Modernize/cleanup 2

.pre-commit-config.yaml

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+default_language_version:
+  python: python3
+# TODO remove _LEGACY once it's gone
+exclude: '\.(tsv|fasta|gb)$|^ingest/vendored/|^_LEGACY'
+repos:
+  - repo: https://github.com/snakemake/snakefmt
+    rev: v0.10.1
+    hooks:
+      - id: snakefmt
+        language_version: python3
+  - repo: https://github.com/rhysd/actionlint
+    rev: v1.6.27
+    hooks:
+      - id: actionlint
+        entry: env SHELLCHECK_OPTS='--exclude=SC2027' actionlint
+  - repo: https://github.com/codespell-project/codespell
+    rev: v2.2.6
+    hooks:
+      - id: codespell
+        additional_dependencies:
+          - tomli
+  - repo: https://github.com/google/yamlfmt
+    rev: v0.12.1
+    hooks:
+      - id: yamlfmt
+  - repo: https://github.com/pappasam/toml-sort
+    rev: v0.23.1
+    hooks:
+      - id: toml-sort-fix
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v4.6.0
+    hooks:
+      - id: trailing-whitespace
+      - id: check-ast
+      - id: check-case-conflict
+      - id: check-docstring-first
+      - id: check-json
+      - id: check-executables-have-shebangs
+      - id: check-merge-conflict
+      - id: check-shebang-scripts-are-executable
+      - id: check-symlinks
+      - id: check-toml
+      - id: check-yaml
+      - id: destroyed-symlinks
+      - id: detect-private-key
+      - id: end-of-file-fixer
+      - id: fix-byte-order-marker
+  - repo: https://github.com/pre-commit/sync-pre-commit-deps
+    rev: v0.0.1
+    hooks:
+      - id: sync-pre-commit-deps
+  - repo: https://github.com/shellcheck-py/shellcheck-py
+    rev: v0.10.0.1
+    hooks:
+      - id: shellcheck

.yamlfmt

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+formatter:
+  type: basic
+  line_ending: lf
+  retain_line_breaks: true
+  max_line_length: 120

README.md

@@ -1,82 +1,12 @@
-# Nextstrain build for Yellow Fever
-
-This build is currently designed for in-the-field running and is not yet generalised for a stable, updated nextstrain.org page.
-
-## Install augur + auspice using conda
-
-```
-curl http://data.nextstrain.org/nextstrain.yml --compressed -o nextstrain.yml
-conda env create -f nextstrain.yml
-conda activate nextstrain
-npm install --global auspice
-```
-
-When you're inside the "nextstrain" environment (via `conda activate nextstrain`) you should have both `augur` & `auspice` installed.
-You can test this by running `augur --version` and `auspice --version`.
-Currently, augur is around `v5.1.1` and auspice is around `v1.36.6`.
-
-
-## Clone this repo
-
-```
-git clone https://github.com/nextstrain/yellow-fever.git
-cd yellow-fever
-mkdir data results auspice
-```
-
-
-## Make input files available
-
-The bioinformatics "pipeline" for YFV starts with 4 main files as input: 
-* `./data/genbankReleased.fasta`
-* `./data/genbankReleased.csv`
-* `./data/newSequences.fasta`
-* `./data/newSequences.csv`
-
-These are not committed to the github repo (they're "gitignored"), so you'll have to put them there.
-
-These files are specified in the first few lines of the Snakemake file, which contains all the commands necessary to run the pipeline.
-It's possible to use >2 sets of input files, or different file names, but you'll have to add / change them in the snakemake file.
-
-
-Additionally, there are 2 other input-like files, also defined in the snakemake file:
-* `./config/auspice_config.json` which contains options -- such as what traits to display as the color-by's on the tree -- which are used to control how auspice will visualise the data.
-* `./config/YFV112.gb` the YFV reference used here -- currently [YF112](https://www.ncbi.nlm.nih.gov/nuccore/1269012770). Please replace this if needed & update the snakemake file accordingly.
-
-
-## Run the pipeline
-
-```
-snakemake --printshellcmds
-```
-
-This will run all the steps defined in the Snakefile 🎉
-
-These steps are (roughly):
-1. __parse__ convert the (potentially multiple) CSV + FASTA files into the correct format for augur (TSV + FASTA). Also performs some field manipulation, such as extracting "country" from the "Sequence_name", extracting collection year, storing which file a sequence came from etcetera.
-2. __align__ Using mafft
-3. __tree__ Using IQ-TREE (cahn change this to RAxML or FastTree if needed)
-4. __refine__ Normally this is where we date the internal nodes, but I haven't enabled this here. It is needed however to label the internal nodes & reroot the tree (see below).
-5. __ancestral__ Infer ancestral mutations on the tree. This step could easily be dropped if desired!
-6. __traits__ Use DTA to infer some traits across the tree. Currently used for "country" only. You can easily add fields to the snakemake file which will perform this for additional traits.
-7. __export__ Create the final JSON for auspice to visualise.
-
-Steps 1-6 produce output in `./results`, while step 7 (export) produces the JSONs in `./auspice`. Both of these directories are gitignored (as well as `./data`) so that files here won't be pushed up to GitHub.
-
-## Visualise the data
-
-```
-auspice view --datasetDir auspice
-```
-Then open a browser at http://localhost:4000
-
-Current color-bys include most of the metadata provided, as well as which file the samples came from, year of collection.
-The GPS co-ordinates are per-strain, so that is the geographic-resolution available. We could also aggregate municipalities if desired (we'd need GPS coordinates for each one if so).
-
-
-## To-Do
-* The tree is rooted on the oldest available sequence ("JF912179", 1980), but there may be a better choice? This is defined in the Snakefile and is really easy to change.
-* Reference sequence used may not be ideal.
+# Nextstrain repository for yellow fever virus
 
