Add example-build

The main motivation for this is to simplify the CI build-args which will 
need to be replicated across augur, docker-base, and conda-base. 

Note the CI config uses the repo's local example_data as inputs and the paths 
are relative to the top level directory, so the workflow can only be run from 
the top level directory.

Author: joverlee521

.github/workflows/ci.yaml

@@ -12,6 +12,4 @@ jobs:
     uses: nextstrain/.github/.github/workflows/pathogen-repo-ci.yaml@v0
     with:
       build-args: |
-        --snakefile segment-focused/Snakefile \
-        -pf test_target  \
-        --config 'inputs=[{"name": "example", "metadata": "example_data/gisaid/metadata.tsv", "sequences": "example_data/gisaid/sequences_{segment}.fasta"}]'
+        --snakefile build-configs/ci/Snakefile

README.md

@@ -297,15 +297,13 @@ additional_inputs:
 
 ### Run a single H5N1 HA all-time analysis
 
-There is a `test_target` rule which will produce a single H5N1 HA "all-time" tree.
-You can combine this with the example data (see above) to run a single build using a small number of sequences:
+There is an example build which will produce a single H5N1 HA "all-time" tree
+using the example data (see above):
 
 
 ``` bash
 snakemake --cores 2 \
-    --snakefile segment-focused/Snakefile \
-    --config 'inputs=[{"name": "example", "metadata": "example_data/gisaid/metadata.tsv", "sequences": "example_data/gisaid/sequences_{segment}.fasta"}]' \
-    -pf test_target
+    --snakefile build-configs/ci/Snakefile
 ```
 
 ### clade labeling

build-configs/ci/Snakefile

@@ -0,0 +1,12 @@
+# This needs to be defined before rules/config.smk so that the `configfile`
+# defined in there will be merged on top of this one. This allows us to use the
+# segment-focused config as the base config that is overridden by the
+# ci/config.yaml, which defines a single build and use example data as inputs.
+configfile: os.path.join(workflow.basedir, '../../segment-focused/config.yaml')
+
+include: "../../rules/config.smk"
+
+include: "../../rules/main.smk"
+
+rule _all:
+    input: rules.all.input

build-configs/ci/config.yaml

@@ -0,0 +1,16 @@
+# Produces single build: auspice/avian-flu_h5n1_ha_all-time.json
+builds:
+  - subtype:
+      - h5n1
+    segment:
+      - ha
+    time:
+      - all-time
+
+# Inputs relative to the top level directory so this will only work running
+# the workflow from the top level directory
+inputs:
+  - name: example-data
+    metadata: example_data/gisaid/metadata.tsv
+    sequences:
+        ha: example_data/gisaid/sequences_ha.fasta