Phylogenetic updates to match pathogen-repo-guide

.github/workflows/ci.yaml

@@ -21,7 +21,7 @@ jobs:
       run: |
         nextstrain build \
           phylogenetic \
-          --configfile profiles/ci/builds.yaml
+          --configfiles build-configs/ci/config.yaml
       artifact-name: output-${{ matrix.runtime }}
       artifact-paths: |
         phylogenetic/auspice/

.github/workflows/rebuild-hmpxv1-big.yaml

@@ -63,5 +63,5 @@ jobs:
           --env SLACK_CHANNELS \
           . \
             notify_on_deploy \
-              --configfiles $BUILD_DIR/config/$BUILD_NAME/config.yaml $BUILD_DIR/config/nextstrain_automation.yaml \
+              --configfiles $BUILD_DIR/defaults/$BUILD_NAME/config.yaml $BUILD_DIR/build-configs/nextstrain-automation/config.yaml \
               $CONFIG_OVERRIDES --directory $BUILD_DIR --snakefile $BUILD_DIR/Snakefile

.github/workflows/rebuild-hmpxv1.yaml

@@ -63,5 +63,5 @@ jobs:
           --env SLACK_CHANNELS \
           . \
             notify_on_deploy \
-            --configfiles $BUILD_DIR/config/$BUILD_NAME/config.yaml $BUILD_DIR/config/nextstrain_automation.yaml \
+            --configfiles $BUILD_DIR/defaults/$BUILD_NAME/config.yaml $BUILD_DIR/build-configs/nextstrain-automation/config.yaml \
             $CONFIG_OVERRIDES --directory $BUILD_DIR --snakefile $BUILD_DIR/Snakefile

.github/workflows/rebuild-mpxv.yaml

@@ -63,5 +63,5 @@ jobs:
           --env SLACK_CHANNELS \
           . \
             notify_on_deploy \
-              --configfiles $BUILD_DIR/config/$BUILD_NAME/config.yaml $BUILD_DIR/config/nextstrain_automation.yaml \
+              --configfiles $BUILD_DIR/defaults/$BUILD_NAME/config.yaml $BUILD_DIR/build-configs/nextstrain-automation/config.yaml \
               $CONFIG_OVERRIDES --directory $BUILD_DIR --snakefile $BUILD_DIR/Snakefile

phylogenetic/README.md

@@ -11,7 +11,7 @@ for Nextstrain's suite of software tools.
 ## Usage
 
 If you're unfamiliar with Nextstrain builds, you may want to follow our
-[Running a Pathogen Workflow guide][] first and then come back here.
+[Running a Pathogen Workflow guide](https://docs.nextstrain.org/en/latest/tutorials/running-a-workflow.html) first and then come back here.
 
 The easiest way to run this pathogen build is using the Nextstrain
 command-line tool from within the `phylogenetic/` directory:
@@ -28,7 +28,7 @@ Once you've run the build, you can view the results with:
 You can run an example build using the example data provided in this repository via:
 
 ```
-nextstrain build .  --configfile profiles/ci/builds.yaml
+nextstrain build .  --configfile build-configs/ci/config.yaml
 ```
 
 When the build has finished running, view the output Auspice trees via:
@@ -61,43 +61,21 @@ nextstrain build . data/sequences.fasta data/metadata.tsv
 Run pipeline to produce the "overview" tree for `/mpox/all-clades` with:
 
 ```bash
-nextstrain build . --configfile config/mpxv/config.yaml
+nextstrain build . --configfile defaults/mpxv/config.yaml
 ```
 
 Run pipeline to produce the "clade IIb" tree for `/mpox/clade-IIb` with:
 
 ```bash
-nextstrain build . --configfile config/hmpxv1/config.yaml
+nextstrain build . --configfile defaults/hmpxv1/config.yaml
 ```
 
 Run pipeline to produce the "lineage B.1" tree for `/mpox/lineage-B.1` with:
 
 ```bash
-nextstrain build . --configfile config/hmpxv1_big/config.yaml
+nextstrain build . --configfile defaults/hmpxv1_big/config.yaml
 ```
 
-### Deploy
-
-⚠️ The below is outdated and needs to be adjusted for the new build names (mpox instead of monkeypox, etc.)
-
-<details>
-
-Run the python script [`scripts/deploy.py`](scripts/deploy.py) to deploy the staging build to production.
-
-This will also automatically create a dated build where each node has a unique (random) ID so it can be targeted in shared links/narratives.
-
-```bash
-python scripts/deploy.py --build-names hmpxv1 mpxv
-```
-
-If a dated build already exists it is not overwritten by default. To overwrite, pass `-f`.
-
-To deploy a locally built build to staging, use the `--staging` flag.
-
-To not deploy a dated build to production, add the `--no-dated` flag.
-
-</details>
-
 ### Visualize results
 
 View results with:
@@ -108,19 +86,30 @@ nextstrain view .
 
 ## Configuration
 
-Configuration takes place in `config/*/config.yaml` files for each build.
-The analysis pipeline is contained in `workflow/snakemake_rule/core.smk`.
+The default configuration takes place in `defaults/*/config.yaml` files for each build.
+The analysis pipeline is contained in `rules/core.smk`.
 This can be read top-to-bottom, each rule specifies its file inputs and output and pulls its parameters from `config`.
 There is little redirection and each rule should be able to be reasoned with on its own.
 
+### Custom build configs
+
+The build-configs directory contains configs and customizations that override and/or extend the default workflow.
+
+- [chores](build-configs/chores/) - internal Nextstrain chores such as [updating the example data](#update-example-data).
+- [ci](build-configs/ci/) - CI build that run the [example build](#example-build) with the [example data](example_data/).
+- [nextstrain-automation](build-configs/nextstrain-automation/) - internal Nextstrain automated builds
+
 ## Update example data
 
-[Example data](./example_data/) is used by [CI](https://github.com/nextstrain/mpox/actions/workflows/ci.yaml). It can also be used as a small subset of real-world data.
+[Example data](./example_data/) is used by [CI](https://github.com/nextstrain/mpox/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 or a new clade/lineage emerges. To update, run:
+Example data should be updated every time metadata schema is changed or a new clade/lineage emerges.
+To update, run:
 
 ```sh
-nextstrain build . update_example_data -F
+nextstrain build . update_example_data -F \
+    --configfiles build-configs/ci/config.yaml build-configs/chores/config.yaml
 ```
 
 ## Data use

phylogenetic/Snakefile

@@ -12,18 +12,16 @@ if version.parse(augur_version) < version.parse(min_augur_version):
 
 if not config:
 
-    configfile: "config/hmpxv1/config.yaml"
+    configfile: "defaults/hmpxv1/config.yaml"
 
 
 build_dir = "results"
-
-
 auspice_dir = "auspice"
 
 prefix = config.get("auspice_prefix", None)
 AUSPICE_PREFIX = ("trial_" + prefix + "_") if prefix is not None else ""
-AUSPICE_FILENAME = AUSPICE_PREFIX + config.get("auspice_name")
-
+# Defaults to the `build_name` if no `auspice_name` is provided in the config
+AUSPICE_FILENAME = AUSPICE_PREFIX + config.get("auspice_name", config["build_name"])
 
 rule all:
     input:
@@ -39,22 +37,10 @@ rule all:
         """
 
 
-if config.get("data_source", None) == "lapis":
-
-    include: "workflow/snakemake_rules/download_via_lapis.smk"
-
-else:
-
-    include: "workflow/snakemake_rules/prepare.smk"
-
-
-include: "workflow/snakemake_rules/chores.smk"
-include: "workflow/snakemake_rules/core.smk"
-
-
-if config.get("deploy_url", False):
-
-    include: "workflow/snakemake_rules/nextstrain_automation.smk"
+include: "rules/prepare_sequences.smk"
+include: "rules/construct_phylogeny.smk"
+include: "rules/annotate_phylogeny.smk"
+include: "rules/export.smk"
 
 
 # Include custom rules defined in the config.

phylogenetic/workflow/snakemake_rules/chores.smk → phylogenetic/build-configs/chores/chores.smk

@@ -1,3 +1,6 @@
+# I was hoping to use the Snakemake `default_target` directive to make this the
+# default target when including this rule via `custom_rules`, but that is
+# currently not possible: https://github.com/snakemake/snakemake/issues/2056
 rule update_example_data:
     """This updates the files under example_data/ based on latest available data from data.nextstrain.org.
 

