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53 lines
2.2 KiB
Text
53 lines
2.2 KiB
Text
#!/usr/bin/env nextflow
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nextflow.enable.dsl = 2
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include { SRST2_SRST2 } from '../../../../modules/srst2/srst2/main.nf'
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workflow test_srst2_srst2_exit {
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input = [
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[ id:'test', single_end:false, db:"test"], // meta map
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[ file(params.test_data['bacteroides_fragilis']['illumina']['test1_1_fastq_gz'], checkIfExists: true),
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file(params.test_data['bacteroides_fragilis']['illumina']['test1_2_fastq_gz'], checkIfExists: true) ],
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// [("")]
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file('https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/delete_me/srst2/resFinder_20180221_srst2.fasta')
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]
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SRST2_SRST2(input)
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}
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workflow test_srst2_srst2_mlst {
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input = [
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[ id:'test', single_end:false, db:"mlst"], // meta map
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[ file("https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/delete_me/srst2/SRR9067271_1.fastq.gz", checkIfExists: true),
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file("https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/delete_me/srst2/SRR9067271_2.fastq.gz", checkIfExists: true) ],
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file('https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/delete_me/srst2/MLST_DB.fas')
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]
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SRST2_SRST2(input)
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}
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workflow test_srst2_srst2_paired_end {
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input = [
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[ id:'test', single_end:false, db:"gene"], // meta map
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[ file(params.test_data['bacteroides_fragilis']['illumina']['test1_1_fastq_gz'], checkIfExists: true),
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file(params.test_data['bacteroides_fragilis']['illumina']['test1_2_fastq_gz'], checkIfExists: true) ],
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file('https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/delete_me/srst2/resFinder_20180221_srst2.fasta') // Change to params.test_data syntax after the data is included in tests/config/test_data.config
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]
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SRST2_SRST2(input)
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}
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workflow test_srst2_srst2_single_end {
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input = [
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[ id:'test', single_end:true, db:"gene" ], // meta map
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file(params.test_data['bacteroides_fragilis']['illumina']['test1_1_fastq_gz'], checkIfExists: true),
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file('https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/delete_me/srst2/resFinder_20180221_srst2.fasta') // Change to params.test_data syntax after the data is included in tests/config/test_data.config
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]
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SRST2_SRST2(input)
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}
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