diff --git a/pipes/WDL/tasks/tasks_assembly.wdl b/pipes/WDL/tasks/tasks_assembly.wdl
index 20a85f600..7d577bd4b 100644
--- a/pipes/WDL/tasks/tasks_assembly.wdl
+++ b/pipes/WDL/tasks/tasks_assembly.wdl
@@ -15,7 +15,7 @@ task assemble {
       String   sample_name = basename(basename(reads_unmapped_bam, ".bam"), ".taxfilt")
       
       Int?     machine_mem_gb
-      String   docker = "quay.io/broadinstitute/viral-assemble:2.3.2.0"
+      String   docker = "quay.io/broadinstitute/viral-assemble:2.3.6.1"
     }
     parameter_meta{
       reads_unmapped_bam: {
@@ -115,7 +115,7 @@ task select_references {
     Int?          skani_s
     Int?          skani_c
 
-    String        docker = "quay.io/broadinstitute/viral-assemble:2.3.2.0"
+    String        docker = "quay.io/broadinstitute/viral-assemble:2.3.6.1"
     Int           machine_mem_gb = 4
     Int           cpu = 2
     Int           disk_size = 100
@@ -206,7 +206,7 @@ task scaffold {
       Float?       scaffold_min_pct_contig_aligned
 
       Int?         machine_mem_gb
-      String       docker="quay.io/broadinstitute/viral-assemble:2.3.2.0"
+      String       docker="quay.io/broadinstitute/viral-assemble:2.3.6.1"
 
       # do this in multiple steps in case the input doesn't actually have "assembly1-x" in the name
       String       sample_name = basename(basename(contigs_fasta, ".fasta"), ".assembly1-spades")
@@ -583,7 +583,7 @@ task align_reads {
     Boolean  skip_mark_dupes = false
 
     Int?     machine_mem_gb
-    String   docker = "quay.io/broadinstitute/viral-core:2.3.2"
+    String   docker = "quay.io/broadinstitute/viral-core:2.4.0"
 
     String   sample_name = basename(basename(basename(reads_unmapped_bam, ".bam"), ".taxfilt"), ".clean")
   }
@@ -720,7 +720,7 @@ task refine_assembly_with_aligned_reads {
       Int      min_coverage = 3
 
       Int      machine_mem_gb = 15
-      String   docker = "quay.io/broadinstitute/viral-assemble:2.3.2.0"
+      String   docker = "quay.io/broadinstitute/viral-assemble:2.3.6.1"
     }
 
     Int disk_size = 375
@@ -845,7 +845,7 @@ task refine_2x_and_plot {
       String? plot_coverage_novoalign_options = "-r Random -l 40 -g 40 -x 20 -t 100 -k"
 
       Int?    machine_mem_gb
-      String  docker = "quay.io/broadinstitute/viral-assemble:2.3.2.0"
+      String  docker = "quay.io/broadinstitute/viral-assemble:2.3.6.1"
 
       # do this in two steps in case the input doesn't actually have "cleaned" in the name
       String  sample_name = basename(basename(reads_unmapped_bam, ".bam"), ".cleaned")
@@ -981,7 +981,7 @@ task run_discordance {
       String out_basename = "run"
       Int    min_coverage = 4
 
-      String docker = "quay.io/broadinstitute/viral-core:2.3.2"
+      String docker = "quay.io/broadinstitute/viral-core:2.4.0"
     }
     parameter_meta {
       reads_aligned_bam: {
diff --git a/pipes/WDL/tasks/tasks_demux.wdl b/pipes/WDL/tasks/tasks_demux.wdl
index 9a63dc521..86d209970 100644
--- a/pipes/WDL/tasks/tasks_demux.wdl
+++ b/pipes/WDL/tasks/tasks_demux.wdl
@@ -6,7 +6,7 @@ task merge_tarballs {
     String       out_filename
 
     Int?         machine_mem_gb
-    String       docker = "quay.io/broadinstitute/viral-core:2.3.2"
+    String       docker = "quay.io/broadinstitute/viral-core:2.4.0"
   }
 
   Int disk_size = 2625
@@ -163,7 +163,7 @@ task illumina_demux {
 
     Int?    machine_mem_gb
     Int     disk_size = 2625
-    String  docker = "quay.io/broadinstitute/viral-core:2.3.2"
+    String  docker = "quay.io/broadinstitute/viral-core:2.4.0"
   }
 
   parameter_meta {
diff --git a/pipes/WDL/tasks/tasks_interhost.wdl b/pipes/WDL/tasks/tasks_interhost.wdl
index e8ca286ce..93e875dba 100644
--- a/pipes/WDL/tasks/tasks_interhost.wdl
+++ b/pipes/WDL/tasks/tasks_interhost.wdl
@@ -160,7 +160,7 @@ task multi_align_mafft_ref {
     Float?       mafft_gapOpeningPenalty
 
     Int?         machine_mem_gb
-    String       docker = "quay.io/broadinstitute/viral-phylo:2.1.20.2"
+    String       docker = "quay.io/broadinstitute/viral-phylo:2.3.6.0"
   }
 
   String         fasta_basename = basename(reference_fasta, '.fasta')
@@ -207,7 +207,7 @@ task multi_align_mafft {
     Float?       mafft_gapOpeningPenalty
 
     Int?         machine_mem_gb
-    String       docker = "quay.io/broadinstitute/viral-phylo:2.1.20.2"
+    String       docker = "quay.io/broadinstitute/viral-phylo:2.3.6.0"
   }
 
   Int disk_size = 200
@@ -351,7 +351,7 @@ task index_ref {
     File?  novocraft_license
 
     Int?   machine_mem_gb
-    String docker = "quay.io/broadinstitute/viral-core:2.3.2"
+    String docker = "quay.io/broadinstitute/viral-core:2.4.0"
   }
 
   Int disk_size = 100
@@ -476,7 +476,7 @@ task merge_vcfs_gatk {
     File        ref_fasta
 
     Int?        machine_mem_gb
-    String      docker = "quay.io/broadinstitute/viral-phylo:2.1.20.2"
+    String      docker = "quay.io/broadinstitute/viral-phylo:2.3.6.0"
 
     String      output_prefix = "merged"
   }
diff --git a/pipes/WDL/tasks/tasks_intrahost.wdl b/pipes/WDL/tasks/tasks_intrahost.wdl
index 83dc49599..10eb1b4f1 100644
--- a/pipes/WDL/tasks/tasks_intrahost.wdl
+++ b/pipes/WDL/tasks/tasks_intrahost.wdl
@@ -136,7 +136,7 @@ task lofreq {
     File      reference_fasta
 
     String    out_basename = basename(aligned_bam, '.bam')
-    String    docker = "quay.io/biocontainers/lofreq:2.1.5--py38h588ecb2_4"
+    String    docker = "quay.io/broadinstitute/viral-phylo:2.3.6.0"
   }
   Int disk_size = 200
   command <<<
@@ -145,8 +145,13 @@ task lofreq {
     lofreq version | grep version | sed 's/.* \(.*\)/\1/g' | tee LOFREQ_VERSION
 
     # make local copies because CWD is writeable but localization dir isn't always
-    cp "~{reference_fasta}" reference.fasta
     cp "~{aligned_bam}" aligned.bam
+    python3<<CODE
+    import shutil
+    import util.file
+    with util.file.fastas_with_sanitized_ids("~{reference_fasta}", use_tmp=True) as sanitized_fastas:
+        shutil.copyfile(sanitized_fastas[0], 'reference.fasta')
+    CODE
 
     # samtools faidx fails if fasta is empty
     if [ $(grep -v '^>' reference.fasta | tr -d '\nNn' | wc -c) == "0" ]; then
@@ -191,7 +196,7 @@ task isnvs_per_sample {
     Boolean removeDoublyMappedReads = true
 
     Int?    machine_mem_gb
-    String  docker = "quay.io/broadinstitute/viral-phylo:2.1.20.2"
+    String  docker = "quay.io/broadinstitute/viral-phylo:2.3.6.0"
 
     String  sample_name = basename(basename(basename(mapped_bam, ".bam"), ".all"), ".mapped")
   }
@@ -234,7 +239,7 @@ task isnvs_vcf {
     Boolean        naiveFilter = false
 
     Int?           machine_mem_gb
-    String         docker = "quay.io/broadinstitute/viral-phylo:2.1.20.2"
+    String         docker = "quay.io/broadinstitute/viral-phylo:2.3.6.0"
   }
 
   parameter_meta {
@@ -308,7 +313,7 @@ task annotate_vcf_snpeff {
     String?        emailAddress
 
