Merge pull request #197 from nextstrain/ingest-tutorial-followup

Fill in missing code-block language
nextstrain · Apr 19, 2024 · e9721fc · e9721fc
2 parents ba9ced1 + 4de29e9
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diff --git a/src/learn/augur-to-auspice.rst b/src/learn/augur-to-auspice.rst
@@ -718,9 +718,9 @@ Select (discrete) colorings are available for filtering in Auspice (both
 via the sidebar UI and listed in the footer) if they are defined in the
 auspice-config JSONs filters list:
 
-.. code-block::
+.. code-block:: json
 
-   "filters": ["country", "region", ...]
+   "filters": ["country", "region", "..."]
 
 Additionally, each mutation and strain name will be automatically
 available in Auspice’s sidebar UI for filtering.

diff --git a/src/tutorials/creating-a-pathogen-repo/creating-an-ingest-workflow.rst b/src/tutorials/creating-a-pathogen-repo/creating-an-ingest-workflow.rst
@@ -36,9 +36,9 @@ This tutorial will only focus on using the guide to set up the ingest workflow.
 3. Follow the `GitHub guide to download the new repository <https://docs.github.com/en/repositories/creating-and-managing-repositories/cloning-a-repository>`_.
 4. Change directory to your new pathogen repository
 
-.. code-block::
+.. code-block:: console
 
-    cd <new-pathogen-repository>
+    $ cd <new-pathogen-repository>
 
 Decide on data source
 =====================
@@ -66,9 +66,9 @@ You can decide whether NCBI Datasets include sufficient data for your pathogen b
 1. Add your pathogen's NCBI taxonomy ID to the ``ncbi_taxon_id`` parameter in the ``ingest/defaults/config.yaml`` config file.
 2. Dump the uncurated metadata by running
 
-.. code-block::
+.. code-block:: console
 
-    nextstrain build ingest dump_ncbi_dataset_report
+    $ nextstrain build ingest dump_ncbi_dataset_report
 
 3. Inspect the generated file ``ingest/data/ncbi_dataset_report_raw.tsv``
 4. If there are other fields in the raw file that you would like to include in the workflow,
@@ -92,7 +92,7 @@ the `NCBI Entrez <https://www.ncbi.nlm.nih.gov/books/NBK25501/>`_ tool to downlo
 4. Switch the `Snakemake ruleorder <https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#handling-ambiguous-rules>`_
    within the ``ingest/rules/fetch_from_ncbi.smk`` file.
 
-.. code-block::
+.. code-block:: python
 
     ruleorder: format_ncbi_datasets_ndjson < parse_genbank_to_ndjson
 
@@ -276,7 +276,7 @@ Geolocation rules
 
 Geolocation rules are defined in a TSV file with the format
 
-.. code-block::
+.. code-block:: none
 
     region/country/division/location<\t>region/country/division/location
 
@@ -289,14 +289,14 @@ If there are rules that can be applied across multiple locations, then a wildcar
 
 Let's say you have the following locations in your NDJSON
 
-.. code-block::
+.. code-block:: none
 
     {“region”: “North America”, “country”: “United States”, “division”: “New York”, “location”: “Buffalo”}
     {“region”: “North America”, “country”: “United States”, “division”: “New York”, “location”: “New York”}
 
 And you provide these geolocation rules
 
-.. code-block::
+.. code-block:: none
 
     North America/United States/New York/New York		North America/United States/New York/New York City
     North America/United States/New York/*	North America/United States/New York State/*
@@ -308,7 +308,7 @@ The third rule has wildcards for both division and location, so it will correct
 
 Running through the ``ingest/vendored/apply-geolocation-rules`` script should produce the following
 
-.. code-block::
+.. code-block:: none
 
     {“region”: “North America”, “country”: “USA”, “division”: “New York State”, “location”: “Buffalo”}
     {“region”: “North America”, “country”: “USA”, “division”: “New York State”, “location”: “New York City”}
@@ -337,7 +337,7 @@ User annotations
 
 The user annotations are defined in a TSV file with the format
 
-.. code-block::
+.. code-block:: none
 
     id<\t>field<\t>value
 
@@ -347,14 +347,14 @@ The ``value`` is the value you are trying to add to the NDJSON record.
 