phylogenetic/build-configs/chores/config.yaml

@@ -0,0 +1,2 @@
+custom_rules:
+  - build-configs/chores/chores.smk

phylogenetic/profiles/ci/builds.yaml → phylogenetic/build-configs/ci/config.yaml

@@ -1,15 +1,15 @@
 custom_rules:
-  - profiles/ci/copy_example_data.smk
+  - build-configs/ci/copy_example_data.smk
 
-reference: "config/reference.fasta"
-genemap: "config/genemap.gff"
-genbank_reference: "config/reference.gb"
-include: "config/hmpxv1/include.txt"
-clades: "config/clades.tsv"
-lat_longs: "config/lat_longs.tsv"
-auspice_config: "config/hmpxv1/auspice_config.json"
-description: "config/description.md"
-tree_mask: "config/tree_mask.tsv"
+reference: "defaults/reference.fasta"
+genemap: "defaults/genemap.gff"
+genbank_reference: "defaults/reference.gb"
+include: "defaults/hmpxv1/include.txt"
+clades: "defaults/clades.tsv"
+lat_longs: "defaults/lat_longs.tsv"
+auspice_config: "defaults/hmpxv1/auspice_config.json"
+description: "defaults/description.md"
+tree_mask: "defaults/tree_mask.tsv"
 
 # Use `accession` as the ID column since `strain` currently contains duplicates¹.
 # ¹ https://github.com/nextstrain/monkeypox/issues/33
@@ -20,7 +20,7 @@ build_name: "hmpxv1"
 auspice_name: "mpox_clade-IIb"
 
 filter:
-  exclude: "config/exclude_accessions.txt"
+  exclude: "defaults/exclude_accessions.txt"
   min_date: 2017
   min_length: 100000
 
@@ -81,4 +81,4 @@ recency: true
 mask:
   from_beginning: 800
   from_end: 6422
-  maskfile: "config/mask.bed"
+  maskfile: "defaults/mask.bed"

phylogenetic/config/nextstrain_automation.yaml → phylogenetic/build-configs/nextstrain-automation/config.yaml

@@ -1,5 +1,8 @@
 # Optional configs to include for automated Nextstrain builds
 # Intended to be used internally by the Nextstrain team
 
+custom_rules:
+  - build-configs/nextstrain-automation/nextstrain-automation.smk
+
 # deploy
 deploy_url: "s3://nextstrain-data"

phylogenetic/config/description.md → phylogenetic/defaults/description.md

@@ -14,7 +14,7 @@ Our bioinformatic processing workflow can be found at [github.com/nextstrain/mpo
 - masking several regions of the genome, including the first 1350 and last 6422 base pairs and multiple repetitive regions of variable length
 - phylogenetic reconstruction using [IQTREE-2](http://www.iqtree.org/)
 - ancestral state reconstruction and temporal inference using [TreeTime](https://github.com/neherlab/treetime)
-- clade assignment via [clade definitions defined here](https://github.com/nextstrain/mpox/blob/master/config/clades.tsv), to label broader MPXV clades I, IIa and IIb and to label hMPXV1 lineages A, A.1, A.1.1, etc...
+- clade assignment via [clade definitions defined here](https://github.com/nextstrain/mpox/blob/master/defaults/clades.tsv), to label broader MPXV clades I, IIa and IIb and to label hMPXV1 lineages A, A.1, A.1.1, etc...
 
 #### Underlying data
 We curate sequence data and metadata from the [NCBI Datasets command line tools](https://www.ncbi.nlm.nih.gov/datasets/docs/v2/download-and-install/),

phylogenetic/config/hmpxv1/config.yaml → phylogenetic/defaults/hmpxv1/config.yaml

@@ -1,12 +1,12 @@
-reference: "config/reference.fasta"
-genemap: "config/genemap.gff"
-genbank_reference: "config/reference.gb"
-include: "config/hmpxv1/include.txt"
-clades: "config/clades.tsv"
-lat_longs: "config/lat_longs.tsv"
-auspice_config: "config/hmpxv1/auspice_config.json"
-description: "config/description.md"
-tree_mask: "config/tree_mask.tsv"
+reference: "defaults/reference.fasta"
+genemap: "defaults/genemap.gff"
+genbank_reference: "defaults/reference.gb"
+include: "defaults/hmpxv1/include.txt"
+clades: "defaults/clades.tsv"
+lat_longs: "defaults/lat_longs.tsv"
+auspice_config: "defaults/hmpxv1/auspice_config.json"
+description: "defaults/description.md"
+tree_mask: "defaults/tree_mask.tsv"
 
