Update docs of nextclade.smk

ingest/workflow/snakemake_rules/nextclade.smk

@@ -1,3 +1,24 @@
+"""
+This part of the workflow handles running Nextclade on the curated metadata
+and sequences.
+
+REQUIRED INPUTS:
+
+    metadata    = data/metadata_all.tsv
+    sequences   = results/sequences_{serotype}.fasta
+    nextclade_datasets = ../nextclade_data/{serotype}
+
+OUTPUTS:
+
+    metadata        = results/metadata_{serotype}.tsv
+    sequences       = results/sequences_{serotype}.fasta
+    nextclade       = results/nextclade_subtypes.tsv
+
+See Nextclade docs for more details on usage, inputs, and outputs if you would
+like to customize the rules:
+https://docs.nextstrain.org/projects/nextclade/page/user/nextclade-cli.html
+"""
+
 SUPPORTED_NEXTCLADE_SEROTYPES = ['denv1', 'denv2', 'denv3', 'denv4']
 SEROTYPE_CONSTRAINTS = '|'.join(SUPPORTED_NEXTCLADE_SEROTYPES)