fixup: update docs

phylogenetic/rules/prepare_sequences_E.smk

@@ -1,17 +1,17 @@
 """
-This part of the workflow prepares sequences for constructing the phylogenetic tree.
+This part of the workflow prepares reference files and sequences for constructing the gene phylogenetic trees.
 REQUIRED INPUTS:
-    metadata_url    = url to metadata.tsv.zst
-    sequences_url   = url to sequences.fasta.zst
     reference   = path to reference sequence or genbank
+    sequences   = path to all sequences from which gene sequences can be extracted
+
 OUTPUTS:
-    prepared_sequences = results/aligned.fasta
+    gene_fasta = reference fasta for the gene (e.g. E gene)
+    gene_genbank = reference genbank for the gene (e.g. E gene)
+    sequences = sequences with gene sequences extracted and aligned to the reference gene sequence
 This part of the workflow usually includes the following steps:
-    - augur index
-    - augur filter
-    - augur align
-    - augur mask
-See Augur's usage docs for these commands for more details.
+    - newreference.py: Creates new gene genbank and gene reference FASTA from the whole genome reference genbank
+    - nextclade: Aligns sequences to the reference gene sequence and extracts the gene sequences to ensure the reference files are valid
+See Nextclade or script usage docs for these commands for more details.
 """
 
 ruleorder: align_and_extract_E > decompress