     Int?           machine_mem_gb
-    String         docker = "quay.io/broadinstitute/viral-phylo:2.1.20.2"
+    String         docker = "quay.io/broadinstitute/viral-phylo:2.3.6.0"
 
     String         output_basename = basename(basename(in_vcf, ".gz"), ".vcf")
   }
diff --git a/pipes/WDL/tasks/tasks_megablast.wdl b/pipes/WDL/tasks/tasks_megablast.wdl
index 7b9822545..d93a359c1 100755
--- a/pipes/WDL/tasks/tasks_megablast.wdl
+++ b/pipes/WDL/tasks/tasks_megablast.wdl
@@ -15,7 +15,7 @@ task trim_rmdup_subsamp {
         Int cpu            = 16
         Int disk_size_gb   = 100 
 
-        String docker      = "quay.io/broadinstitute/viral-assemble:2.3.2.0"
+        String docker      = "quay.io/broadinstitute/viral-assemble:2.3.6.1"
     }
 
     parameter_meta {
@@ -36,7 +36,7 @@ task trim_rmdup_subsamp {
     command <<<
         set -ex o pipefail
         assembly.py --version | tee VERSION
-        #BAM ->FASTQ-> OutBam? https://github.com/broadinstitute/viral-assemble/blob/80bcc1da5c6a0174362ca9fd8bc0b49ee0b4103b/assembly.py#L91
+        #BAM ->FASTQ-> OutBam? https://github.com/broadinstitute/viral-assemble:2.3.6.1
         assembly.py trim_rmdup_subsamp \
         "~{inBam}" \
         "~{clipDb}" \
diff --git a/pipes/WDL/tasks/tasks_ncbi.wdl b/pipes/WDL/tasks/tasks_ncbi.wdl
index abb5a3d1d..31278f662 100644
--- a/pipes/WDL/tasks/tasks_ncbi.wdl
+++ b/pipes/WDL/tasks/tasks_ncbi.wdl
@@ -6,7 +6,7 @@ task download_fasta {
     Array[String]+ accessions
     String         emailAddress
 
-    String         docker = "quay.io/broadinstitute/viral-phylo:2.1.20.2"
+    String         docker = "quay.io/broadinstitute/viral-phylo:2.3.6.0"
   }
 
   command {
@@ -38,7 +38,7 @@ task download_annotations {
     String         emailAddress
     String         combined_out_prefix
 
-    String         docker = "quay.io/broadinstitute/viral-phylo:2.1.20.2"
+    String         docker = "quay.io/broadinstitute/viral-phylo:2.3.6.0"
   }
 
   command <<<
@@ -85,7 +85,7 @@ task annot_transfer {
     File         reference_fasta
     Array[File]+ reference_feature_table
 
-    String       docker = "quay.io/broadinstitute/viral-phylo:2.1.20.2"
+    String       docker = "quay.io/broadinstitute/viral-phylo:2.3.6.0"
   }
 
   parameter_meta {
@@ -139,7 +139,7 @@ task align_and_annot_transfer_single {
     Array[File]+ reference_fastas
     Array[File]+ reference_feature_tables
 
-    String       docker = "quay.io/broadinstitute/viral-phylo:2.1.20.2"
+    String       docker = "quay.io/broadinstitute/viral-phylo:2.3.6.0"
   }
 
   parameter_meta {
@@ -192,7 +192,7 @@ task structured_comments {
 
     File?  filter_to_ids
 
-    String docker = "quay.io/broadinstitute/viral-core:2.3.2"
+    String docker = "quay.io/broadinstitute/viral-core:2.4.0"
   }
   String out_base = basename(assembly_stats_tsv, '.txt')
   command <<<
@@ -272,7 +272,7 @@ task rename_fasta_header {
 
     String out_basename = basename(genome_fasta, ".fasta")
 
-    String docker = "quay.io/broadinstitute/viral-core:2.3.2"
+    String docker = "quay.io/broadinstitute/viral-core:2.4.0"
   }
   command {
     set -e
@@ -437,7 +437,7 @@ task sra_meta_prep {
     Boolean     paired
 
     String      out_name = "sra_metadata.tsv"
-    String      docker="quay.io/broadinstitute/viral-core:2.3.2"
+    String      docker="quay.io/broadinstitute/viral-core:2.4.0"
   }
   Int disk_size = 100
   parameter_meta {
@@ -653,7 +653,7 @@ task biosample_to_genbank {
     File?   filter_to_ids
 