 Let's say you have the following NDJSON records
 
-.. code-block::
+.. code-block:: none
 
     {“accession”: “AAAAA”, “country”: “United States”, “division”: “New York”, “location”: “Buffalo”}
     {“accession”: “BBBBB”, “country”: “United States”, “division”: “New York”, “location”: “Buffalo”}
 
 And you provide these user annotations
 
-.. code-block::
+.. code-block:: none
 
     AAAAA	age	10
     BBBBB	age	12
@@ -365,7 +365,7 @@ third annotation overwrites the existing ``location`` field for the record ``BBB
 
 Running through the ``ingest/vendored/merge-user-metadata`` script should produce the following:
 
-.. code-block::
+.. code-block:: none
 
     {“accession”: “AAAAA”, “country”: “United States”, “division”: “New York”, “location”: “Buffalo”, “age”: 10}
     {“accession”: “BBBBB”, “country”: “United States”, “division”: “New York”, “location”: “Niagara Falls”, “age”: 12}
@@ -448,7 +448,7 @@ config file to include the Nextclade rules from ``ingest/rules/nextclade.smk`` a
 1. Add your Nextclade dataset name to the ``nextclade.dataset_name`` parameter
 2. Run the ingest workflow with the additional config file
 
-.. code-block::
+.. code-block:: bash
 
     nextstrain build ingest --configfile defaults/nextclade_config.yaml
 

diff --git a/src/tutorials/running-a-phylogenetic-workflow.rst b/src/tutorials/running-a-phylogenetic-workflow.rst
@@ -22,7 +22,7 @@ Download the example Zika pathogen repository
 
 :term:`Pathogen workflows<phylogenetic workflow>` are stored in :term:`pathogen repositories<pathogen repository>` (version-controlled folders) to track changes over time. Download the `example Zika pathogen repository <https://github.com/nextstrain/zika-tutorial>`_.
 
-.. code-block::
+.. code-block:: console
 
     $ git clone https://github.com/nextstrain/zika-tutorial
     Cloning into 'zika-tutorial'...
@@ -37,7 +37,7 @@ Run the workflow
 
 Run the workflow with the :term:`Nextstrain CLI`.
 
-.. code-block::
+.. code-block:: console
 
     $ nextstrain build --cpus 1 zika-tutorial/
     Building DAG of jobs...
@@ -53,7 +53,7 @@ Visualize results
 
 View the resulting :term:`phylogenetic dataset` using Nextstrain's visualizations.
 
-.. code-block::
+.. code-block:: console
 
     $ nextstrain view zika-tutorial/auspice/
     ——————————————————————————————————————————————————————————————————————————————

diff --git a/src/tutorials/using-a-pathogen-repo/running-an-ingest-workflow.rst b/src/tutorials/using-a-pathogen-repo/running-an-ingest-workflow.rst
@@ -27,7 +27,7 @@ Download the Zika repository
 All pathogen ingest workflows are stored in :term:`pathogen repositories<pathogen repository>` (version-controlled folders) to track changes over time.
 Download the `Zika repository <https://github.com/nextstrain/zika>`_.
 
-.. code-block::
+.. code-block:: console
 
     $ git clone https://github.com/nextstrain/zika
     Cloning into 'zika'...
@@ -44,13 +44,13 @@ the downloaded data into a format suitable for :term:`phylogenetic workflows <ph
 
 1. Change directory to the Zika pathogen repository downloaded in the previous step
 
-.. code-block::
+.. code-block:: console
 
     $ cd zika
 
 2. Run the default ingest workflow with the :term:`Nextstrain CLI`.
 
-.. code-block::
+.. code-block:: console
 
     $ nextstrain build ingest
     Using profile profiles/default and workflow specific profile profiles/default for setting default command line arguments.
@@ -91,34 +91,34 @@ you can download the uncurated NCBI data.
 
