diff --git a/conf/test.config b/conf/test.config index 777d9bf..016eb2e 100644 --- a/conf/test.config +++ b/conf/test.config @@ -39,6 +39,7 @@ params { run_metaphlan3 = true run_centrifuge = true run_diamond = true + run_krakenuniq = true run_motus = false run_krona = true krona_taxonomy_directory = 'https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/sarscov2/metagenome/krona_taxonomy.tab' diff --git a/conf/test_motus.config b/conf/test_motus.config index d167b94..2428a4c 100644 --- a/conf/test_motus.config +++ b/conf/test_motus.config @@ -38,6 +38,7 @@ params { run_metaphlan3 = false run_centrifuge = false run_diamond = false + run_krakenuniq = false run_motus = true run_profile_standardisation = true } diff --git a/conf/test_nopreprocessing.config b/conf/test_nopreprocessing.config index 357f76f..9a51320 100644 --- a/conf/test_nopreprocessing.config +++ b/conf/test_nopreprocessing.config @@ -38,6 +38,7 @@ params { run_metaphlan3 = true run_centrifuge = true run_diamond = true + run_krakenuniq = true run_motus = false run_krona = true } diff --git a/conf/test_noprofiling.config b/conf/test_noprofiling.config index 59ed0da..3ca715b 100644 --- a/conf/test_noprofiling.config +++ b/conf/test_noprofiling.config @@ -39,6 +39,7 @@ params { run_metaphlan3 = false run_centrifuge = false run_diamond = false + run_krakenuniq = false run_motus = false } diff --git a/conf/test_nothing.config b/conf/test_nothing.config index df09613..47976df 100644 --- a/conf/test_nothing.config +++ b/conf/test_nothing.config @@ -38,6 +38,7 @@ params { run_metaphlan3 = false run_centrifuge = false run_diamond = false + run_krakenuniq = false run_motus = false } diff --git a/subworkflows/local/profiling.nf b/subworkflows/local/profiling.nf index 4ca2c4c..aeee2a4 100644 --- a/subworkflows/local/profiling.nf +++ b/subworkflows/local/profiling.nf @@ -271,7 +271,7 @@ workflow PROFILING { ch_input_for_krakenuniq = ch_input_for_profiling.krakenuniq .map { meta, reads, db_meta, db -> - [[single_end: meta.single_end], reads, db_meta, db] + [[id: db_meta.db_name, single_end: meta.single_end], reads, db_meta, db] } .groupTuple(by: [0,2,3]) .dump(tag: "krakenuniq_premultimap")