     Boolean s_dropout_note = true
-    String  docker = "quay.io/broadinstitute/viral-phylo:2.1.20.2"
+    String  docker = "quay.io/broadinstitute/viral-phylo:2.3.6.0"
   }
   String base = basename(biosample_attributes, ".txt")
   command {
@@ -851,7 +851,7 @@ task prepare_genbank {
     String?      assembly_method_version
 
     Int?         machine_mem_gb
-    String       docker = "quay.io/broadinstitute/viral-phylo:2.1.20.2"
+    String       docker = "quay.io/broadinstitute/viral-phylo:2.3.6.0"
   }
 
   parameter_meta {
diff --git a/pipes/WDL/tasks/tasks_nextstrain.wdl b/pipes/WDL/tasks/tasks_nextstrain.wdl
index 98b1733ab..52d874982 100644
--- a/pipes/WDL/tasks/tasks_nextstrain.wdl
+++ b/pipes/WDL/tasks/tasks_nextstrain.wdl
@@ -11,9 +11,15 @@ task taxid_to_nextclade_dataset_name {
             2697049 : 'sars-cov-2',
             641809  : 'flu_h1n1pdm_ha',
             335341  : 'flu_h3n2_ha',
+            119210  : 'flu_h3n2_ha',
             518987  : 'flu_vic_ha',
             208893  : 'rsv_a',
             208895  : 'rsv_b',
+            11234   : 'nextstrain/measles/N450/WHO-2012',
+            11053   : 'nextstrain/dengue/all',
+            11060   : 'nextstrain/dengue/all',
+            11069   : 'nextstrain/dengue/all',
+            11070   : 'nextstrain/dengue/all',
             10244   : 'MPXV',
             619591  : 'hMPXV'
         }
@@ -43,13 +49,11 @@ task nextclade_one_sample {
         File  genome_fasta
         File? root_sequence
         File? auspice_reference_tree_json
-        File? qc_config_json
+        File? pathogen_json
         File? gene_annotations_json
-        File? pcr_primers_csv
-        File? virus_properties
         String? dataset_name
         Int    disk_size = 50
-        String docker = "nextstrain/nextclade:2.14.0"
+        String docker = "nextstrain/nextclade:3.9.1"
     }
     String basename = basename(genome_fasta, ".fasta")
     command <<<
@@ -67,21 +71,19 @@ task nextclade_one_sample {
             DATASET_ARG="--input-dataset ."
         python3<<CODE1
         import json, os
-        with open('tag.json', 'rt') as inf:
+        with open('pathogen.json', 'rt') as inf:
             datasetinfo = json.load(inf)
         with open('VERSION', 'wt') as outf:
-            outf.write(os.environ['NEXTCLADE_VERSION'] + "; name=" + datasetinfo['name'] + "; tag=" + datasetinfo['tag'] + "\n")
+            outf.write(os.environ['NEXTCLADE_VERSION'] + "; name=" + datasetinfo['attributes']['name'] + "; tag=" + datasetinfo['version']['tag'] + "\n")
         CODE1
         fi
 
         nextclade run \
             $DATASET_ARG \
-            ~{"--input-root-seq " + root_sequence} \
+            ~{"--input-ref " + root_sequence} \
             ~{"--input-tree " + auspice_reference_tree_json} \
-            ~{"--input-qc-config " + qc_config_json} \
-            ~{"--input-gene-map " + gene_annotations_json} \
-            ~{"--input-pcr-primers " + pcr_primers_csv} \
-            ~{"--input-virus-properties " + virus_properties}  \
+            ~{"--input-annotation " + gene_annotations_json} \
+            ~{"--input-pathogen-json " + pathogen_json}  \
             --output-all=. \
             --output-basename "~{basename}" \
             --output-json "~{basename}".nextclade.json \
@@ -136,15 +138,13 @@ task nextclade_many_samples {
         Array[File]+ genome_fastas
         File?        root_sequence
         File?        auspice_reference_tree_json
-        File?        qc_config_json
+        File?        pathogen_json
         File?        gene_annotations_json
-        File?        pcr_primers_csv
-        File?        virus_properties
         String?      dataset_name
         String       basename
         File?        genome_ids_setdefault_blank
         Int          disk_size = 150
-        String       docker = "nextstrain/nextclade:2.14.0"
+        String       docker = "nextstrain/nextclade:3.9.1"
     }
     command <<<
         set -e
@@ -170,12 +170,10 @@ task nextclade_many_samples {
 