 1. Enter an interactive Nextstrain shell to be able to run the NCBI Datasets CLI commands without installing them separately.
 
-.. code-block::
+.. code-block:: console
 
     $ nextstrain shell .
 
 2. Create the ``ingest/data`` directory if it doesn't already exist.
 
-.. code-block::
+.. code-block:: console
 
     $ mkdir -p ingest/data
 
 3. Download the dataset with the pathogen NCBI taxonomy ID.
 
-.. code-block::
+.. code-block:: console
 
     $ datasets download virus genome taxon <taxon-id> \
         --filename ingest/data/ncbi_dataset.zip
 
 4. Extract and format the metadata as a TSV file for easy inspection
 
-.. code-block::
+.. code-block:: console
 
     $ dataformat tsv virus-genome \
         --package ingest/data/ncbi_dataset.zip \
         > ingest/data/raw_metadata.tsv
 
 5. Exit the Nextstrain shell to return to your usual shell environment.
 
-.. code-block::
+.. code-block:: console
 
     $ exit
 
@@ -133,13 +133,13 @@ If you wanted this field to be included in your outputs, you could perform the f
 
 1. Create a new build config directory ``ingest/build-configs/tutorial/``
 
-.. code-block::
+.. code-block:: console
 
     $ mkdir ingest/build-configs/tutorial
 
 2. Copy the default config to ``ingest/build-configs/tutorial/config.yaml``
 
-.. code-block::
+.. code-block:: console
 
     $ cp ingest/defaults/config.yaml ingest/build-configs/tutorial/config.yaml
 
@@ -168,7 +168,7 @@ Any of the config parameters can be overridden in a custom config file.
 
 4. Run the ingest workflow again with the custom config file.
 
-.. code-block::
+.. code-block:: console
 
     $ nextstrain build ingest --configfile build-configs/tutorial/config.yaml --forceall
     Using profile profiles/default and workflow specific profile profiles/default for setting default command line arguments.
@@ -190,7 +190,7 @@ We'll walk through an example customization that joins additional metadata to th
 
 1. Create an additional metadata file ``ingest/build-configs/tutorial/additional-metadata.tsv``
 
-.. code-block::
+.. code-block:: none
 
     genbank_accession    column_A    column_B    column_C
     AF013415    AAAAA    BBBBB    CCCCC
@@ -207,7 +207,7 @@ We'll walk through an example customization that joins additional metadata to th
 
 2. Create a new rules file ``ingest/build-configs/tutorial/merge-metadata.smk``
 
-.. code-block::
+.. code-block:: python
 
     rule merge_metadata:
       input:
@@ -234,7 +234,7 @@ default ``?`` value in the new columns.
 
 3. Add the following to the custom config file ``ingest/build-configs/tutorial/config.yaml``
 
-.. code-block::
+.. code-block:: yaml
 
     custom_rules:
       - build-configs/tutorial/merge-metadata.smk
@@ -243,7 +243,7 @@ The ``custom_rules`` config tells the ingest workflow to include your custom rul
 
 4. Run the ingest workflow again with the customized rule.
 
-.. code-block::
+.. code-block:: console
 
     $ nextstrain build ingest merge_metadata --configfile build-configs/tutorial/config.yaml
     Using profile profiles/default and workflow specific profile profiles/default for setting default command line arguments.
@@ -261,7 +261,7 @@ Next steps
 * Run the `zika phylogenetic workflow <https://github.com/nextstrain/zika/tree/main/phylogenetic>`_ with new ingested data as input
   by running
 
-  .. code-block::
+  .. code-block:: console
 
       $ mv ingest/results/* phylogenetic/data/
       $ nextstrain build phylogenetic