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Add KU to the test profiles and add id to KU processes
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commit
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6 changed files with 6 additions and 1 deletions
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@ -39,6 +39,7 @@ params {
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run_metaphlan3 = true
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run_metaphlan3 = true
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run_centrifuge = true
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run_centrifuge = true
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run_diamond = true
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run_diamond = true
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run_krakenuniq = true
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run_motus = false
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run_motus = false
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run_krona = true
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run_krona = true
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krona_taxonomy_directory = 'https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/sarscov2/metagenome/krona_taxonomy.tab'
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krona_taxonomy_directory = 'https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/sarscov2/metagenome/krona_taxonomy.tab'
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@ -38,6 +38,7 @@ params {
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run_metaphlan3 = false
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run_metaphlan3 = false
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run_centrifuge = false
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run_centrifuge = false
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run_diamond = false
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run_diamond = false
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run_krakenuniq = false
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run_motus = true
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run_motus = true
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run_profile_standardisation = true
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run_profile_standardisation = true
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}
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}
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@ -38,6 +38,7 @@ params {
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run_metaphlan3 = true
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run_metaphlan3 = true
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run_centrifuge = true
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run_centrifuge = true
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run_diamond = true
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run_diamond = true
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run_krakenuniq = true
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run_motus = false
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run_motus = false
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run_krona = true
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run_krona = true
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}
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}
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@ -39,6 +39,7 @@ params {
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run_metaphlan3 = false
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run_metaphlan3 = false
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run_centrifuge = false
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run_centrifuge = false
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run_diamond = false
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run_diamond = false
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run_krakenuniq = false
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run_motus = false
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run_motus = false
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}
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}
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@ -38,6 +38,7 @@ params {
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run_metaphlan3 = false
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run_metaphlan3 = false
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run_centrifuge = false
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run_centrifuge = false
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run_diamond = false
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run_diamond = false
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run_krakenuniq = false
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run_motus = false
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run_motus = false
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}
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}
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@ -271,7 +271,7 @@ workflow PROFILING {
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ch_input_for_krakenuniq = ch_input_for_profiling.krakenuniq
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ch_input_for_krakenuniq = ch_input_for_profiling.krakenuniq
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.map {
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.map {
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meta, reads, db_meta, db ->
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meta, reads, db_meta, db ->
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[[single_end: meta.single_end], reads, db_meta, db]
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[[id: db_meta.db_name, single_end: meta.single_end], reads, db_meta, db]
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}
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}
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.groupTuple(by: [0,2,3])
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.groupTuple(by: [0,2,3])
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.dump(tag: "krakenuniq_premultimap")
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.dump(tag: "krakenuniq_premultimap")
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