nf-core_modules/tests/modules/cat/fastq/main.nf
Harshil Patel b932210f27
Fix flash and cat/fastq modules (#759)
* Fix version commands: round 3

* Fix seqkit/split2 modules

* Fix flash and cat/fastq modules

* Remove md5sums on gz files
2021-09-28 21:14:11 +01:00

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Text

#!/usr/bin/env nextflow
nextflow.enable.dsl = 2
include { CAT_FASTQ } from '../../../../modules/cat/fastq/main.nf' addParams( options: [publish_dir:'cat'] )
workflow test_cat_fastq_single_end {
input = [
[ id:'test', single_end:true ], // meta map
[ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
file(params.test_data['sarscov2']['illumina']['test2_1_fastq_gz'], checkIfExists: true) ]
]
CAT_FASTQ ( input )
}
workflow test_cat_fastq_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),
file(params.test_data['sarscov2']['illumina']['test2_1_fastq_gz'], checkIfExists: true),
file(params.test_data['sarscov2']['illumina']['test2_2_fastq_gz'], checkIfExists: true) ]
]
CAT_FASTQ ( input )
}