diff --git a/bifrost/bifrost_listener/aggregation.py b/bifrost/bifrost_listener/aggregation.py index df77a3e..0c0627d 100644 --- a/bifrost/bifrost_listener/aggregation.py +++ b/bifrost/bifrost_listener/aggregation.py @@ -109,6 +109,7 @@ def agg_pipeline(changed_ids=None): "sero_enterobase": "$categories.serotype.report.enterobase_serotype1", "sero_seqsero": "$categories.serotype.report.seqsero_serotype", "sero_antigen_seqsero": "$categories.serotype.summary.antigenic_profile", + "sero_serotype_finder": "$categories.bifrost_sp_ecoli.summary.OH", "sero_d_tartrate": "$categories.serotype.summary.D-tartrate_pos10", "mlst_schema": {"$arrayElemAt": ["$mlstlookup.schema", 0]}, # "siblings": "$siblings", @@ -253,10 +254,16 @@ def agg_pipeline(changed_ids=None): "trst": "$categories.bifrost_sp_cdiff.summary.TRST", "tcda": "$categories.bifrost_sp_cdiff.summary.tcdA", "tcdb": "$categories.bifrost_sp_cdiff.summary.tcdB", - "cdta_cdtb": "$categories.bifrost_sp_cdiff.summary.cdtA/B", - "del117": "$categories.bifrost_sp_cdiff.summary.117del", + "cdta_cdtb": { + "$concat": [ + "$categories.bifrost_sp_cdiff.summary.cdtA", + "/", + "$categories.bifrost_sp_cdiff.summary.cdtB" + ] + }, + "del_117": "$categories.bifrost_sp_cdiff.summary.117del", "a117t": "$categories.bifrost_sp_cdiff.summary.A117T", - "cdiff_details": "$categories.bifrost_sp_cdiff.summary.tcdA:tcdB:tcdC:cdtA:cdtB", + "cdiff_details": "$categories.bifrost_sp_cdiff.summary.cov_info", "adhaesion": "$categories.bifrost_sp_ecoli.summary.eae", "toxin": "$categories.bifrost_sp_ecoli.summary.stx", "toxin_details": "$categories.bifrost_sp_ecoli.summary.verbose", @@ -272,13 +279,9 @@ def agg_pipeline(changed_ids=None): }, "virulence_genes": { "$concat": [ - "$categories.bifrost_sp_ecoli.summary.wzx", - ",", - "$categories.bifrost_sp_ecoli.summary.wzy", - ",", - "$categories.bifrost_sp_ecoli.summary.fliC", - ",", "$categories.bifrost_sp_ecoli.summary.ehx", + ",", + "$categories.bifrost_sp_ecoli.summary.other", ]}, "bifrost_min_read_check": { "$let": {