From bd393f11ae575755b941d4358386390216538bdd Mon Sep 17 00:00:00 2001
From: Thomas Sibley <tsibley@fredhutch.org>
Date: Wed, 4 Sep 2024 11:37:07 -0700
Subject: [PATCH] ingest: Use raw-string for Nextclade metadata merge rule
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Preserving the line-breaks makes the command much more readable in
Snakemake output¹, which is important since I'm changing this rule right
now.

The \n previously interpreted by Python is now interpreted by `tr`,
which is preferable.

¹ <https://docs.nextstrain.org/en/latest/reference/snakemake-style-guide.html#use-triple-quoted-command-definitions>

Ported-from: <https://github.com/nextstrain/measles/commit/762acdb2b54ce7bb47cf69e72b70e1e2051a6ae4>
Related-to: <https://github.com/nextstrain/measles/pull/52>
Related-to: <https://github.com/nextstrain/pathogen-repo-guide/issues/65>
---
 ingest/rules/nextclade.smk | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/ingest/rules/nextclade.smk b/ingest/rules/nextclade.smk
index 8bda056..3117028 100644
--- a/ingest/rules/nextclade.smk
+++ b/ingest/rules/nextclade.smk
@@ -72,7 +72,7 @@ rule join_metadata_and_nextclade:
         metadata_id_field=config["curate"]["output_id_field"],
         nextclade_id_field=config["nextclade"]["id_field"],
     shell:
-        """
+        r"""
         export SUBSET_FIELDS=`grep -v '^#' {input.nextclade_field_map} | awk '{{print $1}}' | tr '\n' ',' | sed 's/,$//g'`
 
         csvtk -tl cut -f $SUBSET_FIELDS \