From a6bce9f37d2e467ce8c9b8bcf7c2595c5dda4180 Mon Sep 17 00:00:00 2001 From: aineniamh Date: Sun, 3 May 2020 10:47:05 +0100 Subject: [PATCH] --addprofile added, doesn't break even if one seq --- pangolin/scripts/assign_query_lineage.smk | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pangolin/scripts/assign_query_lineage.smk b/pangolin/scripts/assign_query_lineage.smk index 5196c51..fbd3ed3 100644 --- a/pangolin/scripts/assign_query_lineage.smk +++ b/pangolin/scripts/assign_query_lineage.smk @@ -39,7 +39,7 @@ rule profile_align_query: output: temp(config["tempdir"] + "/{query}.aln.fasta") shell: - "mafft --add {input.query:q} {input.aln:q} > {output:q}" + "mafft --addprofile {input.query:q} {input.aln:q} > {output:q}" rule iqtree_with_guide_tree: input: