Ecosyste.ms: Issues

An open API service for providing issue and pull request metadata for open source projects.

GitHub / nextstrain/mpox issues and pull requests

#97 - ingest: Update schedule to run daily at 4pm UTC

Pull Request - State: closed - Opened by joverlee521 over 2 years ago

#96 - Push aligned sequences up to data.nextstrain.org for download availability

Issue - State: open - Opened by emmahodcroft over 2 years ago
Labels: enhancement

#95 - clades: Proposal to designate 5 B.1 sublineages (B.1.1 - B.1.5)

Pull Request - State: closed - Opened by corneliusroemer over 2 years ago - 4 comments

#94 - Chore/reverse complement

Pull Request - State: closed - Opened by rneher over 2 years ago

#93 - Subsample MPXV clades

Pull Request - State: closed - Opened by trvrb over 2 years ago - 1 comment

#92 - Revert "fix: duplicate metadata output from chores"

Pull Request - State: closed - Opened by victorlin over 2 years ago

#91 - Rename nextclade2 to nextclade

Pull Request - State: closed - Opened by ivan-aksamentov over 2 years ago - 1 comment

#90 - feat: use reverse complemented sequences

Pull Request - State: closed - Opened by corneliusroemer over 2 years ago

#89 - feat(ingest): add retry reverse complement and annotation

Pull Request - State: closed - Opened by corneliusroemer over 2 years ago

#87 - fix: duplicate metadata output from chores

Pull Request - State: closed - Opened by corneliusroemer over 2 years ago - 1 comment

#86 - chore: update example data, generated by chores.smk

Pull Request - State: closed - Opened by corneliusroemer over 2 years ago - 2 comments

#85 - workflow: give input data files unique names

Pull Request - State: open - Opened by ktmeaton over 2 years ago - 2 comments

#84 - chore: format using snakefmt

Pull Request - State: closed - Opened by corneliusroemer over 2 years ago - 5 comments

#83 - LAPIS data: cannot reindex on an axis with duplicate labels

Issue - State: closed - Opened by ktmeaton over 2 years ago - 3 comments
Labels: bug, dependency

#82 - Change of reference, shorter ITR

Pull Request - State: closed - Opened by babarlelephant over 2 years ago

#81 - remove hxmpv1 exclude file, use clade to filter

Pull Request - State: closed - Opened by rneher over 2 years ago - 2 comments

#80 - feat: reverse complement sequences if annotated in metadata

Pull Request - State: closed - Opened by corneliusroemer over 2 years ago

#79 - feat(ingest): reverse reverse-complemented sequences

Pull Request - State: closed - Opened by corneliusroemer over 2 years ago

#78 - Subsample example data

Pull Request - State: closed - Opened by victorlin over 2 years ago - 1 comment

#77 - ingest: notify Slack with metadata diff

Issue - State: closed - Opened by joverlee521 over 2 years ago
Labels: enhancement

#76 - ingest: include `url` field

Issue - State: open - Opened by joverlee521 over 2 years ago - 2 comments
Labels: enhancement

#74 - feat: rename nextalign -> nextalign2 to work with base image

Pull Request - State: closed - Opened by corneliusroemer over 2 years ago

#73 - chore: make submission_date scale temporal, parallel to mpxv change

Pull Request - State: closed - Opened by corneliusroemer over 2 years ago - 3 comments

#72 - Include "accession" in metadata

Pull Request - State: closed - Opened by trvrb over 2 years ago - 1 comment

#71 - Separate clade definitions and lineage definitions

Pull Request - State: open - Opened by trvrb over 2 years ago

#70 - Provision colors separately for mpxv and hmpxv1 build targets

Pull Request - State: closed - Opened by trvrb over 2 years ago

#69 - feat: use GFF3 genemap instead of genbank reference so that genenames are OPG

Pull Request - State: closed - Opened by corneliusroemer over 2 years ago - 2 comments

#68 - ingest: Include more data from GenBank

Issue - State: open - Opened by chaoran-chen over 2 years ago
Labels: enhancement

