Merge pull request #11 from nextstrain/add-phylogenetic-ci

Add CI GH Action to Phylogenetic

phylogenetic/build-configs/ci/config.yaml

@@ -0,0 +1,7 @@
+# This configuration file contains the custom configurations parameters
+# for the CI workflow to run with the example data.
+
+# Custom rules to run as part of the CI automated workflow
+# The paths should be relative to the phylogenetic directory.
+custom_rules:
+  - build-configs/ci/copy_example_data.smk

phylogenetic/build-configs/ci/copy_example_data.smk

@@ -14,4 +14,4 @@ rule copy_example_data:
 # Add a Snakemake ruleorder directive here if you need to resolve ambiguous rules
 # that have the same output as the copy_example_data rule.
 
-# ruleorder: copy_example_data > ...
+ruleorder: copy_example_data > decompress

phylogenetic/example_data/metadata.tsv

@@ -0,0 +1,21 @@
+accession	accession_version	strain	date	region	country	division	location	length	host	host_latin_name	host_family	host_genus	host_group	host_common_name	date_released	date_updated	sra_accessions	authors	abbr_authors	institution
+MN726865	MN726865.1	Z-14-136	2014-XX-XX	Asia	Philippines			11653	Domestic Dog	Canis lupus familiaris	Canidae	Canis	carnivores	dog	2019-12-25	2019-12-25		Brunker,K.,Miranda,M.E.	Brunker et al.	University of Glasgow, IBAHCM
+MT895955	MT895955.1	ERA-M-MF1	2019-XX-XX	Asia	China			11931	Other Mammal	Mus musculus	Muridae	Mus	rodents	house mouse	2021-11-17	2021-11-17		Xu,L.,Zhang,Y.	Xu et al.	Shanghai Public Health Clinical Center & Institute of Biomedical Sciences, Fudan University
+OK340700	OK340700.1	18_4347	2018-09-26	North America	USA			11856	Bat	Eptesicus fuscus	Vespertilionidae	Eptesicus	bats	big brown bat	2022-01-04	2022-01-04		Hyeon,J.Y.,Risatti,G.R.,Helal,Z.H.,McGinnis,H.,Sims,M.,Hunt,A.,Chung,D.H.,Kim,J.,Desiato,J.,Lee,D.H.,Lee,D.-H.,Risatti,G.	Hyeon et al.	University of Connecticut, Department of Pathobiology and Veterinary Science
+ON630696	ON630696.1	200808957	2008-07-10	South America	Peru			11832	Cattle	Bos taurus	Bovidae	Bos	even-toed ungulates & whales	domestic cattle	2023-02-07	2023-02-14		Viana,M.,Benavides,J.A.,Broos,A.,Ibanez Loayza,D.,Nino,R.,Bone,J.,da Silva Filipe,A.,Orton,R.,Valderrama Bazan,W.,Matthiopoulos,J.,Streicker,D.G.	Viana et al.	MRC-University of Glasgow Centre for Virus Research
+ON630706	ON630706.1	201600571	2016-01-15	South America	Peru			11832	Cattle	Bos taurus	Bovidae	Bos	even-toed ungulates & whales	domestic cattle	2023-02-07	2023-02-14		Viana,M.,Benavides,J.A.,Broos,A.,Ibanez Loayza,D.,Nino,R.,Bone,J.,da Silva Filipe,A.,Orton,R.,Valderrama Bazan,W.,Matthiopoulos,J.,Streicker,D.G.	Viana et al.	MRC-University of Glasgow Centre for Virus Research
