[DROP] Add CI and example data

.github/workflows/ci.yaml

@@ -0,0 +1,9 @@
+name: CI
+
+on:
+ - push
+ - pull_request
+
+jobs:
+ pathogen-ci:
+ uses: nextstrain/.github/.github/workflows/pathogen-repo-ci.yaml@victorlin/copy-example-data-recursively

.gitignore

@@ -0,0 +1,25 @@
+# Files created by the pipeline, which we want to keep out of git
+# (or at least out of _this_ git repo).
+data/
+results/
+auspice/
+build/
+
+# Snakemake
+.snakemake/
+logs/
+
+# Python
+*.pyc
+.tox/
+.cache/
+
+# OS generated files
+.DS_Store
+.DS_Store?
+._*
+.Spotlight-V100
+.Trashes
+Icon?
+ehthumbs.db
+Thumbs.db

README.md

@@ -35,3 +35,13 @@ Follow the standard [installation instructions](https://docs.nextstrain.org/en/l
 ## Data Use
 
 We gratefully acknowledge the authors, originating and submitting laboratories of the genetic sequences and metadata for sharing their work. Please note that although data generators have generously shared data in an open fashion, that does not mean there should be free license to publish on this data. Data generators should be cited where possible and collaborations should be sought in some circumstances.
+
+### Update example data
+
+[Example data](./example_data/) is used by [CI](https://github.com/nextstrain/rsv/actions/workflows/ci.yaml). It can also be used as a small subset of real-world data.
+
+Example data should be updated every time metadata schema is changed. To update, run:
+
+```sh
+nextstrain build --docker . update_example_data -F
+```

Snakefile

@@ -12,6 +12,8 @@ rule all:
  subtype = config.get("subtypes",['a']),
  build = config.get("buildstorun", ['genome']))
 
+include: "workflow/snakemake_rules/chores.smk"
+
 include: "workflow/snakemake_rules/core.smk"
 
 include: "workflow/snakemake_rules/export.smk"

