILD.out.index, save_unaligned, sort )
|
|
}
|
|
|
|
workflow test_bowtie2_align_paired_end_large_index {
|
|
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)
|
|
save_unaligned = false
|
|
sort = false
|
|
|
|
BOWTIE2_BUILD ( fasta )
|
|
BOWTIE2_ALIGN ( input, BOWTIE2_BUILD.out.index, save_unaligned, sort )
|
|
}
|