ingest/config.yaml: Add all NCBI Datasets fields

Provides an easy way for first time users to get the uncurated metadata
from NCBI Datasets commands by running the ingest workflow with the
specified target `data/ncbi_dataset_report.tsv`.

Afterwards, users can easily remove fields that are not needed as part
the workflow to reduce the file size and save space.

Prompted by @jameshadfield in review of the tutorial¹ and
resolves #30.

¹ nextstrain/docs.nextstrain.org#195 (comment)

ingest/README.md

@@ -25,6 +25,22 @@ This produces the default outputs of the ingest workflow:
 - metadata      = results/metadata.tsv
 - sequences     = results/sequences.fasta
 
+### Uncurated metadata
+
+To see the uncurated metadata from NCBI Datasets, you can specify the intermediate
+target of the workflow with:
+
+```
+nextstrain build ingest data/ncbi_dataset_report.tsv --notemp
+```
+
+> [!Note]
+> This outputs the computer friendly mnemonics instead of the human readable
+> names of the [NCBI Dataset fields](https://www.ncbi.nlm.nih.gov/datasets/docs/v2/reference-docs/command-line/dataformat/tsv/dataformat_tsv_virus-genome/#fields).
+
+Inspect the `ingest/data/ncbi_dataset_report.tsv` file to see the uncurated
+metadata from NCBI Datasets.
+
 ## Defaults
 
 The defaults directory contains all of the default configurations for the ingest workflow.

ingest/defaults/config.yaml

@@ -13,24 +13,60 @@ ncbi_taxon_id: ""
 # The list of NCBI Datasets fields to include from NCBI Datasets output
 # These need to be the mneumonics of the NCBI Datasets fields, see docs for full list of fields
 # https://www.ncbi.nlm.nih.gov/datasets/docs/v2/reference-docs/command-line/dataformat/tsv/dataformat_tsv_virus-genome/#fields
+#
+# The default includes all available fields to be able to easily see the
+# uncurated metadata by running the workflow with the target `data/ncbi_dataset_report.tsv`
+# Remove any fields that are not needed in your workflow to reduce file size and save space.
 # Note: the "accession" field MUST be provided to match with the sequences
 ncbi_datasets_fields:
   - accession
-  - sourcedb
-  - sra-accs
-  - isolate-lineage
-  - geo-region
+  - bioprojects
+  - biosample-acc
+  - completeness
+  - gene-count
   - geo-location
-  - isolate-collection-date
-  - release-date
-  - update-date
-  - length
+  - geo-region
+  - host-common-name
+  - host-infraspecific-breed
+  - host-infraspecific-cultivar
+  - host-infraspecific-ecotype
+  - host-infraspecific-isolate
+  - host-infraspecific-sex
+  - host-infraspecific-strain
   - host-name
+  - host-pangolin
+  - host-tax-id
+  - is-annotated
+  - is-complete
+  - is-lab-host
+  - is-vaccine-strain
+  - isolate-collection-date
+  - isolate-lineage
   - isolate-lineage-source
-  - biosample-acc
-  - submitter-names
+  - lab-host
+  - length
+  - matpeptide-count
+  - mol-type
+  - nucleotide-completeness
+  - protein-count
+  - purpose-of-sampling
+  - release-date
+  - sourcedb
+  - sra-accs
   - submitter-affiliation
   - submitter-country
+  - submitter-names
+  - update-date
+  - virus-common-name
+  - virus-infraspecific-breed
+  - virus-infraspecific-cultivar
+  - virus-infraspecific-ecotype
+  - virus-infraspecific-isolate
+  - virus-infraspecific-sex
+  - virus-infraspecific-strain
+  - virus-name
+  - virus-pangolin
+  - virus-tax-id
 
 # Config parameters related to the curate pipeline
 curate: