mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-12-26 15:38:17 -05:00
4f1c1601cf
* Specify more guidelines on input channels * Linting * Updates based on code review * Update README.md * Fix broken sentence * Add bwa/aln module * Also output reads as required with SAI * Add sampe * Fix container paths * Update based on code review from @grst * Update input docs
20 lines
854 B
Text
20 lines
854 B
Text
#!/usr/bin/env nextflow
|
|
|
|
nextflow.enable.dsl = 2
|
|
|
|
include { BWA_INDEX } from '../../../../modules/bwa/index/main.nf' addParams( options: [:] )
|
|
include { BWA_ALN } from '../../../../modules/bwa/aln/main.nf' addParams( options: [:] )
|
|
include { BWA_SAMPE } from '../../../../modules/bwa/sampe/main.nf' addParams( options: [:] )
|
|
|
|
workflow test_bwa_sampe {
|
|
|
|
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)
|
|
|
|
BWA_INDEX ( fasta )
|
|
BWA_ALN ( input, BWA_INDEX.out.index )
|
|
BWA_SAMPE ( BWA_ALN.out.sai, BWA_INDEX.out.index )
|
|
}
|