Merge pull request #27 from nextstrain/fixup-include-samples

fixup: use include file in `augur filter`
nextstrain · Apr 30, 2024 · 73dd4bc · 73dd4bc
2 parents 15957d4 + c8547a2
commit 73dd4bc
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diff --git a/phylogenetic/rules/prepare_sequences.smk b/phylogenetic/rules/prepare_sequences.smk
@@ -59,6 +59,7 @@ rule filter:
             --metadata {input.metadata} \
             --metadata-id-columns {params.strain_id} \
             --exclude {input.exclude} \
+            --include {input.include} \
             --output {output.sequences} \
             --group-by {params.group_by} \
             --sequences-per-group {params.sequences_per_group} \

diff --git a/phylogenetic/rules/prepare_sequences_N450.smk b/phylogenetic/rules/prepare_sequences_N450.smk
@@ -51,6 +51,7 @@ rule filter_N450:
             --metadata {input.metadata} \
             --metadata-id-columns {params.strain_id} \
             --exclude {input.exclude} \
+            --include {input.include} \
             --output {output.sequences} \
             --group-by {params.group_by} \
             --subsample-max-sequences {params.subsample_max_sequences} \