example_data/a/metadata.tsv

@@ -0,0 +1,51 @@
+strain accession genbank_accession_rev date region country division location host date_submitted sra_accession abbr_authors reverse authors institution F_coverage G_coverage genome_coverage
+KM042386 KM042386 KM042386.1 2013-01-14 North America USA Tennessee Homo sapiens 2014-08-08 Das et al Das,S., Halpin,R.A., Bera,J., Puri,V., Fedorova,N., Tsitrin,T., Stockwell,T., Amedeo,P., Bishop,B., Katzel,D., Schobel,S., Shrivastava,S., Hartert,T., Moore,M., Chappell,J., Larkin,E., Wentworth,D.E., Anderson,L.J. 1.0 1.0 0.996
+OM062646 OM062646 OM062646.1 Asia China Xiamen Homo sapiens 2022-02-13 Sun et al Sun,Y., Lei,S., Wang,Y., Qiang,H., Yin,Y., Jiang,Z., Zhu,M., Chen,X., Ye,H., Zheng,Z., Xia,N. 0.0 0.856 0.053
+KJ890469 KJ890469 KJ890469.1 2012-02-XX North America USA Homo sapiens 2014-09-03 Avadhanula et al Avadhanula,V., Chemaly,R.F., Shah,D.P., Ghantoji,S.S., Azzi,J.M., Aideyan,L.O., Mei,M., Piedra,P.A. 0.0 0.27 0.017
+AB687647 AB687647 AB687647.1 2007-XX-XX Asia Japan Fukui Homo sapiens 2011-12-14 Nakamura et al Nakamura,M., Sugawara,T., Toho,M., Kawabata,M., Tsuchida,S., Maegawa,K., Hanaoka,N., Okusa,Y., Adhikary,A.K., Okabe,N., Fujimoto,T. 0.0 0.27 0.018
+KJ627339 KJ627339 KJ627339.1 2009-03-11 South America Peru Piura Homo sapiens 2014-04-07 Wentworth et al Wentworth,D.E., Halpin,R.A., Bera,J., Lin,X., Fedorova,N., Tsitrin,T., McLellan,M., Stockwell,T., Amedeo,P., Bishop,B., Gupta,N., Hoover,J., Katzel,D., Schobel,S., Shrivastava,S., Garcia,J., Laguna-Torres,V.A., Leguia,M., Benavides,J.G., Halsey,E. 1.0 1.0 0.997
+OP690220 OP690220 OP690220.1 2019-XX-XX Asia Taiwan Homo sapiens 2023-05-01 Lee et al Lee,C.Y. 1.0 0.0 0.114
+AB551041 AB551041 AB551041.1 Asia Japan Kanagawa Yokohama 2011-12-23 Fujitsuka et al Fujitsuka,A., Tsukagoshi,H., Arakawa,M., Goto-Sugai,K., Ryo,A., Okayama,Y., Mizuta,K., Nishina,A., Yoshizumi,M., Kaburagi,Y., Noda,M., Tashiro,M., Okabe,N., Mori,M., Yokota,S., Kimura,H., Sugai,K. 0.0 0.246 0.016
+HQ699280 HQ699280 HQ699280.1 2009-12-XX Asia South Korea Homo sapiens 2011-07-13 Baek et al Baek,Y.H., Choi,E.H., Song,M.S., Pascua,P.N., Kwon,H.I., Park,S.J., Lee,J.H., Woo,S.I., Ahn,B.H., Han,H.S., Hahn,Y.S., Shin,K.S., Jang,H.L., Kim,S.Y., Choi,Y.K., Park,S.-J., Song,M.-S., Choi,Y.-K. 0.0 1.0 0.059
+KF246608 KF246608 KF246608.1 2012-10-10 Asia India Homo sapiens 2014-01-22 Choudhary et al Choudhary,M.L., Anand,S.P., Wadhwa,B.S., Chadha,M.S. 0.988 1.0 0.177
+KU955245 KU955245 KU955245.1 2010-XX-XX Asia China Homo sapiens 2019-03-31 Jia et al Jia,B., Xiao,Y., Wang,Y., Chen,L., Zhang,J., Ren,L., Wang,J. 0.0 1.0 0.059
+KT326792 KT326792 KT326792.1 2014-12-16 Europe Spain Homo sapiens 2016-07-31 Calderon et al Calderon,A., Pozo,F., Calvo,C., Garcia-Garcia,M., Gonzalez,M., Molinero,M., Casas,I. 0.0 1.0 0.059
+OM062752 OM062752 OM062752.1 Asia China Xiamen Homo sapiens 2022-02-13 Sun et al Sun,Y., Lei,S., Wang,Y., Qiang,H., Yin,Y., Jiang,Z., Zhu,M., Chen,X., Ye,H., Zheng,Z., Xia,N. 0.01 0.893 0.057
+KJ672457 KJ672457 KJ672457.1 2013-01-07 North America USA Tennessee Homo sapiens 2014-05-09 Das et al Das,S., Halpin,R.A., Bera,J., Fedorova,N., Tsitrin,T., Stockwell,T., Amedeo,P., Bishop,B., Gupta,N., Hoover,J., Katzel,D., Schobel,S., Shrivastava,S., Hartert,T., Moore,M., Chappell,J., Larkin,E., Wentworth,D.E., Anderson,L.J. 1.0 1.0 0.996
