Merge pull request #245 from nextstrain/nextclade3

Use nextclade3 for phylogenetic workflow

phylogenetic/build-configs/ci/config.yaml

@@ -2,7 +2,7 @@ custom_rules:
   - build-configs/ci/copy_example_data.smk
 
 reference: "defaults/reference.fasta"
-genemap: "defaults/genemap.gff"
+genome_annotation: "defaults/genome_annotation.gff3"
 genbank_reference: "defaults/reference.gb"
 include: "defaults/hmpxv1/include.txt"
 clades: "defaults/clades.tsv"
@@ -20,7 +20,6 @@ build_name: "hmpxv1"
 auspice_name: "mpox_clade-IIb"
 
 filter:
-  exclude: "defaults/exclude_accessions.txt"
   min_date: 2017
   min_length: 100000
 

phylogenetic/defaults/exclude_accessions.txt

@@ -75,7 +75,4 @@ PP098578
 
 HM172544	# cidofovir-resistant lab strain that is derived from DQ011155 (h/t Andrew Rambaut)
 
-TMP0003	# Overdiverged 23MPX1786C
-TMP0045	# Overdiverged RDC-NKV-GOM-MPOX-004
-
 NC_003310	# Overdiverged RefSeq NC_003310

phylogenetic/defaults/hmpxv1/config.yaml

@@ -1,5 +1,5 @@
 reference: "defaults/reference.fasta"
-genemap: "defaults/genemap.gff"
+genome_annotation: "defaults/genome_annotation.gff3"
 genbank_reference: "defaults/reference.gb"
 include: "defaults/hmpxv1/include.txt"
 clades: "defaults/clades.tsv"
@@ -17,7 +17,6 @@ build_name: "hmpxv1"
 auspice_name: "mpox_clade-IIb"
 
 filter:
-  exclude: "defaults/exclude_accessions.txt"
   min_date: 2017
   min_length: 100000
 

phylogenetic/defaults/hmpxv1_big/config.yaml

@@ -1,5 +1,5 @@
 reference: "defaults/reference.fasta"
-genemap: "defaults/genemap.gff"
+genome_annotation: "defaults/genome_annotation.gff3"
 genbank_reference: "defaults/reference.gb"
 include: "defaults/hmpxv1_big/include.txt"
 clades: "defaults/clades.tsv"
@@ -17,7 +17,6 @@ build_name: "hmpxv1_big"
 auspice_name: "mpox_lineage-B.1"
 
 filter:
-  exclude: "defaults/exclude_accessions.txt"
   min_date: 2022
   min_length: 180000
 

phylogenetic/defaults/mpxv/config.yaml

@@ -1,7 +1,7 @@
 auspice_config: "defaults/mpxv/auspice_config.json"
 include: "defaults/mpxv/include.txt"
 reference: "defaults/reference.fasta"
-genemap: "defaults/genemap.gff"
+genome_annotation: "defaults/genome_annotation.gff3"
 genbank_reference: "defaults/reference.gb"
 lat_longs: "defaults/lat_longs.tsv"
 description: "defaults/description.md"
@@ -17,7 +17,6 @@ build_name: "mpxv"
 auspice_name: "mpox_all-clades"
 
 filter:
-  exclude: "defaults/exclude_accessions.txt"
   min_date: 1950
   min_length: 100000
 

phylogenetic/rules/annotate_phylogeny.smk

@@ -48,15 +48,15 @@ rule translate:
     input:
         tree=build_dir + "/{build_name}/tree.nwk",
         node_data=build_dir + "/{build_name}/nt_muts.json",
-        genemap=config["genemap"],
+        genome_annotation=config["genome_annotation"],
     output:
         node_data=build_dir + "/{build_name}/aa_muts.json",
     shell:
         """
         augur translate \
             --tree {input.tree} \
             --ancestral-sequences {input.node_data} \
-            --reference-sequence {input.genemap} \
+            --reference-sequence {input.genome_annotation} \
             --output {output.node_data}
         """
 

phylogenetic/rules/prepare_sequences.smk

@@ -5,7 +5,7 @@ REQUIRED INPUTS:
 
     include     = path to file of sequences to in force include
     reference   = path to reference sequence FASTA for Nextclade alignment
-    genemap     = path to genemap GFF for Nextclade alignment
+    genome_annotation     = path to genome_annotation GFF for Nextclade alignment
     maskfile    = path to maskfile of sites to be masked
 
