phylogenetic: Add profile for CI example build

Adds custom rule to copy over the example data to be able to run
the build with example data. This allows users to run the example build
without having to manually copy over the data.

phylogenetic/README.md

@@ -9,6 +9,20 @@ Follow the [standard installation instructions](https://docs.nextstrain.org/en/l
 
 ## Usage
 
+### Example build
+
+You can run an example build using the example data provided in this repository via:
+
+```
+nextstrain build .  --configfile profiles/ci/builds.yaml
+```
+
+When the build has finished running, view the output Auspice trees via:
+
+```
+nextstrain view .
+```
+
 ### Provision input data
 
 Input sequences and metadata can be retrieved from data.nextstrain.org

phylogenetic/profiles/ci/builds.yaml

@@ -0,0 +1,83 @@
+custom_rules:
+  - profiles/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"
+
+# Use `accession` as the ID column since `strain` currently contains duplicates¹.
+# ¹ https://github.com/nextstrain/monkeypox/issues/33
+strain_id_field: "accession"
+display_strain_field: "strain"
+
+build_name: "hmpxv1"
+auspice_name: "mpox_clade-IIb"
+
+filter:
+  exclude: "config/exclude_accessions.txt"
+  min_date: 2017
+  min_length: 100000
+
+
+### Set 1: Non-B.1 sequences: use all
+### Set 2: B.1 sequences: small sample across year/country, maybe month
+subsample:
+  non_b1:
+    group_by: "--group-by lineage year country"
+    sequences_per_group: "--sequences-per-group 50"
+    other_filters: "outbreak!=hMPXV-1 clade!=IIb"
+    exclude_lineages:
+      - B.1
+      - B.1.1
+      - B.1.2
+      - B.1.3
+      - B.1.4
+      - B.1.5
+      - B.1.6
+      - B.1.7
+      - B.1.8
+      - B.1.9
+      - B.1.10
+      - B.1.11
+      - B.1.12
+      - B.1.13
+      - B.1.14
+      - B.1.15
+      - B.1.16
+      - B.1.17
+      - B.1.18
+      - B.1.19
+      - B.1.20
+      - C.1
+  b1:
+    group_by: "--group-by country year"
+    sequences_per_group: "--subsample-max-sequences 100"
+    other_filters: "--exclude-where outbreak!=hMPXV-1 clade!=IIb"
+
+## align
+max_indel: 10000
+seed_spacing: 1000
+
+## treefix
+fix_tree: true
+treefix_root: "--root MK783032"
+
+## refine
+timetree: true
+root: "MK783032 MK783030"
+clock_rate: 5.7e-5
+clock_std_dev: 2e-5
+
+## recency
+recency: true
+
+mask:
+  from_beginning: 800
+  from_end: 6422
+  maskfile: "config/mask.bed"

phylogenetic/profiles/ci/copy_example_data.smk

@@ -0,0 +1,15 @@
+rule copy_example_data:
+    input:
+        sequences="example_data/sequences.fasta",
+        metadata="example_data/metadata.tsv",
+    output:
+        sequences="data/sequences.fasta",
+        metadata="data/metadata.tsv",
+    shell:
+        """
+        cp -f {input.sequences} {output.sequences}
+        cp -f {input.metadata} {output.metadata}
+        """
+
+
+ruleorder: copy_example_data > decompress