Phylogenetic: Create phylogenetic trees between recombination breakpoints

ingest/defaults/config.yaml

@@ -150,7 +150,7 @@ gene_coverage:
   id_field: "seqName"
   coverage:
     cdsCoverage_field: "cdsCoverage"
-    genes: "p48,NTPase,p22,VPg,3CLpro,RdRp,VP1,VP2"
+    genes: "p48,NTPase,p22,VPg,3CLpro,RdRp,VP1,VP2,ORF1,ORF2,ORF3"
     round_digits: 3
 
 # Nextclade parameters to include if you are running Nextclade as a part of your ingest workflow

phylogenetic/build-configs/ci/config.yaml

@@ -2,7 +2,7 @@
 # for the CI workflow to run with the example data.
 
 # {group} represents different genotypes to be analyzed
-groups: ['all']
+groups: ['GII.2']
 # {gene} represents the norovirus genes to focus on in each build
 genes: ['genome', 'VP1']
 

phylogenetic/defaults/GII.4/exclude.txt

@@ -0,0 +1,13 @@
+KX158286
+JX846924
+MK073894
+KJ407072
+NC_039475
+KC597139
+KJ196286
+MH218591
+KT589391
+MG557657 # Low quality, may break all/VPg
+KX158285 # Perhaps too diverged, may break GII.4/genome
+OR951134 # False positive GII.4, remove after nextclade tuning
+MF373609 # False positive GII.4, remove after nextclade tuning

phylogenetic/defaults/all/config.yaml

@@ -8,4 +8,8 @@
 # {group} represents different genotypes to be analyzed
 groups: ['all']
 # {gene} represents the norovirus genes to focus on in each build
-genes: ['3CLpro', 'NTPase', 'p22', 'p48', 'RdRp', 'VP1', 'VP2', 'VPg']
+genes: ['genome', '3CLpro', 'NTPase', 'p22', 'p48', 'RdRp', 'VP1', 'VP2', 'VPg']
+
+# Timetree still performs better than outgroup
+# refine:
+#   outgroup: NC_027026_outgroup

phylogenetic/defaults/all/reference.gff3

@@ -14,7 +14,11 @@ NC_039477_REF	Genbank	gene	3029	3571	.	+	.	ID=gene-3CLpro;Name=3CLpro
 NC_039477_REF	Genbank	CDS	3029	3571	.	+	.	ID=cds-3CLpro;Parent=gene-3CLpro;Name=3CLpro
 NC_039477_REF	Genbank	gene	3572	5101	.	+	.	ID=gene-RdRp;Name=RdRp
 NC_039477_REF	Genbank	CDS	3572	5101	.	+	.	ID=cds-RdRp;Parent=gene-RdRp;Name=RdRp
+NC_039477_REF	Genbank	gene	5085	6707	.	+	.	ID=gene-ORF2;Name=ORF2
+NC_039477_REF	Genbank	CDS	5085	6707	.	+	.	ID=cds-ORF2;Parent=gene-ORF2;Name=ORF2
 NC_039477_REF	Genbank	gene	5085	6707	.	+	.	ID=gene-VP1;Name=VP1
 NC_039477_REF	Genbank	CDS	5085	6707	.	+	.	ID=cds-VP1;Parent=gene-VP1;Name=VP1
+NC_039477_REF	Genbank	gene	6707	7513	.	+	.	ID=gene-ORF3;Name=ORF3
+NC_039477_REF	Genbank	CDS	6707	7513	.	+	.	ID=cds-ORF3;Parent=gene-ORF3;Name=ORF3
 NC_039477_REF	Genbank	gene	6707	7513	.	+	.	ID=gene-VP2;Name=VP2
 NC_039477_REF	Genbank	CDS	6707	7513	.	+	.	ID=cds-VP2;Parent=gene-VP2;Name=VP2

phylogenetic/defaults/config.yaml

@@ -6,9 +6,9 @@
 
 # Define wildcards used for building trees in the workflow, also used in the intermediate files or auxillariary default file names.
 # {group} represents different genotypes to be analyzed
-groups: ['GII.6', 'GII.4', 'GII.2', 'GII.3', 'GII.17', 'all']
+groups: ['GII.6', 'GII.4', 'GII.2', 'GII.3', 'GII.17']
 # {gene} represents the norovirus genes to focus on in each build
-genes: ['genome']
+genes: ['ORF1', 'ORF2', 'ORF3', 'RdRp', 'VP1']
 
 inputs:
   - name: ncbi
@@ -20,20 +20,20 @@ strain_id_field: "accession"
 reference: defaults/{group}/reference.gb
 
 filter:
-  exclude: defaults/exclude.txt
+  exclude:
+    default: defaults/exclude.txt
+    GII.4: defaults/GII.4/exclude.txt
   min_coverage: 0.8
   filter_params: --group-by year VP1_nextclade RdRp_nextclade --sequences-per-group 30 --min-date 1950 --exclude-ambiguous-dates-by year --query-columns is_lab_host:str --exclude-where is_lab_host='true'
 
 refine:
   root:
     default: best --timetree --date-confidence --clock-filter-iqd 4 --date-inference marginal
+    # Estimated from auspice build https://github.com/nextstrain/norovirus/issues/22#issuecomment-3221851561
     all:
       p48: DQ366347 --timetree --date-confidence --clock-filter-iqd 4 --date-inference marginal
       VP2: best --timetree --date-confidence
       genome: best --timetree --date-confidence
-    GII.4:
-      genome: mid_point --timetree --date-confidence
-  # Estimated from auspice build https://github.com/nextstrain/norovirus/issues/22#issuecomment-3221851561
   clock_rate:
     all:
       genome: 0.00328
@@ -46,15 +46,16 @@ refine:
       VP1: 0.00136
       VP2: 0.00228
     GII.2:
-      genome: 0.000211
+      RdRp: 0.000346
     GII.3:
-      genome: 0.000688
+      RdRp: 0.00156
     GII.4:
-      genome: 0.000874
+      RdRp: 0.00177
     GII.6:
-      genome: 0.000135
+      RdRp: 0.00199
     GII.17:
-      genome: 0.00142
+      RdRp: 0.00133
+
 
 traits:
   default: region country ORF1_type ORF2_type VP1_nextclade VP1_group VP1_type VP1_variant RdRp_nextclade RdRp_group RdRp_type RdRp_variant host

phylogenetic/defaults/description.md

@@ -1,15 +1,22 @@
 We gratefully acknowledge the authors, originating and submitting laboratories of the genetic sequences and metadata for sharing their work. Please note that although data generators have generously shared data in an open fashion, that does not mean there should be free license to publish on this data. Data generators should be cited where possible and collaborations should be sought in some circumstances. Please try to avoid scooping someone else's work. Reach out if uncertain.
 
-**We maintain 14 views of norovirus evolution:**
+**We provide divergence tree views of norovirus evolution across all samples:**
 
