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Add automation workflows #5

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merged 9 commits into from
Oct 24, 2024
Merged

Add automation workflows #5

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6042eb6
Add upload ingest rules
j23414 Sep 25, 2024
755d11d
Add example data
j23414 Sep 26, 2024
242ee57
Add phylogenetic ci
j23414 Sep 26, 2024
dd077a7
Add phylogenetic nextstrain automation
j23414 Sep 26, 2024
12a7b3d
Add github actions
j23414 Sep 26, 2024
72cd56c
Download s3 data for phylogenetic workflow
j23414 Oct 4, 2024
1c00e9a
inline the root sequence
j23414 Oct 4, 2024
49e5bfc
Refactor ingest config to match pathogen-repo-guide
j23414 Oct 12, 2024
b28766f
Add is_lab_host column
j23414 Oct 12, 2024
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Add example data
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@j23414
j23414 committed Sep 26, 2024
commit 755d11da79cd976e420a75be39649eb4a9daf857
19 changes: 19 additions & 0 deletions phylogenetic/example_data/metadata.tsv
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accession strain date date_released date_updated region country division location length host sra_accessions abbr_authors institution submitter_country sample_type
AF212302.2 XXXX-XX-XX 2000-06-01 2001-12-10 18246 Chua et al. Centers for Disease Control and Prevention, Measles Virus Section USA
AJ564621.1 NV/MY/99/VRI-2794 XXXX-XX-XX 2004-01-05 2023-07-14 18246 AbuBakar et al. Abubakar S., Medical Microbiology, University Malaya, Faculty Of Medicine, 50603 Kuala Lumpur Malaysia
AJ564622.1 NV/MY/99/VRI-1413 XXXX-XX-XX 2004-01-05 2023-07-14 18246 AbuBakar et al. Abubakar S., Medical Microbiology, University Malaya, Faculty Of Medicine, 50603 Kuala Lumpur Malaysia
AJ564623.1 NV/MY/99/UM-0128 XXXX-XX-XX 2004-01-05 2023-07-14 18246 AbuBakar et al. Abubakar S., Medical Microbiology, University Malaya, Faculty Of Medicine, 50603 Kuala Lumpur Malaysia
AJ627196.1 NV/MY/99/VRI-0626 XXXX-XX-XX 2005-01-07 2005-04-15 Asia Malaysia 18246 Sus scrofa AbuBakar et al. Abubakar S., Medical Microbiology, University Malaya, Faculty of Medicine, 50603 Kuala Lumpur Malaysia
AY029767.1 UMMC1 XXXX-XX-XX 2001-09-07 1900-01-01 Asia Malaysia 18246 Chan et al. University of Malaya, Department of Medical Microbiology Malaysia
AY029768.1 UMMC2 XXXX-XX-XX 2001-09-07 1900-01-01 Asia Malaysia 18246 Chan et al. University of Malaya, Department of Medical Microbiology Malaysia
AY988601.1 2004-XX-XX 2005-06-01 2005-09-26 Asia Bangladesh 18252 Homo sapiens Harcourt et al. Centers for Disease Control and Prevention, Division of Viral and Rickettsial Diseases USA
FJ513078.1 Ind-Nipah-07-FG 2007-XX-XX 2009-12-31 2011-05-02 Asia India 18252 Homo sapiens Arankalle et al. National Institute of Virology, Hepatitis India lung
JN808857.1 NIVBGD2008MANIKGONJ 2008-XX-XX 2012-02-04 2012-02-04 Asia Bangladesh Manikgonj 18252 Homo sapiens Lo et al. Centers for Disease Control and Prevention, Viral Special Pathogens Branch USA oronasopharynx
JN808863.1 NIVBGD2008RAJBARI 2008-XX-XX 2012-02-04 2012-02-04 Asia Bangladesh Dhaka Rajbari 18252 Homo sapiens Lo et al. Centers for Disease Control and Prevention, Viral Special Pathogens Branch USA oronasopharynx
JN808864.1 NIVBGD2010FARIDPUR 2010-XX-XX 2012-02-04 2012-02-04 Asia Bangladesh Dhaka Faridpur 18167 Homo sapiens Lo et al. Centers for Disease Control and Prevention, Viral Special Pathogens Branch USA oronasopharynx
KY425646.1 IRF0160 1999-XX-XX 2017-01-15 2017-01-15 Asia Malaysia Kuala Lumpur 18212 Homo sapiens Johnson et al. National Institute of Allergy and Infectious Diseases, National Institutes of Health, Integrated Research Facility - Frederick USA
KY425655.1 IRF0158 1999-XX-XX 2017-01-15 2017-01-15 Asia Malaysia Kuala Lumpur 18214 Homo sapiens Honko et al. National Institute of Allergy and Infectious Diseases, National Institutes of Health, Integrated Research Facility - Frederick USA
MH396625.1 2018-05-17 2018-11-01 2018-11-01 Asia India Kozhikode District Kerala State 18210 Homo sapiens Yadav et al. National Institute of Virology, Maximum Containment Laboratory India oronasopharynx
MH523640.1 2018-05-17 2019-04-01 2019-04-01 Asia India Kozhikode District Kerala State 18132 Homo sapiens Yadav et al. National Institute of Virology, Maximum Containment Laboratory India lung
MH523641.1 2018-05-21 2019-04-01 2019-04-01 Asia India Kozhikode District Kerala State 18027 Homo sapiens Yadav et al. National Institute of Virology, Maximum Containment Laboratory India oronasopharynx
MH523642.1 Nipah virus 2018-05-17 2019-04-01 2019-04-01 Asia India Kozhikode District Kerala State 18242 Homo sapiens Yadav et al. National Institute of Virology, Maximum Containment Laboratory India oronasopharynx
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