 OUTPUTS:
@@ -56,12 +56,12 @@ rule filter:
     input:
         sequences="data/sequences.fasta",
         metadata="data/metadata.tsv",
+        exclude="defaults/exclude_accessions.txt",
     output:
         sequences=build_dir + "/{build_name}/good_sequences.fasta",
         metadata=build_dir + "/{build_name}/good_metadata.tsv",
         log=build_dir + "/{build_name}/good_filter.log",
     params:
-        exclude=config["filter"]["exclude"],
         min_date=config["filter"]["min_date"],
         min_length=config["filter"]["min_length"],
         strain_id=config["strain_id_field"],
@@ -73,7 +73,7 @@ rule filter:
             --metadata-id-columns {params.strain_id} \
             --output-sequences {output.sequences} \
             --output-metadata {output.metadata} \
-            --exclude {params.exclude} \
+            --exclude {input.exclude} \
             --min-date {params.min_date} \
             --min-length {params.min_length} \
             --query "(QC_rare_mutations == 'good' | QC_rare_mutations == 'mediocre')" \
@@ -93,9 +93,11 @@ rule subsample:
             "sequences_per_group"
         ],
         other_filters=lambda w: config["subsample"][w.sample].get("other_filters", ""),
-        exclude=lambda w: f"--exclude-where {' '.join([f'lineage={l}' for l in config['subsample'][w.sample]['exclude_lineages']])}"
-        if "exclude_lineages" in config["subsample"][w.sample]
-        else "",
+        exclude=lambda w: (
+            f"--exclude-where {' '.join([f'lineage={l}' for l in config['subsample'][w.sample]['exclude_lineages']])}"
+            if "exclude_lineages" in config["subsample"][w.sample]
+            else ""
+        ),
         strain_id=config["strain_id_field"],
     shell:
         """
@@ -156,30 +158,35 @@ rule reverse_reverse_complements:
 rule align:
     """
     Aligning sequences to {input.reference}
-      - filling gaps with N
     """
     input:
         sequences=build_dir + "/{build_name}/reversed.fasta",
         reference=config["reference"],
-        genemap=config["genemap"],
+        genome_annotation=config["genome_annotation"],
     output:
         alignment=build_dir + "/{build_name}/aligned.fasta",
-        insertions=build_dir + "/{build_name}/insertions.fasta",
     params:
-        max_indel=config["max_indel"],
-        seed_spacing=config["seed_spacing"],
+        # Alignment params from all-clades nextclade dataset
+        excess_bandwidth=100,
+        terminal_bandwidth=300,
+        window_size=40,
+        min_seed_cover=0.1,
+        allowed_mismatches=8,
+        gap_alignment_side="left",
     threads: workflow.cores
     shell:
         """
-        nextalign run \
+        nextclade3 run \
             --jobs {threads} \
-            --reference {input.reference} \
-            --genemap {input.genemap} \
-            --max-indel {params.max_indel} \
-            --seed-spacing {params.seed_spacing} \
-            --retry-reverse-complement \
+            --input-ref {input.reference} \
+            --input-annotation {input.genome_annotation} \
+            --excess-bandwidth {params.excess_bandwidth} \
+            --terminal-bandwidth {params.terminal_bandwidth} \
+            --window-size {params.window_size} \
+            --min-seed-cover {params.min_seed_cover} \
+            --allowed-mismatches {params.allowed_mismatches} \
+            --gap-alignment-side {params.gap_alignment_side} \
             --output-fasta - \
-            --output-insertions {output.insertions} \
             {input.sequences} | seqkit seq -i > {output.alignment}
         """