WIP: Add rule to create column for accessions

Author: j23414

ingest/rules/curate.smk

@@ -116,10 +116,27 @@ rule curate:
                 --output-seq-field {params.sequence_field} ) 2>> {log}
         """
 
+rule add_metadata_columns:
+    """Add columns to metadata
+    Notable columns:
+    - [NEW] url: URL linking to the NCBI GenBank record ('https://www.ncbi.nlm.nih.gov/nuccore/*').
+    """
+    input:
+        metadata = "data/all_metadata.tsv"
+    output:
+        metadata = "data/all_metadata_added.tsv"
+    shell:
+        """
+        csvtk mutate2 -t \
+          -n url \
+          -e '"https://www.ncbi.nlm.nih.gov/nuccore/" + $accession' \
+          {input.metadata} \
+        > {output.metadata}
+        """
 
 rule subset_metadata:
     input:
-        metadata="data/all_metadata.tsv",
+        metadata="data/all_metadata_added.tsv",
     output:
         subset_metadata="data/subset_metadata.tsv",
     params: