diff --git a/phylogenetic/config/auspice_config_all.json b/phylogenetic/config/auspice_config_all.json index fa5fd966..d55a202f 100644 --- a/phylogenetic/config/auspice_config_all.json +++ b/phylogenetic/config/auspice_config_all.json @@ -3,7 +3,7 @@ "maintainers": [ {"name": "Trevor Bedford", "url": "http://bedford.io/team/trevor-bedford/"} ], - "build_url": "https://github.com/nextstrain/dengue", + "build_url": "https://github.com/nextstrain/dengue", "colorings": [ { "key": "gt", @@ -44,5 +44,8 @@ "country", "region", "author" + ], + "metadata_columns": [ + "genbank_accession" ] } diff --git a/phylogenetic/config/auspice_config_denv1.json b/phylogenetic/config/auspice_config_denv1.json index 19182bca..ae608416 100644 --- a/phylogenetic/config/auspice_config_denv1.json +++ b/phylogenetic/config/auspice_config_denv1.json @@ -43,5 +43,8 @@ "country", "region", "author" + ], + "metadata_columns": [ + "genbank_accession" ] } diff --git a/phylogenetic/config/auspice_config_denv2.json b/phylogenetic/config/auspice_config_denv2.json index a50dced9..6244d130 100644 --- a/phylogenetic/config/auspice_config_denv2.json +++ b/phylogenetic/config/auspice_config_denv2.json @@ -43,5 +43,8 @@ "country", "region", "author" + ], + "metadata_columns": [ + "genbank_accession" ] } diff --git a/phylogenetic/config/auspice_config_denv3.json b/phylogenetic/config/auspice_config_denv3.json index 42849eec..27d648ee 100644 --- a/phylogenetic/config/auspice_config_denv3.json +++ b/phylogenetic/config/auspice_config_denv3.json @@ -43,5 +43,8 @@ "country", "region", "author" + ], + "metadata_columns": [ + "genbank_accession" ] } diff --git a/phylogenetic/config/auspice_config_denv4.json b/phylogenetic/config/auspice_config_denv4.json index ee89e5e8..be3a933d 100644 --- a/phylogenetic/config/auspice_config_denv4.json +++ b/phylogenetic/config/auspice_config_denv4.json @@ -43,5 +43,8 @@ "country", "region", "author" + ], + "metadata_columns": [ + "genbank_accession" ] } diff --git a/phylogenetic/config/config_dengue.yaml b/phylogenetic/config/config_dengue.yaml index 3824415b..d6f3f6d8 100644 --- a/phylogenetic/config/config_dengue.yaml +++ b/phylogenetic/config/config_dengue.yaml @@ -1,4 +1,4 @@ -strain_id_field: "accession" +strain_id_field: "genbank_accession" display_strain_field: "strain" filter: diff --git a/phylogenetic/example_data/metadata_all.tsv b/phylogenetic/example_data/metadata_all.tsv index ba8c0c35..01a411da 100644 --- a/phylogenetic/example_data/metadata_all.tsv +++ b/phylogenetic/example_data/metadata_all.tsv @@ -1,4 +1,4 @@ -strain virus accession date region country division city db segment authors url title journal paper_url +strain virus genbank_accession date region country division city db segment authors url title journal paper_url DENV1/VIETNAM/BIDV1862/2008 dengue FJ410220 2008-XX-XX Southeast Asia Vietnam Vietnam Vietnam ? genome Alvarado et al. ? ? ? ? DENV3/WALLIS_AND_FUTUNA/1404838/1989 dengue JQ920487 1989-08-14 ? Wallis And Futuna French Overseas Collectivity Wallis And Futuna ? genome Aubry et al. ? ? ? ? DENV/BRAZIL/SJRP778/2013 dengue KT438585 2013-02-04 South America Brazil Brazil Brazil ? genome Araujo et al. ? ? ? ? diff --git a/phylogenetic/example_data/metadata_denv1.tsv b/phylogenetic/example_data/metadata_denv1.tsv index b697eb54..0574a0c7 100644 --- a/phylogenetic/example_data/metadata_denv1.tsv +++ b/phylogenetic/example_data/metadata_denv1.tsv @@ -1,4 +1,4 @@ -strain virus accession date region country division city db segment authors url title journal paper_url +strain virus genbank_accession date region country division city db segment authors url title journal paper_url DENV1/INDIA/237/1962 dengue JF297572 1962-XX-XX South Asia India India India ? genome Cecilia et al. ? ? ? ? DENV1/CHINA/RL6/2013 dengue KJ470727 2013-09-XX China China China China ? genome Guo et al. ? ? ? ? DENV1/THAILAND/AILANDKPPKDV08491NC04528V0L/2007 dengue JQ993108 2007-XX-XX Southeast Asia Thailand Thailand Thailand ? genome Aldstadt et al. ? ? ? ? diff --git a/phylogenetic/example_data/metadata_denv2.tsv b/phylogenetic/example_data/metadata_denv2.tsv index 31f88305..5c694c00 100644 --- a/phylogenetic/example_data/metadata_denv2.tsv +++ b/phylogenetic/example_data/metadata_denv2.tsv @@ -1,4 +1,4 @@ -strain virus accession date region country division city db segment authors url title journal paper_url +strain virus genbank_accession date region country division city db segment authors url title journal paper_url DENV2/INDONESIA/MKS0084/2007 dengue KC762660 2007-11-21 Southeast Asia Indonesia Makassar Makassar ? genome Bifani et al. ? ? ? ? DENV2/TAIWAN/71/2002 dengue EF016253 2002-XX-XX China Taiwan Taiwan Taiwan ? genome Ke et al. ? ? ? ? DENV2/PAKISTAN/8D/2011 dengue JX042512 2011-XX-XX West Asia Pakistan Pakistan Pakistan ? genome Alvi et al. ? ? ? ? diff --git a/phylogenetic/example_data/metadata_denv3.tsv b/phylogenetic/example_data/metadata_denv3.tsv index 911e8cef..18c5b0aa 100644 --- a/phylogenetic/example_data/metadata_denv3.tsv +++ b/phylogenetic/example_data/metadata_denv3.tsv @@ -1,4 +1,4 @@ -strain virus accession date region country division city db segment authors url title journal paper_url +strain virus genbank_accession date region country division city db segment authors url title journal paper_url DENV3/PUERTO_RICO/BIDV1615/2004 dengue FJ373302 2004-XX-XX North America Puerto Rico Puerto Rico Puerto Rico ? genome Alvarado et al. ? ? ? ? DENV3/THAILAND/BIDV2323/2001 dengue FJ744734 2001-XX-XX Southeast Asia Thailand Kamphaeng Phet Kamphaeng Phet ? genome Alvarado et al. ? ? ? ? DENV3/BANGLADESH/JACOB/NA dengue AY656673 ? South Asia Bangladesh Bangladesh Bangladesh ? genome Aaskov et al. ? ? ? ? diff --git a/phylogenetic/example_data/metadata_denv4.tsv b/phylogenetic/example_data/metadata_denv4.tsv index d3175b21..9d9ce386 100644 --- a/phylogenetic/example_data/metadata_denv4.tsv +++ b/phylogenetic/example_data/metadata_denv4.tsv @@ -1,4 +1,4 @@ -strain virus accession date region country division city db segment authors url title journal paper_url +strain virus genbank_accession date region country division city db segment authors url title journal paper_url DENV4/ECUADOR/FSE2098/2006 dengue GQ139572 2006-XX-XX South America Ecuador Ecuador Ecuador ? genome Alava et al. ? ? ? ? DENV4/BRAZIL/SJRP580/2012 dengue KP188562 2012-12-10 South America Brazil Brazil Brazil ? genome Araujo et al. ? ? ? ? DENV4/BRAZIL/GUSP0670/2013 dengue KP704043 2013-03-17 South America Brazil Brazil Brazil ? genome Balarini et al. ? ? ? ? diff --git a/phylogenetic/rules/prepare_sequences.smk b/phylogenetic/rules/prepare_sequences.smk index 9c163a61..5cb14c75 100644 --- a/phylogenetic/rules/prepare_sequences.smk +++ b/phylogenetic/rules/prepare_sequences.smk @@ -21,8 +21,8 @@ rule download: metadata = "data/metadata_{serotype}.tsv.zst" params: - sequences_url = "https://data.nextstrain.org/files/dengue/sequences_{serotype}.fasta.zst", - metadata_url = "https://data.nextstrain.org/files/dengue/metadata_{serotype}.tsv.zst" + sequences_url = "https://data.nextstrain.org/files/workflows/dengue/sequences_{serotype}.fasta.zst", + metadata_url = "https://data.nextstrain.org/files/workflows/dengue/metadata_{serotype}.tsv.zst" shell: """ curl -fsSL --compressed {params.sequences_url:q} --output {output.sequences}