+##TODO## finish updating this
+This repository is in the process of being upgraded to follow the
+[pathogen repo
+guide](https://github.com/nextstrain/pathogen-repo-guide/).
 
+## Installation
 
+Follow the [standard installation
+instructions](https://docs.nextstrain.org/en/latest/install.html) for
+Nextstrain's suite of software tools.

ingest/README.md

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+# Ingest
+
+This workflow ingests public data from NCBI and outputs curated
+metadata and sequences that can be used as input for the phylogenetic
+workflow.
+
+## Workflow Usage
+
+The workflow can be run from the top level pathogen repo directory:
+
+```bash
+nextstrain build ingest
+```
+
+Alternatively, the workflow can also be run from within the ingest
+directory:
+
+```bash
+cd ingest
+nextstrain build .
+```
+
+This produces the default outputs of the ingest workflow:
+
+- metadata      = results/metadata.tsv
+- sequences     = results/sequences.fasta
+
+### Dumping the full raw metadata from NCBI Datasets
+
+The workflow has a target for dumping the full raw metadata from NCBI
+Datasets.
+
+```bash
+nextstrain build ingest dump_ncbi_dataset_report
+```
+
+This will produce the file `ingest/data/ncbi_dataset_report_raw.tsv`,
+which you can inspect to determine what fields and data to use if you
+want to configure the workflow for your pathogen.
+
+## Defaults
+
+The defaults directory contains all of the default configurations for
+the ingest workflow.
+
+[defaults/config.yaml](defaults/config.yaml) contains all of the
+default configuration parameters used for the ingest workflow. Use
+Snakemake's `--configfile`/`--config` options to override these
+default values.
+
+## Snakefile and rules
+
+The rules directory contains separate Snakefiles (`*.smk`) as modules
+of the core ingest workflow. The modules of the workflow are in
+separate files to keep the main ingest [Snakefile](Snakefile) succinct
+and organized.
+
+The `workdir` is hardcoded to be the ingest directory so all filepaths
+for inputs/outputs should be relative to the ingest directory.
+
+Modules are all
+[included](https://snakemake.readthedocs.io/en/stable/snakefiles/modularization.html#includes)
+in the main Snakefile in the order that they are expected to run.
+
+### Nextclade
+
+Nextstrain is pushing to standardize ingest workflows with Nextclade
+runs to include Nextclade outputs in our publicly hosted data.
+However, if a Nextclade dataset does not already exist, it requires
+curated data as input, so we are making Nextclade steps optional here.
+
+If Nextclade config values are included, the Nextclade rules will
+create the final metadata TSV by joining the Nextclade output with the
+metadata. If Nextclade configs are not included, we rename the subset
+metadata TSV to the final metadata TSV.
+
+To run Nextclade rules, include the `defaults/nextclade_config.yaml`
+config file with:
+
+```bash
+nextstrain build ingest --configfile defaults/nextclade_config.yaml
+```
+
+> [!TIP]
+> If the Nextclade dataset is stable and you always want to run the
+> Nextclade rules as part of ingest, we recommend moving the Nextclade
+> related config parameters from the `defaults/nextclade_config.yaml`
+> file to the default config file `defaults/config.yaml`.
+
+## Build configs
+
+The build-configs directory contains custom configs and rules that
+override and/or extend the default workflow.
+
+- [nextstrain-automation](build-configs/nextstrain-automation/) - automated internal Nextstrain builds.
+
+## Vendored
+
+This repository uses
+[`git subrepo`](https://github.com/ingydotnet/git-subrepo) to manage copies
+of ingest scripts in [vendored](vendored), from
+[nextstrain/ingest](https://github.com/nextstrain/ingest).
+
+See [vendored/README.md](vendored/README.md#vendoring) for
+instructions on how to update the vendored scripts.