 | group | genome | p48 | NTPase | p22 | VPg | 3CLpro | RdRp | VP1 | VP2 |
 |:--|:--|:--|:--|:--|:--|:--|:--|:--|:--|
 | all | [genome](https://nextstrain.org/norovirus/all/genome) | [p48](https://nextstrain.org/norovirus/all/p48) | [NTPase](https://nextstrain.org/norovirus/all/NTPase) | [p22](https://nextstrain.org/norovirus/all/p22) | [VPg](https://nextstrain.org/norovirus/all/VPg) | [3CLpro](https://nextstrain.org/norovirus/all/3CLpro) | [RdRp](https://nextstrain.org/norovirus/all/RdRp/) | [VP1](https://nextstrain.org/norovirus/all/VP1) | [VP2](https://nextstrain.org/norovirus/all/VP2) |
-| GII.2 | [genome](https://nextstrain.org/norovirus/GII.2/genome) | | | | | | | | |
-| GII.3 | [genome](https://nextstrain.org/norovirus/GII.3/genome) | | | | | | | | |
-| GII.4 | [genome](https://nextstrain.org/norovirus/GII.4/genome) | | | | | | | | |
-| GII.6 | [genome](https://nextstrain.org/norovirus/GII.6/genome) | | | | | | | | |
-| GII.17 | [genome](https://nextstrain.org/norovirus/GII.17/genome) | | | | | | | | |
+
+**We provide timetree views by genogroup:**
+
+Since novovirus is known to have recombination breakpoints between ORF1-ORF2 (between the RdRp and VP1 genes) and less frequently between ORF2-ORF3, the treetime views are by breakpoint region.
+
+| group  | ORF1 | ORF2 | ORF3 | RdRp | VP1 |
+|:--|:-- |:--|:--|:--|:--|
+| GII.2  | [ORF1](https://nextstrain.org/norovirus/GII.2/ORF1/) | [ORF2](https://nextstrain.org/norovirus/GII.2/ORF2/) | [ORF3](https://nextstrain.org/norovirus/GII.2/ORF3/) | [RdRp](https://nextstrain.org/norovirus/GII.2/RdRp/) | [VP1](https://nextstrain.org/norovirus/GII.2/VP1/) |
+| GII.3  | [ORF1](https://nextstrain.org/norovirus/GII.3/ORF1/) | [ORF2](https://nextstrain.org/norovirus/GII.3/ORF2/) | [ORF3](https://nextstrain.org/norovirus/GII.3/ORF3/) | [RdRp](https://nextstrain.org/norovirus/GII.3/RdRp/) | [VP1](https://nextstrain.org/norovirus/GII.3/VP1/) |
+| GII.4  | [ORF1](https://nextstrain.org/norovirus/GII.4/ORF1/) | [ORF2](https://nextstrain.org/norovirus/GII.4/ORF2/) | [ORF3](https://nextstrain.org/norovirus/GII.4/ORF3/) | [RdRp](https://nextstrain.org/norovirus/GII.4/RdRp/) | [VP1](https://nextstrain.org/norovirus/GII.4/VP1/) |
+| GII.6  | [ORF1](https://nextstrain.org/norovirus/GII.6/ORF1/) | [ORF2](https://nextstrain.org/norovirus/GII.6/ORF2/) | [ORF3](https://nextstrain.org/norovirus/GII.6/ORF3/) | [RdRp](https://nextstrain.org/norovirus/GII.6/RdRp/) | [VP1](https://nextstrain.org/norovirus/GII.6/VP1/) |
+| GII.17 | [ORF1](https://nextstrain.org/norovirus/GII.17/ORF1/) | [ORF2](https://nextstrain.org/norovirus/GII.17/ORF2/) | [ORF3](https://nextstrain.org/norovirus/GII.17/ORF3/) | [RdRp](https://nextstrain.org/norovirus/GII.17/RdRp/) | [VP1](https://nextstrain.org/norovirus/GII.17/VP1/) |
 
