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43 lines
1.4 KiB
Text
43 lines
1.4 KiB
Text
#!/usr/bin/env nextflow
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nextflow.enable.dsl = 2
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include { MOTUS_DOWNLOADDB } from '../../../../modules/motus/downloaddb/main.nf'
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include { MOTUS_PROFILE } from '../../../../modules/motus/profile/main.nf'
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workflow test_motus_profile_single_end {
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input = [
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[ id:'test', single_end:true ], // meta map
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file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true)
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]
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MOTUS_DOWNLOADDB(file('https://raw.githubusercontent.com/motu-tool/mOTUs/master/motus/downloadDB.py'))
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MOTUS_PROFILE ( input, MOTUS_DOWNLOADDB.out.db )
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}
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workflow test_motus_profile_paired_end {
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input = [
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[ id:'test', single_end:false ], // meta map
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[ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
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file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true) ]
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]
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MOTUS_DOWNLOADDB(file('https://raw.githubusercontent.com/motu-tool/mOTUs/master/motus/downloadDB.py'))
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MOTUS_PROFILE ( input, MOTUS_DOWNLOADDB.out.db)
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}
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workflow test_motus_profile_bam {
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input = [
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[ id:'test', single_end:false ], // meta map
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[ file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true) ]
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]
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MOTUS_DOWNLOADDB(file('https://raw.githubusercontent.com/motu-tool/mOTUs/master/motus/downloadDB.py'))
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MOTUS_PROFILE ( input, MOTUS_DOWNLOADDB.out.db)
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}
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