| PREVIEW = config.get("preview", False) | |
| YEAR = config.get("year", '2024') | |
| VIDRL_PATH = "../fludata/VIDRL-Melbourne-WHO-CC/raw-data" | |
| H1N1_PATH = f"{VIDRL_PATH}/A/H1N1pdm/HI" | |
| H3N2_PATH = f"{VIDRL_PATH}/A/H3N2/HI" | |
| H3N2_FRA = f"{VIDRL_PATH}/A/H3N2/FRA" | |
| VIC_PATH = f"{VIDRL_PATH}/B/Victoria/HI" |
| subtypes = ['h1n1pdm'] | |
| segments = ['ha', 'na'] | |
| times = ['pandemic'] | |
| rule all: | |
| input: | |
| expand("data/{subtype}/{segment}/{time}.done", subtype=subtypes, segment=segments, time=times) | |
| rule copy_aws_files: | |
| output: touch("data/{subtype}/{segment}/{time}.done") |
| <!doctype html> | |
| <html lang="en"> | |
| <head> | |
| <meta charset="utf-8"> | |
| <meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"> | |
| <meta name="description" content=""> | |
| <meta name="author" content=""> | |
| <title>Snakemake Report</title> |
| subtypes = ['h3n2', 'h1n1pdm', 'vic', 'yam'] | |
| segments = ['ha', 'na'] | |
| times = ['12y', '6y', '3y', '2y', '6m'] | |
| rule all: | |
| input: | |
| expand("data/{subtype}/{segment}/{time}.done", subtype=subtypes, segment=segments, time=times) | |
| rule copy_aws_files: | |
| output: touch("data/{subtype}/{segment}/{time}.done") |
In walking through git subrepo pull with @j23414 for nextstrain/mpox#182,
we ran into unexpected merge conflicts.
$ git subrepo pull ingest/vendored -dv
>>> git rev-parse --verify HEAD
* Assert that working copy is clean: /Users/jlee2346/Repos/nextstrain/monkeypox
* Check for worktree with branch subrepo/ingest/vendored
* Fetch the upstream: https://github.com/nextstrain/ingest (main).
>>> git fetch --no-tags --quiet https://github.com/nextstrain/ingest main
| #!/bin/bash | |
| bucket="nextstrain-data" | |
| s3_prefix="files/workflows/forecasts-ncov" | |
| s3_trial_prefix="trial/seq-counts-workflow" | |
| data_provenances=("open" "gisaid") | |
| variants=("nextstrain_clades" "pango_lineages") | |
| georesolutions=("global" "usa") |
| rule all: | |
| input: "data/rule_all.txt" | |
| rule a: | |
| output: touch("data/rule_a.txt") | |
| rule b: | |
| input: "data/rule_a.txt" | |
| output: "data/rule_a_hardlink.txt" |
| ID | city | latitude | longitude | lineage | lineage__color |
|---|---|---|---|---|---|
| AAA | Auckland | -37 | 174 | B.1.1 | #F020E2 |
| BBB | Auckland | -39 | 175 | C.12 | #20C9F0 |
| CCC | Wellington | -41 | 174 | C.12 | #20C9F0 |
a colours TSV mapping lineage -> hex. (Including some form of colour averaging if there are multiple hexes per lineage, which happens.)
| #!/bin/bash | |
| # Modified for TSV based on the comment from @paulfitz at | |
| # https://github.com/paulfitz/daff/issues/127#issuecomment-433538271 | |
| if [[ -z "$2" ]]; then | |
| echo "Call as foo.tsv foo.sqlite" | |
| exit 1 | |
| fi | |
| header=$(head -n1 $1) | |
| header=$(echo $header | sed "s/ /, /g") |
| QUERY PLAN | |
| ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ | |
| Nested Loop Left Join (cost=1312.91..99487.74 ro |