 #### Nextclade group, type, and variant assignment
 

phylogenetic/defaults/outgroup.fasta

@@ -0,0 +1,2 @@
+>NC_027026_outgroup
+gtgatcaccttgggatggcttccaagccattccaagttgagtcttgcgacttcatgtttgaagtccatgttctccacatgtgctacctcagggtagcaccgagagaacagtttcttgatgactgtactataagtgcagttaccaaatattatttgcaccacgtgcccctacataatagaaatggcatggactgcgagtttgaggctgaggggttgctgtcccggttattcgggacggccggttccccctcactggattcgcagtccgctttcaaggagcttttcggctttgacaccgatgagcaaatgccattgtcccttgaagaattggccaaattgcaaggcgaaatcaccgcctcgcttcaaatgaacaataaccaattcgttgctaaacatggtaaggccaaggtgcaggcccttttggaccagctcaacacactggtcccccgtgacatcagtgaggctgaaagacgccgtcgagaattctttgagaggcagactgctgctgccttcgctgaactcccaaatgatgacacatttaccgaacaagattggaagtcctattggtatgcaatgtggcggcgagttgtgggtggttgcaaatcatactaccatggtctgccccgttggagctctttcaagacacggctctcgcgtgccacagagcccctccgccaggtgttagcagttgctgcacagacctttgatcaatgtgtacaaactgaccctcgcatcttggctatgaattgtgtgactgccttgaaacccactgttttaaccatgatataccagcaacatcacaacacacccagtgggtggcttgcaacccttacggccctctgggaggttttccaaccttccctccctgcattaggcactttaggtactggtgttgccacaaccttggggctcgtcgtcaacaccttgtcacggttcttccagaaactttgtgcttacatttctgaaacatttcttcccgaatctccaacaaccccaggctgggttgccattgtggctggtgttctgctgttacttttgaaactctcctgcatccccaaagtgttttcccactggagcacgcttctcaagttggccagtggtatcacaacagtcattggagcaacacgagccgtggactggatcatggggaaaattcgcgacgcgcgccattcttccatgtgtaaacagttccttagccgtgtgtctgcactgttggagctccactactcaaagactgtcacaggtgttgcagagaacacagagctcctcaagtgtttcgaccagctcattgatgaaggagaagaattggtctctgaaataggaggtggttctttagccgcaataatacgcagtggtgttgacacactccagagggtttccacagaaatcaaagccacaatccaactggacaacccgcgtccagtgcccgtatgtgtgatattctccggacctccaggtattggaaaaacctctttagcataccacatggccaagggcattggtctcacctccaacttttctttggcaaacgatcatcatgatggatatacaggtaaccctgtagctatatgggatgaatatgatactgacaaggatggcaaatttgtggagcagatgatatccctggtcaacacacagccttgtgtcctcaattgtgaccgaccagaaaataagggcaagctttttacatccaagttcattttctgcactaccaattacacgaccagtgtgctcccagacaatccacgtgctggcgcattctaccgtcgagtcatcactgtagatgtgcgatctcctgaaattgaggattggatggcagcacaccctggtaggtcccctccgaaaactctcttcaaaagcgattgctcccacttgaaattaatggttaggccatatatggggtacaaccctgacggggatactctagctggcaaacgcgtaaagcccaccccaatcaccatagctgggcttcatgacatgattgacaaaaagtttgaggagcaatcaggggaggtccggggcatttggatcactgtgccccggcgtagtgtgcaaacagcccttgttgctgtcaagaagttttgtgtagcccatcaagcgttgtgccacgtcacatccactccttctcctgaaattctacagtgtgccactttctcgtgtgttgttgtgtcagatgcgcacccgccacctggtgctccacttttgcacatcaagaatgcacatcttgaagtagaccacactggccaagctgtcaccagcatttcagagagcctgcttggtatgtttattacagagcaacgtgtttcatccaagttgcaaagggatatcatgtacaaagtgtggtcaccttttacattaatgcagactgagccattgaatacacagtccctacccccagttaggcgcataatttatgctgacacgcccatggatttcattgggggtttaaggcaccaccttggctttagttcaattcctggtctgtggcgtgcccttaagcatctcccagacacgccctcaatgatagagtggatcactgaccacctttctcaagtgcagtttcccaacaaccccgaatcaaccctatttagaacaggcaatggtgatgtcatattctatacttatggttctttttatgctctaggcacttgtgcccgtgtgcctgtagttagtggtgacacagttagccctctcccaaatgtccccctaaaaatgacttggtttgaaacactgaaggccctttgctcgtcagcattgcgcttgttcacggccatctcaccatttgccatagccgttgctaatgtcacttatctcaccacccgaggatcacgtgaagaacaagccaaaggcaagacaaaacatggtcgtggcgcccgccatgcccgtgggcgatccacagcgcttaatgatgatgagtacaatgagtggatggacttgcgccgcgactggcgtgaagaaatgactgctgacgagttcttacacctaagggatgaagcttatgaaggtatcatcaatgaccgcacccagcggtacaacacctggcttaacctgcgcaacatgcgcttaggcgctggagcgtaccaacatgcaacaatcataggcaagggtggtgtgcgcaatgagatcatacgcacccaagtgctgaaggctcccaggaaaggaaaatggtcacacattgattcttctggccccatgaattattttgatgaggcaccgaccccactagtggaatttgagtgtgatggtgcccatgttgggtggggggtgcaccttgggaacgggcgcgtggtgacagtcacccatgtggccacatcatctaacactgtgaacgggctgccatttaaggtcaaggacaccgacggggagacctgccaggtttatgccactctaggtaacttgccacactaccagcttggggatggtgcgcctgtttactacacaaccaggtaccaccctgtgcttgtgattggtgaagggcaatttgacacacctacaacgactgtcaacggtttccacgttcgcattaccaattcatatccaacaaagaaaggtgattgtggactaccatacttcaatgcactgcgccaggtggttgcccttcatgctgctggcagtacagatgggtcaaccaagttggcgcaacgagttgctgagaaaccgcaaacaggggatgcattcgtctggaagggattgcccgttgttcgtggtagtgatgtcggcggactccccactggcactcgctaccatcgctccccagcttggccagagatgcgatctgacgagactcattcaccagctccttttggttctggtgacaagcggtatgaattctcacaagtggagatgcttgttaacaacttgagaccataccttgaggaagttccaggggtgcctccagcattacttaatagagctattgttcacacccgcaattacctacaatcaataattggcactgaacaaagtgaaccacttacttatgccatggcatcatcaatgttggaaaaaggcacctcctgtggtccccacattactggccttaagggtgattactgggatgatgaaacacaacagtacacagggtcacttcgagaacatctggaagcggtctggaacaaggctatgttagggacaccaccaagccacgattacaaattggcactcaaagatgagttaagaccaaatgagaaaaatgaacagggtaagaggcgcctgctgtggggtgctgatgctgggcttactctcgtgtgttgtgctgctctcaaaccagcagccgcacgactgcaaactgttgtgcctatgacacctgttgcagtcggcatcaacatggattctgcacacatagaagttatgaatgagtcccttaaggggcgtgtgctttatgcattagattatagcaagtgggacagcacccaatctgcagctgtgacagcagcctcacttgagatccttgcatccttcatgacaccaactccaattgtctcatcagctattgaggccctgaaggcacccgctagaggcatggtcaacgatgccatcttcatagctcgatccggtttgccatctggcatgccgttcacaagtgtggtcaactccatcaaccacatgctttacatctctgcagctattcttcaggcatacgaagcacataatctcccatatagtgacaatgtttttaacattgaaaccattcacacctatggtgatgattgcctgtacgggttcacccccgcaacagcctctctcatgcaggtaatcatagaaaacctacgctcatatggcctgaaacccacagcagctgataagggcgaaaccattgccccagtgcaaactcctgtttttctcaagcgcacgttcgcaacaacaccacatggactgcgcgctttgcttgacacctcttccattcttaggcagttcttctgggtgaaagcccaacgcacatgtgatgtctattctgctcctacaattgacaccaaatctcgggctgcgcagctcgaggtggcattggcctatgctagtcaacatggtcatgagttcttcaacaaagcacgtgaaatcgctgagaaaacaagtgcagctgaggggtatgttctggtgaataccaactacgaacaagcaactgcatgttacaacagctggtacataggaggcactacaccagaaatgcccgctaccaatgaaggctgcgggctaatagtgtttgagatggagggcaatggctccccacgaggaggtaaccagcctcaatcccacaatggtggcacttcacctgctcaggctgcaccgcctggcacgactggccctgcggaagcaccccttgtacctgttaatcctgaacagcccaattccattgcccaacgcatggagctggctgttgccacaggagcaacaacctcaaatgtccctgaatgtgtgcggaactgctttgctctccttcgtacgattccttggaattctcgacagccccagggatctcttctcacagctgtttctttacaccctgacatcaacccgtacacaaaacatcttgctcaaatgtttgccggatggggaggggcaatggatgtccgtgtcacgatctcaggctcgggcttatttgcagggaagcttgtgtgtgggatacttcctcctggagttaatcccactcttgtcagcgatccgggggttctgccacacgctttggtagatgcccgcgtgactgaaccagcatgcttcaacgtgcctgatgtccgcgccgtcgactaccatcgcactgacggcgatgaggcaactgcaacacttggcatttgggtgctccaaccactaatcaaccccttctccactgaagctgtttcaaccgcttggatttcaattgagaccaaaccaggtggtgattttgatctttgcttgatgaaacctcctaaccaagccatggataacggcacatctccatcgttcctcttgccacgccgtttacaacgttcaagaggcaaccgcgctggtggctatgcagttggaatggtcattgtgggctcagcacaccaggtgaaccgccacttcactgctcttggcacaacatttggttggtctaccgcaccttacgaacccatgcgatgtgcttttggtggagtacatcaagggcgtgacaccaacccaaaaattggctactactgggaggttggtgctgaccagcgtggcccgctttttccaaacattgttaatcattggcctgattttgcagtcaacaccaaatacacatggccagatgccgactatataccccatagtgcggttgttggaaccttggtttccttccaggacaatggagatgtttctgaggatcaagtggctactgcatttgcaatttcaatgaacactccaagtgggagcacaactggacgcggcacagtcagagaagcatttgatccatccacaatgcatttggtccgcaccaatggtaccactcaaccatctgggtggccaaccggctcaaacactggaaatggttacttcacaccaatgtggggtcatggtcagggtaatgcaattaatgataagatcaccaacatggagggggctaattatacatttggaggctctggccaaaacaacatagtcttgtgggttgaaagaatcttctcagaccatcctggtaaaaccacactttactcatcacaattggacagcactgcggccattttccagtcaggcccagtcaatatacctgagaacatgatggctgtctacaatgtcaccactaatggggctgactttcaagttggcatccgtcgtgatggctacatggtcacatctggaacaattggtactcagcaggagcttgaccctgacaccactttcacttatgttggacttttccccctttctgcctcattggttggcccacatgggaattctggacgggcccagatagcatggtcatgagctggttggtaggcactttgcaatctcttggtgggctcactgacgttgcgtccaccatttctggcatggtttatcaacatagacatcttgaccaactgaaaagacagaatgatctacaagaacagtggatggcccgcaatgaacaactgcagcgagatgcaatgcaattaactcaggatttggcagtcaatgccccagcgatgagagtgcaggccgctctcaatgctgggtttgatgtggttagtgcgcgccagcttgccggttcaactgagcgaaggatcaacggctatttggatcagccaattcgcactattgatcaggcaatggcagtgcagtctaggggcaatttgacttcgttgtcgaacgcccttgccacttaccaaaaaggcactcaatttggactcaaacaacccaaaggatttaagagcccaattgctgctgaacaatctcgtggtccaaccattacacttggccctcccccaccatctactaatctataaatcaatcttttataaatttgtgcaaatttctttttcttcctcatggtcgcacacgcgttcgggtgcgttgcagtcaattaagcgattgacgccatctttgg

