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https://github.com/MillironX/nf-core_modules.git
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b02e648c22
* Add motus/merge module, missing test yml * Fix prefix * Fix polymersase * Update test meta.yml * Try new version system * Typo fix * Clairfy docs for the version file * Switch to directory auto detection * Now with the change and not just meta * Remove now unneeded input parameter from test * Fix input type check * Try adding db requirement to fix docker issue * Update modules/motus/merge/main.nf * Fix input * Apply suggestions from code review * Fix md5sums * Replace debugging db location with actual * Fix contains due to further varialbility * Indenting
29 lines
1 KiB
Text
29 lines
1 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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include { MOTUS_MERGE } from '../../../../modules/motus/merge/main.nf'
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workflow test_motus_merge {
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input = Channel.fromList(
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[
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[
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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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[
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[ id:'test2', 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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]
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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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MOTUS_MERGE ( MOTUS_PROFILE.out.out.map{it[1]}.collect(), MOTUS_DOWNLOADDB.out.db, MOTUS_PROFILE.out.versions.first(), false )
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}
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