ingest/Snakefile

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+"""
+This is the main ingest Snakefile that orchestrates the full ingest workflow
+and defines its default outputs.
+"""
+
+
+# The workflow filepaths are written relative to this Snakefile's base
+# directory
+workdir: workflow.current_basedir
+
+
+# Use default configuration values. Override with Snakemake's
+# --configfile/--config options.
+configfile: "defaults/config.yaml"
+
+
+# This is the default rule that Snakemake will run when there are no
+# specified targets. The default output of the ingest workflow is
+# usually the curated metadata and sequences. Nextstrain-maintained
+# ingest workflows will produce metadata files with the standard
+# Nextstrain fields and additional fields that are pathogen specific.
+# We recommend using these standard fields in custom ingests as well
+# to minimize the customizations you will need for the downstream
+# phylogenetic workflow.
+
+
+# TODO: Add link to centralized docs on standard Nextstrain metadata fields
+rule all:
+    input:
+        "results/sequences.fasta",
+        "results/metadata.tsv",
+
+
+# Note that only PATHOGEN-level customizations should be added to
+# these core steps, meaning they are custom rules necessary for all
+# builds of the pathogen. If there are build-specific customizations,
+# they should be added with the custom_rules imported below to ensure
+# that the core workflow is not complicated by build-specific rules.
+include: "rules/fetch_from_ncbi.smk"
+include: "rules/curate.smk"
+
+
+# We are pushing to standardize ingest workflows with Nextclade runs
+# to include Nextclade outputs in our publicly hosted data. However,
+# if a Nextclade dataset does not already exist, creating one requires
+# curated data as input, so we are making Nextclade steps optional
+# here.
+#
+# If Nextclade config values are included, the nextclade rules will
+# create the final metadata TSV by joining the Nextclade output with
+# the metadata. If Nextclade configs are not included, we rename the
+# subset metadata TSV to the final metadata TSV. To run nextclade.smk
+# rules, include the `defaults/nextclade_config.yaml` config file with
+# `nextstrain build ingest --configfile
+# defaults/nextclade_config.yaml`.
+if "nextclade" in config:
+
+    include: "rules/nextclade.smk"
+
+else:
+
+    rule create_final_metadata:
+        input:
+            metadata="data/subset_metadata.tsv",
+        output:
+            metadata="results/metadata.tsv",
+        shell:
+            """
+            mv {input.metadata} {output.metadata}
+            """
+
+
+# Allow users to import custom rules provided via the config.
+# This allows users to run custom rules that can extend or override
+# the workflow. A concrete example of using custom rules is the
+# extension of the workflow with rules to support the Nextstrain
+# automation that uploads files and sends internal Slack
+# notifications. For extensions, the user will have to specify the
+# custom rule targets when running the workflow. For overrides, the
+# custom Snakefile will have to use the `ruleorder` directive to allow
+# Snakemake to handle ambiguous rules
+# https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#handling-ambiguous-rules
+if "custom_rules" in config:
+    for rule_file in config["custom_rules"]:
+
+        include: rule_file

ingest/build-configs/nextstrain-automation/README.md

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+# Nextstrain automation
+
+> [!NOTE]
+> External users can ignore this directory!
+> This build config/customization is tailored for the internal Nextstrain team
+> to extend the core ingest workflow for automated workflows.
+
+## Update the config
+
+Update the [config.yaml](config.yaml) for your pathogen:
+
+1. Edit the `s3_dst` param to add the pathogen repository name.
+2. Edit the `files_to_upload` param to a mapping of files you need to upload for your pathogen.
+The default includes suggested files for uploading curated data and Nextclade outputs.
+
+## Run the workflow
+
+Provide the additional config file to the Snakemake options in order to
+include the custom rules from [upload.smk](upload.smk) in the workflow.
+Specify the `upload_all` target in order to run the additional upload rules.
+
+The upload rules will require AWS credentials for a user that has permissions
+to upload to the Nextstrain data bucket.
+
+The customized workflow can be run from the top level pathogen repo directory with:
+```
+nextstrain build \
+    --env AWS_ACCESS_KEY_ID \
+    --env AWS_SECRET_ACCESS_KEY \
+    ingest \
+        upload_all \
+        --configfile build-configs/nextstrain-automation/config.yaml
+```
+
+## Automated GitHub Action workflows
+
+Additional instructions on how to use this with the shared `pathogen-repo-build`
+GitHub Action workflow to come!