+KU962191 KU962191 KU962191.1 2013-XX-XX Asia China Homo sapiens 2019-03-31 Jia et al Jia,B., Xiao,Y., Wang,Y., Chen,L., Zhang,J., Ren,L., Wang,J. 0.0 0.27 0.017
+OM062902 OM062902 OM062902.1 Asia China Xiamen Homo sapiens 2022-02-13 Sun et al Sun,Y., Lei,S., Wang,Y., Qiang,H., Yin,Y., Jiang,Z., Zhu,M., Chen,X., Ye,H., Zheng,Z., Xia,N. 0.956 0.0 0.108
+MF445942 MF445942 MF445942.1 2013-02-18 Asia China Homo sapiens 2019-12-31 Su et al Su,Y., Wu,Y., Tian,R., Liang,G. 0.968 0.0 0.11
+KY711325 KY711325 KY711325.1 2016-XX-XX Asia Saudi Arabia Homo sapiens 2019-04-01 Al Hassinah et al Al Hassinah,S.M., Ahmed,A., Alsenaidy,A.M., Haq,S.H., Somily,A.M. 0.014 0.221 0.018
+OM062674 OM062674 OM062674.1 Asia China Xiamen Homo sapiens 2022-02-13 Sun et al Sun,Y., Lei,S., Wang,Y., Qiang,H., Yin,Y., Jiang,Z., Zhu,M., Chen,X., Ye,H., Zheng,Z., Xia,N. 0.0 0.856 0.053
+OP690353 OP690353 OP690353.1 2019-XX-XX Asia Taiwan Homo sapiens 2023-05-01 Lee et al Lee,C.Y. 0.0 0.619 0.039
+KX533638 KX533638 KX533638.1 2013-09-06 Asia China Homo sapiens 2017-09-28 Song et al Song,J., Zhang,Y., Wang,H., Shi,J., Sun,L., Zhang,X., Yang,Z., Guan,W., Zhang,H., Yu,P., Xie,Z., Cui,A., Ng,T.I., Xu,W. 0.0 0.267 0.017
+KC858164 KC858164 KC858164.1 2011-01-20 Europe Italy Ancona Homo sapiens 2013-07-23 Bagnarelli et al Bagnarelli,P., Trotta,D., Ferreri,M.L., Pierangeli,A. 0.0 0.41 0.026
+LC367154 LC367154 LC367154.1 2014-08-12 Asia Japan Kanagawa Yokohama Homo sapiens 2018-01-25 Saikusa et al Saikusa,M., Kawakami,C., Usuku,S., Sasao,T., Okubo,I. 1.0 0.0 0.114
+KP284607 KP284607 KP284607.1 2013-12-XX Europe Italy Homo sapiens 2015-05-16 Esposito et al Esposito,S., Piralla,A., Zampiero,A., Bianchini,S., Di Pietro,G., Scala,A., Pinzani,R., Fossali,E., Baldanti,F., Principi,N. 0.0 0.27 0.017
+KC858196 KC858196 KC858196.1 2011-01-11 Europe Italy Roma Homo sapiens 2013-07-23 Bagnarelli et al Bagnarelli,P., Trotta,D., Ferreri,M.L., Pierangeli,A. 0.0 0.41 0.026
+KX765886 KX765886 KX765886.1 2015-06-18 Oceania New Zealand Christchurch Homo sapiens 2016-10-01 Shabman et al Shabman,R., Das,S.R., Shilts,M., Fedorova,N., Puri,V., Shrivastava,S., Amedeo,P., Williams,M., Barratt,K., Mitchell,J., Jennings,L. 1.0 1.0 0.998
+OM062942 OM062942 OM062942.1 Asia China Xiamen Homo sapiens 2022-02-13 Sun et al Sun,Y., Lei,S., Wang,Y., Qiang,H., Yin,Y., Jiang,Z., Zhu,M., Chen,X., Ye,H., Zheng,Z., Xia,N. 0.956 0.0 0.108
+AB160928 AB160928 AB160928.1 Asia Japan Hokkaido Sapporo 2004-01-27 Kuroiwa et al Kuroiwa,Y., Nagai,K., Okita,L., Tsutsumi,H., Yui,I., Nakayama,T., Kase,T. 0.0 0.193 0.013
+KU962877 KU962877 KU962877.1 2008-XX-XX Asia China Homo sapiens 2019-03-31 Jia et al Jia,B., Xiao,Y., Wang,Y., Chen,L., Zhang,J., Ren,L., Wang,J. 0.0 0.27 0.017
+KX533849 KX533849 KX533849.1 2010-11-13 Asia China Homo sapiens 2017-09-28 Song et al Song,J., Zhang,Y., Wang,H., Shi,J., Sun,L., Zhang,X., Yang,Z., Guan,W., Zhang,H., Yu,P., Xie,Z., Cui,A., Ng,T.I., Xu,W. 0.0 0.267 0.017
+LC037539 LC037539 LC037539.1 2012-10-15 Asia Japan Niigata Homo sapiens 2015-03-26 Hibino et al Hibino,A., Saito,R., Taniguchi,K., Zaraket,H., Shobugawa,Y., Matsui,T., Suzuki,H., Shoubugawa,Y., Sano,Y. 0.0 0.246 0.016
+MG930252 MG930252 MG930252.1 2013-XX-XX Europe Germany Wuerzburg Homo sapiens 2018-03-19 Prifert et al Prifert,C., Streng,A., Schultz,J., Liese,J.G., Weissbrich,B., Hofmann,D. 0.0 0.27 0.017
+OK649594 OK649594 OK649594.1 1995-XX-XX North America USA Homo sapiens 2021-11-07 Wang et al Wang,L., Ng,T.F.F., Castro,C.J., Marine,R.L., Magana,L.C., Esona,M., Peret,T.C.T., Thornburg,N.J. 1.0 1.0 0.998