#67 - add updated clades

Pull Request - State: closed - Opened by rneher over 2 years ago - 3 comments

#66 - Update country colors via script

Pull Request - State: closed - Opened by jameshadfield over 2 years ago

#65 - Fix typo

Pull Request - State: closed - Opened by jameshadfield over 2 years ago - 1 comment

#64 - Fix alignment for nextalign v2

Pull Request - State: closed - Opened by huddlej over 2 years ago

#63 - Support for GISAID data

Issue - State: open - Opened by huddlej over 2 years ago - 3 comments
Labels: documentation

#62 - Remove Finnish Virological sequences from repo

Pull Request - State: closed - Opened by trvrb over 2 years ago - 4 comments

#61 - ingest: remove Finnish extra data as they are now on Genbank

Pull Request - State: closed - Opened by corneliusroemer over 2 years ago - 1 comment

#60 - Delete Finland-MPX-37+42.ndjson

Pull Request - State: closed - Opened by chaoran-chen over 2 years ago - 1 comment

#59 - Add recency colouring (sequence submission)

Pull Request - State: closed - Opened by jameshadfield over 2 years ago

#58 - Add nextclade annotations to metadata

Pull Request - State: closed - Opened by rneher over 2 years ago - 4 comments

#57 - mpxv temporal colouring scale

Pull Request - State: closed - Opened by jameshadfield over 2 years ago - 8 comments

#56 - Masking more sites

Issue - State: closed - Opened by babarlelephant over 2 years ago - 2 comments
Labels: bug

#55 - ingest/apply-geolocation-rules: update general rules logic

Pull Request - State: closed - Opened by joverlee521 over 2 years ago - 3 comments

#54 - ingest: Add tests

Pull Request - State: closed - Opened by victorlin over 2 years ago - 1 comment

#53 - Fix typos in `apply-geolocation-rules`

Pull Request - State: closed - Opened by victorlin over 2 years ago

#52 - CloudFront Invalidation

Pull Request - State: closed - Opened by joverlee521 over 2 years ago - 2 comments

#51 - Update description in page footer

Pull Request - State: closed - Opened by trvrb over 2 years ago

#50 - Update split profiles for "overview" vs "outbreak"

Pull Request - State: closed - Opened by trvrb over 2 years ago

#49 - Nomenclature

Pull Request - State: closed - Opened by rneher over 2 years ago

#47 - Force line endings to be LF on check out

Pull Request - State: closed - Opened by huddlej over 2 years ago

#46 - can not see the map?

Issue - State: closed - Opened by liamxg over 2 years ago - 1 comment
Labels: bug

#45 - Robust transform-date-fields

Pull Request - State: closed - Opened by joverlee521 over 2 years ago - 3 comments

#44 - ingest: Split monolith transform rule

Issue - State: open - Opened by joverlee521 over 2 years ago
Labels: enhancement

#43 - Add `institution` to MPX metadata

Pull Request - State: closed - Opened by emmahodcroft over 2 years ago - 2 comments

#42 - Add --cpus option

Pull Request - State: closed - Opened by pvanheus over 2 years ago - 1 comment

#41 - ingest/transform: add `apply-geolocation-rules`

Pull Request - State: closed - Opened by joverlee521 over 2 years ago - 1 comment

#40 - feat(ingest): output dates with `-XX` for unknown month/date

Pull Request - State: closed - Opened by corneliusroemer over 2 years ago

#38 - Ingest to output fasta sequences with accessions as ID

Pull Request - State: closed - Opened by corneliusroemer over 2 years ago

#37 - ingest: run NextClade and include in output files

Issue - State: closed - Opened by joverlee521 over 2 years ago - 1 comment
Labels: enhancement

#36 - ingest: thread Slack notifications

Issue - State: open - Opened by joverlee521 over 2 years ago - 1 comment
Labels: enhancement

#35 - ingest: use location hierarchy to help geolocation curation

Issue - State: closed - Opened by joverlee521 over 2 years ago - 3 comments
Labels: enhancement

#34 - ingest: adopt geolocation rules

Issue - State: closed - Opened by joverlee521 over 2 years ago
Labels: enhancement

