No need to reverse complement in build, as ingest already reverse com…

…plements
nextstrain · Sep 22, 2023 · 5998739 · 5998739
1 parent 9fe0536
commit 5998739
Show file tree

Hide file tree

Showing 2 changed files with 1 addition and 49 deletions.
diff --git a/scripts/reverse_reversed_sequences.py b/scripts/reverse_reversed_sequences.py
diff --git a/workflow/snakemake_rules/core.smk b/workflow/snakemake_rules/core.smk
@@ -102,29 +102,14 @@ rule combine_samples:
         """
 
 
-rule separate_reverse_complement:
-    input:
-        metadata=build_dir + "/{build_name}/metadata.tsv",
-        sequences=build_dir + "/{build_name}/filtered.fasta",
-    output:
-        build_dir + "/{build_name}/reversed.fasta",
-    shell:
-        """
-        python3 scripts/reverse_reversed_sequences.py \
-            --metadata {input.metadata} \
-            --sequences {input.sequences} \
-            --output {output}
-        """
-
-
 rule align:
     message:
         """
         Aligning sequences to {input.reference}
           - filling gaps with N
         """
     input:
-        sequences=rules.separate_reverse_complement.output,
+        sequences=rules.combine_samples.output.sequences,
         reference=config["reference"],
         genemap=config["genemap"],
     output:
@@ -142,7 +127,6 @@ rule align:
             --genemap {input.genemap} \
             --max-indel {params.max_indel} \
             --seed-spacing {params.seed_spacing} \
-            --retry-reverse-complement \
             --output-fasta - \
             --output-insertions {output.insertions} \
             {input.sequences} | seqkit seq -i > {output.alignment}