+ON814541	ON814541.1	DS-T	2017-07-01	Asia	India			11859	Other Carnivore	Panthera tigris	Felidae	Panthera	carnivores	tiger	2023-03-20	2023-03-20		Sahoo,D.M.,Kumar,D.,Singh,K.P.	Sahoo et al.	Indian Veterinary Research Institute, ICAR
+OP515227	OP515227.1	W107	2012-05-10	Asia	Cambodia	Kampong Popil		11881	Domestic Dog	Canis lupus familiaris	Canidae	Canis	carnivores	dog	2023-07-26	2023-07-26		Layan,M.,Dacheux,L.,Lemey,P.,Brunker,K.,Ma,L.,Troupin,C.,Dussart,P.,Chevalier,V.,Wood,J.,Duong,V.,Li,S.,Bourhy,H.,Dellicour,S.	Layan et al.	Institut Pasteur, Unit Lyssavirus Epidemiology and Neuropathology, National Reference Center for Rabies, WHO Collaborating Centre for Reference and Research on Rabies
+OQ410148	OQ410148.1	AH21-1092	2021-XX-XX	North America	USA	Minnesota		11926	Human	Homo sapiens	Hominidae	Homo	primates	human	2023-05-08	2023-05-08		Holzbauer,S.M.,Schrodt,C.A.,Prabhu,R.M.,Asch-Kendrick,R.J.,Ireland,M.,Klumb,C.,Firestone,M.J.,Liu,G.,Harry,K.,Ritter,J.M.,Levine,M.Z.,Orciari,L.A.,Wilkins,K.,Yager,P.,Gigante,C.M.,Ellison,J.A.,Zhao,H.,Niezgoda,M.,Li,Y.,Levis,R.,Scott,D.,Satheshkumar,P.S.,Petersen,B.W.,Rao,A.K.,Bell,W.R.,Bjerk,S.M.,Forrest,S.,Gao,W.,Dasheiff,R.,Russell,K.,Pappas,M.,Kiefer,J.,Bickler,W.,Wiseman,A.,Jurantee,J.,Reichard,R.R.,Smith,K.E.,Lynfield,R.,Scheftel,J.,Wallace,R.M.,Bonwitt,J.	Holzbauer et al.	Centers for Disease Control and Prevention, Division of High-Consequence Pathogens and Pathology
+OR271010	OR271010.1	MAK-CAP-010	2022-06-17	Africa	Kenya	Makueni	Makueni, Kavati	11404	Other Ungulate	Capra hircus	Bovidae	Capra	even-toed ungulates & whales	goat	2023-09-20	2023-09-20		Kimita,G.,Wambugu,E.N.,Masakhwe,C.A.,Thumbi,S.M.,Waitumbi,J.N.	Kimita et al.	USAMRD-A/KEMRI, Basic Science Laboratory
+PP516874	PP516874.1	NNV-RAB-H13	2022-XX-XX	Asia	India			11782	Human	Homo sapiens	Hominidae	Homo	primates	human	2024-03-27	2024-04-29		Dhanya,K.K.,Varun,C.N.,Chandel,S.,Siddalingaiah,N.,Ananda,A.M.,Mani,R.S.	Dhanya et al.	NIMHANS, Department of Neurovirology
+KX148220	KX148220.1	15001AFS	2013-XX-XX	Africa	South Africa			11805	Other Carnivore	Herpestidae	Herpestidae		carnivores	mongooses	2016-11-28	2016-11-28		Troupin,C.,Dacheux,L.,Tanguy,M.,Sabeta,C.,Blanc,H.,Bouchier,C.,Vignuzzi,M.,Duchene,S.,Holmes,E.C.,Bourhy,H.	Troupin et al.	Institut Pasteur, Unit Lyssavirus Dynamics and Host Adaptation, WHO Collaborating Centre for Reference and Research on Rabies
+KX148236	KX148236.1	93011MAU	1993-XX-XX	Africa	Mauritania			11802	Domestic Dog	Canis lupus familiaris	Canidae	Canis	carnivores	dog	2016-11-28	2016-11-28		Troupin,C.,Dacheux,L.,Tanguy,M.,Sabeta,C.,Blanc,H.,Bouchier,C.,Vignuzzi,M.,Duchene,S.,Holmes,E.C.,Bourhy,H.	Troupin et al.	Institut Pasteur, Unit Lyssavirus Dynamics and Host Adaptation, WHO Collaborating Centre for Reference and Research on Rabies
+LC717416	LC717416.1		1965-XX-XX	Asia	Japan			11901	?		?	?	?	?	2022-12-09	2022-12-09		Horiya,M.,Posadas-Herrera,G.,Takayama-Ito,M.,Yamaguchi,Y.,Iizuka-Shiota,I.,Kato,H.,Okamoto,A.,Saijo,M.,Lim,C.K.	Horiya et al.	Department of Virology 1; 1-23-1 Toyama Shinjuku-ku, Tokyo, Tokyo 162-8640
+MF143200	MF143200.2	ME.2013.0109	2013-04-25	North America	USA	Windham	Cumberland, Me	11924	Raccoon	Procyon lotor	Procyonidae	Procyon	carnivores	raccoon	2017-09-13	2021-06-09		Trewby,H.,Nadin-Davis,S.A.,Real,L.A.,Biek,R.	Trewby et al.	University of Glasgow, IBAHCM
+MK540728	MK540728.1	NY.2010.1439R	2010-XX-XX	North America	USA	New York		11924	Raccoon	Procyon lotor	Procyonidae	Procyon	carnivores	raccoon	2019-09-03	2021-06-08		Nadin-Davis,S.,Buchanan,T.,Nituch,L.,Fehlner-Gardiner,C.,Nadin-Davis,S.A.	Nadin-Davis et al.	Ottawa Laboratory Fallowfield, Canadian Food Inspection Agency, Rabies Centre of Expertise
+MK760754	MK760754.1	93-A-27	2014-04-19	Asia	Iran	Kurdistan	Saqqez	11723	Domestic Dog	Canis lupus familiaris	Canidae	Canis	carnivores	dog	2019-10-01	2019-10-01		Dellicour,S.,Troupin,C.,Jahanbakhsh,F.,Salama,A.,Massoudi,S.,Moghaddam,M.K.,Baele,G.,Lemey,P.,Gholami,A.,Bourhy,H.	Dellicour et al.	Institut Pasteur, Unit Lyssavirus Dynamics and Host Adaptation, WHO Collaborating Centre for Reference and Research on Rabies
+MN233898	MN233898.1		1989-XX-XX	North America	USA	Alaska		11926	Fox (Vulpes sp.)	Vulpes vulpes	Canidae	Vulpes	carnivores	red fox	2020-03-18	2021-06-08		Nadin-Davis,S.A.,Falardeau,E.,Flynn,A.,Whitney,H.,Marshall,H.D.,Fallardeau,E.,Marshall,H.,Fehlner-Gardiner,C.	Nadin-Davis et al.	Ottawa Laboratory Fallowfield, Canadian Food Inspection Agency, Rabies Centre of Expertise
+JQ944704	JQ944704.1	184VNO	2009-XX-XX	Europe	Russia			11923	Other Carnivore	Nyctereutes procyonoides	Canidae	Nyctereutes	carnivores	raccoon dog	2012-07-14	2012-07-14		Chupin,S.,Chernyshova,E.,Metlin,A.	Chupin et al.	FGBI Federal Centre for Animal Health, Laboratory for Diagnosis of Farm Animal and Fish Diseases
+KT119676	KT119676.1	07171RCA_2007_312	2007-04-24	Africa	Central African Republic	Bangui		5053	Domestic Dog	Canis lupus familiaris	Canidae	Canis	carnivores	dog	2016-01-30	2016-01-30		Bourhy,H.,Lepelletier,A.,Talbi,C.	Bourhy et al.	Institut Pasteur, Lyssavirus Dynamics and Host Adaptation
+JQ685926	JQ685926.1	AZ2408	2005-XX-XX	North America	USA			11824	Bat	Eptesicus fuscus	Vespertilionidae	Eptesicus	bats	big brown bat	2012-07-11	2012-07-11		Kuzmin,I.V.,Shi,M.,Orciari,L.A.,Yager,P.A.,Velasco-Villa,A.,Kuzmina,N.A.,Streicker,D.G.,Bergman,D.L.,Rupprecht,C.E.	Kuzmin et al.	Centers for Disease Control and Prevention, Rabies Program