+OM857211 OM857211 OM857211.1 2021-01-28 Oceania Australia Homo sapiens 2022-04-06 Eden et al Eden,J.-S., Sikazwe,C., Levy,A., Deng,Y.-M., Dhanasekaran,V., Smith,D.W., Kok,J., Barr,I.G. 1.0 1.0 0.472
+KC677874 KC677874 KC677874.1 2012-08-30 North America Cuba Homo sapiens 2014-09-25 Valdes et al Valdes,O., Corso,M., Pinon,A., Acosta,B., Savon,C., Gonzalez,G., Mune,M., Hernandez,B., Echevarria,Y., Oropesa,S. 0.0 1.0 0.059
+KU962706 KU962706 KU962706.1 2012-XX-XX Asia China Homo sapiens 2019-03-31 Jia et al Jia,B., Xiao,Y., Wang,Y., Chen,L., Zhang,J., Ren,L., Wang,J. 0.0 0.27 0.017
+KU962830 KU962830 KU962830.1 2008-XX-XX Asia China Homo sapiens 2019-03-31 Jia et al Jia,B., Xiao,Y., Wang,Y., Chen,L., Zhang,J., Ren,L., Wang,J. 0.0 0.27 0.017
+LC037573 LC037573 LC037573.1 2012-11-21 Asia Japan Niigata Homo sapiens 2015-03-26 Hibino et al Hibino,A., Saito,R., Taniguchi,K., Zaraket,H., Shobugawa,Y., Matsui,T., Suzuki,H., Shoubugawa,Y., Sano,Y. 0.0 0.246 0.016
+EF650645 EF650645 EF650645.1 Asia China 2007-08-08 Feng et al Feng,D., Xu,J., Zhao,S. 0.0 1.0 0.067
+MZ747634 MZ747634 MZ747634.1 2021-XX-XX Asia Taiwan Homo sapiens 2022-01-26 Lee et al Lee,C.Y., Wu,T.H., Fang,Y.P., Chang,J.C., Wang,H.C., Lin,S.J., Mai,C.H., Chang,Y.C., Chou,T.Y., Lee,C.-Y. 0.0 0.619 0.039
+MT236166 MT236166 MT236166.1 2019-XX-XX South America Brazil São Paulo Sp Homo sapiens 2021-03-20 Dorlass et al Dorlass,E.G., Mesquita,F.S., Thomazelli,L.M., Durigon,E.L., Oliveira,D.B. 0.0 0.797 0.051
+KX533834 KX533834 KX533834.1 2010-12-05 Asia China Homo sapiens 2017-09-28 Song et al Song,J., Zhang,Y., Wang,H., Shi,J., Sun,L., Zhang,X., Yang,Z., Guan,W., Zhang,H., Yu,P., Xie,Z., Cui,A., Ng,T.I., Xu,W. 0.0 0.267 0.017
+OK458598 OK458598 OK458598.1 2009-04-14 Africa Kenya Homo sapiens 2021-12-13 Wangui et al Wangui,J.M., Nokes,J.D., Opot,B.H., Opanda,S.M., Agoti,C.N., Otieno,J.R., Bulimo,W.D. 0.0 0.656 0.042
+KC297345 KC297345 KC297345.1 2012-XX-XX Asia China Homo sapiens 2013-10-02 Cui et al Cui,G., Zhu,R., Qian,Y., Deng,J., Zhao,L., Sun,Y., Wang,F. 0.0 1.0 0.06
+KU962680 KU962680 KU962680.1 2011-XX-XX Asia China Homo sapiens 2019-03-31 Jia et al Jia,B., Xiao,Y., Wang,Y., Chen,L., Zhang,J., Ren,L., Wang,J. 0.0 0.27 0.017
+OM062669 OM062669 OM062669.1 Asia China Xiamen Homo sapiens 2022-02-13 Sun et al Sun,Y., Lei,S., Wang,Y., Qiang,H., Yin,Y., Jiang,Z., Zhu,M., Chen,X., Ye,H., Zheng,Z., Xia,N. 0.0 0.856 0.053
+KU254617 KU254617 KU254617.1 2015-02-XX Asia China Jilin Homo sapiens 2016-07-05 Zheng et al Zheng,Y., Liu,L., Wang,S., Li,Z., Hou,M., Li,J., Yu,X.-F., Zhang,W., Hua,S. 0.0 0.27 0.017
+LC037513 LC037513 LC037513.1 2012-09-12 Asia Japan Niigata Homo sapiens 2015-03-26 Hibino et al Hibino,A., Saito,R., Taniguchi,K., Zaraket,H., Shobugawa,Y., Matsui,T., Suzuki,H., Shoubugawa,Y., Sano,Y. 0.0 0.246 0.016
+MT236271 MT236271 MT236271.1 2017-XX-XX South America Brazil São Paulo Sp Homo sapiens 2021-03-20 Dorlass et al Dorlass,E.G., Mesquita,F.S., Thomazelli,L.M., Durigon,E.L., Oliveira,D.B. 0.0 0.721 0.046
+AB860234 AB860234 AB860234.1 2011-10-31 Asia South Korea Homo sapiens 2013-10-23 Kim et al Kim,Y.J., Kim,D.W., Lee,W.J., Yun,M.R., Lee,H.Y., Lee,H.S., Jung,H.D., Kim,K. 0.0 0.743 0.047
+KM586833 KM586833 KM586833.1 2012-10-15 Asia China Guangdong Guangzhou Homo sapiens 2014-12-07 Xie et al Xie,J.H., Zhu,B., Zhong,J.Y., Chen,Y., Zhang,Y.Y. 0.0 1.0 0.061