nf-core_modules/tests/modules/bbmap/bbsplit/main.nf
Jose Espinosa-Carrasco 5b1cea7f7f
Add bbmap/bbsplit module (#771)
* Add bbmap/bbsplit module

* Conda complains about md5sum

* Apply suggestions from code review

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-09-30 13:37:35 +01:00

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#!/usr/bin/env nextflow
nextflow.enable.dsl = 2
include { BBMAP_BBSPLIT as BBMAP_BBSPLIT_INDEX } from '../../../../modules/bbmap/bbsplit/main.nf' addParams( options: [:] )
include { BBMAP_BBSPLIT as BBMAP_BBSPLIT_SPLIT } from '../../../../modules/bbmap/bbsplit/main.nf' addParams( options: [:] )
workflow test_bbmap_bbsplit {
input = [
[ id:'test', single_end:true ], // meta map
file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true)
]
bbsplit_fasta_list = [
['human'],
file('https://raw.githubusercontent.com/nf-core/test-datasets/rnaseq/reference/chr22_23800000-23980000.fa', checkIfExists: true)
]
fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
BBMAP_BBSPLIT_INDEX ( [ [:], [] ], [], fasta, bbsplit_fasta_list, true )
BBMAP_BBSPLIT_SPLIT ( input, BBMAP_BBSPLIT_INDEX.out.index, fasta, bbsplit_fasta_list, true )
}