 # Use `accession` as the ID column since `strain` currently contains duplicates¹.
 # ¹ https://github.com/nextstrain/mpox/issues/33
@@ -17,7 +17,7 @@ build_name: "hmpxv1"
 auspice_name: "mpox_clade-IIb"
 
 filter:
-  exclude: "config/exclude_accessions.txt"
+  exclude: "defaults/exclude_accessions.txt"
   min_date: 2017
   min_length: 100000
 
@@ -78,4 +78,4 @@ recency: true
 mask:
   from_beginning: 800
   from_end: 6422
-  maskfile: "config/mask.bed"
+  maskfile: "defaults/mask.bed"

phylogenetic/config/hmpxv1_big/config.yaml → phylogenetic/defaults/hmpxv1_big/config.yaml

@@ -1,12 +1,12 @@
-reference: "config/reference.fasta"
-genemap: "config/genemap.gff"
-genbank_reference: "config/reference.gb"
-include: "config/hmpxv1_big/include.txt"
-clades: "config/clades.tsv"
-lat_longs: "config/lat_longs.tsv"
-auspice_config: "config/hmpxv1_big/auspice_config.json"
-description: "config/description.md"
-tree_mask: "config/tree_mask.tsv"
+reference: "defaults/reference.fasta"
+genemap: "defaults/genemap.gff"
+genbank_reference: "defaults/reference.gb"
+include: "defaults/hmpxv1_big/include.txt"
+clades: "defaults/clades.tsv"
+lat_longs: "defaults/lat_longs.tsv"
+auspice_config: "defaults/hmpxv1_big/auspice_config.json"
+description: "defaults/description.md"
+tree_mask: "defaults/tree_mask.tsv"
 
 # Use `accession` as the ID column since `strain` currently contains duplicates¹.
 # ¹ https://github.com/nextstrain/mpox/issues/33
@@ -17,7 +17,7 @@ build_name: "hmpxv1_big"
 auspice_name: "mpox_lineage-B.1"
 
 filter:
-  exclude: "config/exclude_accessions.txt"
+  exclude: "defaults/exclude_accessions.txt"
   min_date: 2022
   min_length: 180000
 
@@ -57,4 +57,4 @@ recency: true
 mask:
   from_beginning: 800
   from_end: 6422
-  maskfile: "config/mask.bed"
+  maskfile: "defaults/mask.bed"

phylogenetic/config/mpxv/config.yaml → phylogenetic/defaults/mpxv/config.yaml

@@ -1,12 +1,12 @@
-auspice_config: "config/mpxv/auspice_config.json"
-include: "config/mpxv/include.txt"
-reference: "config/reference.fasta"
-genemap: "config/genemap.gff"
-genbank_reference: "config/reference.gb"
-lat_longs: "config/lat_longs.tsv"
-description: "config/description.md"
-clades: "config/clades.tsv"
-tree_mask: "config/tree_mask.tsv"
+auspice_config: "defaults/mpxv/auspice_config.json"
+include: "defaults/mpxv/include.txt"
+reference: "defaults/reference.fasta"
+genemap: "defaults/genemap.gff"
+genbank_reference: "defaults/reference.gb"
+lat_longs: "defaults/lat_longs.tsv"
+description: "defaults/description.md"
+clades: "defaults/clades.tsv"
+tree_mask: "defaults/tree_mask.tsv"
 
 # Use `accession` as the ID column since `strain` currently contains duplicates¹.
 # ¹ https://github.com/nextstrain/mpox/issues/33
@@ -17,7 +17,7 @@ build_name: "mpxv"
 auspice_name: "mpox_all-clades"
 
 filter:
-  exclude: "config/exclude_accessions.txt"
+  exclude: "defaults/exclude_accessions.txt"
   min_date: 1950
   min_length: 100000
 
@@ -74,4 +74,4 @@ recency: true
 mask:
   from_beginning: 1350
   from_end: 6422
-  maskfile: "config/mask_overview.bed"
+  maskfile: "defaults/mask_overview.bed"