wip: try rooting by two nodes

nextstrain · Jun 10, 2024 · 2b5a0fc · 2b5a0fc
1 parent 03aea77
commit 2b5a0fc
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Showing 2 changed files with 8 additions and 8 deletions.
diff --git a/nextclade/config/config_dengue.yaml b/nextclade/config/config_dengue.yaml
@@ -26,10 +26,10 @@ outgroup: "config/outgroup.fasta"
 refine:
   root_id:
     all: "Reconstructed_root_sequence_of_https_nextstrain_org_dengue/all/genome"
-    denv1: "Reconstructed_root_sequence_of_https_nextstrain_org_dengue/denv1/genome"
-    denv2: "Reconstructed_root_sequence_of_https_nextstrain_org_dengue/denv2/genome"
-    denv3: "Reconstructed_root_sequence_of_https_nextstrain_org_dengue/denv3/genome"
-    denv4: "Reconstructed_root_sequence_of_https_nextstrain_org_dengue/denv4/genome"
+    denv1: ['Reconstructed_root_sequence_of_https_nextstrain_org_dengue/denv1/genome', 'Reconstructed_root_sequence_of_https_nextstrain_org_dengue/all/genome']
+    denv2: ['Reconstructed_root_sequence_of_https_nextstrain_org_dengue/denv2/genome', 'Reconstructed_root_sequence_of_https_nextstrain_org_dengue/all/genome']
+    denv3: ['Reconstructed_root_sequence_of_https_nextstrain_org_dengue/denv3/genome', 'Reconstructed_root_sequence_of_https_nextstrain_org_dengue/all/genome']
+    denv4: ['Reconstructed_root_sequence_of_https_nextstrain_org_dengue/denv4/genome', 'Reconstructed_root_sequence_of_https_nextstrain_org_dengue/all/genome']
 
 traits:
   sampling_bias_correction: '3'

diff --git a/nextclade/rules/construct_phylogeny.smk b/nextclade/rules/construct_phylogeny.smk
@@ -46,10 +46,10 @@ rule refine:
         date_inference = "marginal",
         clock_filter_iqd = 4,
         strain_id = config.get("strain_id_field", "strain"),
-        root_flag = lambda wildcard: (
-            f"--root '{config['refine']['root_id'][wildcard.serotype]}'"
+        root_args = lambda wildcard: (
+            " ".join(f"'{id}'" for id in config['refine']['root_id'][wildcard.serotype])
             if wildcard.serotype in config["refine"]['root_id']
-            else "--root min_dev"
+            else "min_dev"
         )
     shell:
         """
@@ -63,5 +63,5 @@ rule refine:
             --divergence-unit mutations \
             --keep-polytomies \
             --use-fft \
-            {params.root_flag}
+            --root {params.root_args}
         """