Ensure all text files (except ingest/vendored) have end-of-file newlines

A long-standing Unix convention that when broken can lead to confusing and incorrect behaviour from many commands when they read such files. The offending files in ingest/vendored will be fixed when we next update it from upstream. Updating it now would necessitate a slew of unrelated changes to this repo.
nextstrain · Oct 30, 2024 · a6c33c5 · a6c33c5
1 parent e416110
commit a6c33c5
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Showing 5 changed files with 3 additions and 5 deletions.
diff --git a/nextclade/rules/construct_phylogeny.smk b/nextclade/rules/construct_phylogeny.smk
@@ -53,4 +53,3 @@ rule refine:
             --clock-filter-iqd {params.clock_filter_iqd} \
             --stochastic-resolve
         """
-
diff --git a/phylogenetic/defaults/dropped_strains.txt b/phylogenetic/defaults/dropped_strains.txt
@@ -1,2 +1,2 @@
 HM562901 # temara.MOR/24.03
-HM562900 # Mvs/Toulon.FRA/08.07
+HM562900 # Mvs/Toulon.FRA/08.07
diff --git a/phylogenetic/rules/construct_phylogeny.smk b/phylogenetic/rules/construct_phylogeny.smk
@@ -53,4 +53,3 @@ rule refine:
             --clock-filter-iqd {params.clock_filter_iqd} \
             --stochastic-resolve
         """
-
diff --git a/phylogenetic/rules/prepare_sequences.smk b/phylogenetic/rules/prepare_sequences.smk
@@ -86,4 +86,4 @@ rule align:
             --fill-gaps \
             --remove-reference
         """
-
+
diff --git a/phylogenetic/rules/prepare_sequences_N450.smk b/phylogenetic/rules/prepare_sequences_N450.smk
@@ -57,4 +57,4 @@ rule filter_N450:
             --subsample-max-sequences {params.subsample_max_sequences} \
             --min-date {params.min_date} \
             --min-length {params.min_length}
-        """
+        """
Original file line number	Diff line number	Diff line change
Expand Up		@@ -53,4 +53,3 @@ rule refine:
		--clock-filter-iqd {params.clock_filter_iqd} \
		--stochastic-resolve
		"""
Original file line number	Diff line number	Diff line change
Expand Up		@@ -86,4 +86,4 @@ rule align:
		--fill-gaps \
		--remove-reference
		"""