#33 - ingest: deduplicate sequences using strain names

Issue - State: open - Opened by joverlee521 over 2 years ago - 1 comment
Labels: enhancement

#32 - ingest: canonicalize strain names

Issue - State: open - Opened by joverlee521 over 2 years ago - 1 comment
Labels: enhancement

#31 - Ingest Finnish sequences

Pull Request - State: closed - Opened by joverlee521 over 2 years ago - 1 comment

#30 - metadata for German sequences RKI011-025 (no spurious mutations)

Pull Request - State: closed - Opened by babarlelephant over 2 years ago

#29 - feat: this adds the possibility to specify the column used as strain id

Pull Request - State: closed - Opened by rneher over 2 years ago

#28 - port old annotations

Pull Request - State: closed - Opened by rneher over 2 years ago

#27 - Adding exclusions

Pull Request - State: closed - Opened by theosanderson over 2 years ago - 4 comments

#26 - Ingest pipeline

Pull Request - State: closed - Opened by joverlee521 over 2 years ago - 3 comments

#25 - fix: change LAPIS URL - gen-spectrum.org -> genspectrum.org

Pull Request - State: closed - Opened by corneliusroemer over 2 years ago

#24 - make time tree optional

Pull Request - State: closed - Opened by rneher over 2 years ago

#22 - improving the protein names in reference.gb

Pull Request - State: closed - Opened by babarlelephant over 2 years ago - 2 comments

#21 - better protein names in reference.gb

Pull Request - State: closed - Opened by babarlelephant over 2 years ago

#20 - Update metadata.tsv

Pull Request - State: closed - Opened by chaoran-chen over 2 years ago

#19 - metadata for a few 2003 sequences that are not in the nextstrain tree

Pull Request - State: closed - Opened by babarlelephant over 2 years ago - 2 comments

#18 - Update metadata.tsv

Pull Request - State: closed - Opened by chaoran-chen over 2 years ago - 1 comment

#17 - Add sequences to metadata.tsv

Pull Request - State: closed - Opened by chaoran-chen over 2 years ago

#16 - lat_long.tsv

Pull Request - State: closed - Opened by babarlelephant over 2 years ago

#15 - Allpox

Pull Request - State: closed - Opened by rneher over 2 years ago

#14 - Lapis2

Pull Request - State: closed - Opened by rneher over 2 years ago - 1 comment

#13 - Will you be updating outbreak.fasta ?

Issue - State: closed - Opened by tseemann over 2 years ago - 2 comments
Labels: enhancement

#12 - Add LAPIS entry point

Pull Request - State: closed - Opened by jameshadfield over 2 years ago - 3 comments

#11 - sequences.fasta has 2 duplicates

Issue - State: closed - Opened by tseemann over 2 years ago - 1 comment
Labels: bug

#10 - README: Add --docker and --cpus 1 to the example `nextstrain build` invocation

Pull Request - State: closed - Opened by tsibley over 2 years ago - 1 comment

#9 - Add metadata

Pull Request - State: closed - Opened by chaoran-chen over 2 years ago - 1 comment

#8 - Simplify installation and build invocation; add CI

Pull Request - State: closed - Opened by tsibley over 2 years ago

#7 - Update metadata.tsv

Pull Request - State: closed - Opened by babarlelephant over 2 years ago - 1 comment

#6 - Possible clade misannotations

Issue - State: closed - Opened by theosanderson over 2 years ago - 3 comments
Labels: bug

#5 - Fix metadata.tsv

Pull Request - State: closed - Opened by chaoran-chen over 2 years ago - 1 comment

#4 - Add region column

Pull Request - State: closed - Opened by chaoran-chen over 2 years ago - 2 comments

#3 - Add clade

Pull Request - State: closed - Opened by chaoran-chen over 2 years ago - 1 comment

#2 - Fix date formatting

Pull Request - State: closed - Opened by chaoran-chen over 2 years ago - 1 comment

#1 - README says 'not public'

Issue - State: closed - Opened by lynnlangit over 2 years ago - 1 comment
Labels: documentation