phylogenetic/rules/construct_phylogeny.smk

@@ -19,11 +19,41 @@ This part of the workflow usually includes the following steps:
 See Augur's usage docs for these commands for more details.
 """
 
+rule add_outgroup:
+    """Add outgroup"""
+    input:
+        alignment = "results/{group}/{gene}/aligned.fasta",
+        outgroup = "defaults/outgroup.fasta",
+    output:
+        alignment_with_outgroup = "results/{group}/{gene}/aligned_with_outgroup.fasta",
+    log:
+        "logs/{group}/{gene}/add-outgroup.txt",
+    benchmark:
+        "benchmarks/{group}/{gene}/add-outgroup.txt",
+    shell:
+        """
+        augur align \
+            --sequences {input.outgroup} \
+            --existing-alignment {input.alignment} \
+            --output {output.alignment_with_outgroup} \
+            2>&1 | tee {log}
+        """
+
+def _alignment(wildcards):
+    """
+    Based on if outgroup rooting is specified in the config file, return the needed alignment file
+    """
+    outgroup = config['refine'].get('outgroup', "")
+    if outgroup != "":
+        return "results/{group}/{gene}/aligned_with_outgroup.fasta"
+    else:
+        return "results/{group}/{gene}/aligned.fasta"
+
 
 rule tree:
     """Building tree"""
     input:
-        alignment = "results/{group}/{gene}/aligned.fasta"
+        alignment = lambda wildcards: _alignment(wildcards),
     output:
         tree = "results/{group}/{gene}/tree_raw.nwk"
     benchmark:
@@ -52,20 +82,26 @@ def _clock_rate_params(wildcards):
 
     else leave blank
     """
-    clock_rate = config['refine']['clock_rate'].get(wildcards.group, {}).get(wildcards.gene, "")
+    clock_rate = config['refine'].get('clock_rate', {}).get(wildcards.group, {}).get(wildcards.gene, "")
     if clock_rate !="":
         return f' --clock-rate {clock_rate} '
     else:
         return ""
 
+def _root_params(wildcards):
+    outgroup = config['refine'].get('outgroup', '')
+    if outgroup !="":
+        return f'{outgroup} --remove-outgroup'
+    else:
+        return config['refine']['root'].get(wildcards.group, {}).get(wildcards.gene, config['refine']['root']['default']),
 
 rule refine:
     """
     Refining tree
     """
     input:
         tree = "results/{group}/{gene}/tree_raw.nwk",
-        alignment = "results/{group}/{gene}/aligned.fasta",
+        alignment = lambda wildcards: _alignment(wildcards),
         metadata = "results/{group}/{gene}/filtered.tsv"
     output:
         tree = "results/{group}/{gene}/tree.nwk",
@@ -75,7 +111,7 @@ rule refine:
     log:
         "logs/{group}/{gene}/refine.txt",
     params:
-        root = lambda wildcards: config['refine']['root'].get(wildcards.group, {}).get(wildcards.gene, config['refine']['root']['default']),
+        root = lambda wildcards: _root_params(wildcards),
         clock_rate_params = lambda wildcards: _clock_rate_params(wildcards),
         id_field = config['strain_id_field'],
     shell:
@@ -90,6 +126,6 @@ rule refine:
             --metadata-id-columns {params.id_field} \
             --output-tree {output.tree:q} \
             --output-node-data {output.node_data:q} \
-            --stochastic-resolve \
-            {params.clock_rate_params}
+            {params.clock_rate_params} \
+            --stochastic-resolve
         """

phylogenetic/rules/prepare_sequences.smk

@@ -47,7 +47,7 @@ rule filter:
     input:
         sequences = "results/sequences.fasta",
         metadata = "results/metadata.tsv",
-        exclude = config['filter']['exclude']
+        exclude = lambda wildcards: config['filter']['exclude'].get(wildcards.group, config['filter']['exclude']['default']),
     output:
         sequences = "results/{group}/{gene}/filtered.fasta",
         metadata = "results/{group}/{gene}/filtered.tsv",