         nextclade run \
             $DATASET_ARG \
-            ~{"--input-root-seq " + root_sequence} \
+            ~{"--input-ref " + root_sequence} \
             ~{"--input-tree " + auspice_reference_tree_json} \
-            ~{"--input-qc-config " + qc_config_json} \
-            ~{"--input-gene-map " + gene_annotations_json} \
-            ~{"--input-pcr-primers " + pcr_primers_csv} \
-            ~{"--input-virus-properties " + virus_properties}  \
+            ~{"--input-annotation " + gene_annotations_json} \
+            ~{"--input-pathogen-json " + pathogen_json}  \
             --output-all=. \
             --output-basename "~{basename}" \
             --output-json "~{basename}".nextclade.json \
@@ -323,7 +321,7 @@ task derived_cols {
         String?       lab_highlight_loc
         Array[File]   table_map = []
 
-        String        docker = "quay.io/broadinstitute/viral-core:2.3.2"
+        String        docker = "quay.io/broadinstitute/viral-core:2.4.0"
         Int           disk_size = 50
     }
     parameter_meta {
@@ -891,7 +889,7 @@ task filter_sequences_to_list {
 
         String       out_fname = sub(sub(basename(sequences, ".zst"), ".vcf", ".filtered.vcf"), ".fasta$", ".filtered.fasta")
         # Prior docker image: "nextstrain/base:build-20240318T173028Z"
-        String       docker = "quay.io/broadinstitute/viral-core:2.3.2"
+        String       docker = "quay.io/broadinstitute/viral-core:2.4.0"
         Int          disk_size = 750
     }
     parameter_meta {
@@ -992,7 +990,7 @@ task mafft_one_chr {
         Boolean  large = false
         Boolean  memsavetree = false
 
-        String   docker = "quay.io/broadinstitute/viral-phylo:2.1.20.2"
+        String   docker = "quay.io/broadinstitute/viral-phylo:2.3.6.0"
         Int      mem_size = 500
         Int      cpus = 64
         Int      disk_size = 750
@@ -1080,7 +1078,7 @@ task mafft_one_chr_chunked {
         Int      batch_chunk_size = 2000
         Int      threads_per_job = 2
 
-        String   docker = "quay.io/broadinstitute/viral-phylo:2.1.20.2"
+        String   docker = "quay.io/broadinstitute/viral-phylo:2.3.6.0"
         Int      mem_size = 32
         Int      cpus = 64
         Int      disk_size = 750
diff --git a/pipes/WDL/tasks/tasks_read_utils.wdl b/pipes/WDL/tasks/tasks_read_utils.wdl
index a42aad19e..ce72165e2 100644
--- a/pipes/WDL/tasks/tasks_read_utils.wdl
+++ b/pipes/WDL/tasks/tasks_read_utils.wdl
@@ -84,7 +84,7 @@ task group_bams_by_sample {
 task get_bam_samplename {
   input {
     File    bam
-    String  docker = "quay.io/broadinstitute/viral-core:2.3.2"
+    String  docker = "quay.io/broadinstitute/viral-core:2.4.0"
   }
   Int   disk_size = round(size(bam, "GB")) + 50
   command <<<
@@ -111,7 +111,7 @@ task get_sample_meta {
   input {
     Array[File] samplesheets_extended
 
-    String      docker = "quay.io/broadinstitute/viral-core:2.3.2"
+    String      docker = "quay.io/broadinstitute/viral-core:2.4.0"
   }
   Int disk_size = 50
   command <<<
@@ -172,7 +172,7 @@ task merge_and_reheader_bams {
       File?        reheader_table
       String       out_basename = basename(in_bams[0], ".bam")
 
-      String       docker = "quay.io/broadinstitute/viral-core:2.3.2"
+      String       docker = "quay.io/broadinstitute/viral-core:2.4.0"
       Int          disk_size = 750
       Int          machine_mem_gb = 4
     }
@@ -244,7 +244,7 @@ task rmdup_ubam {
     String  method = "mvicuna"
 
     Int     machine_mem_gb = 7
-    String  docker = "quay.io/broadinstitute/viral-core:2.3.2"
+    String  docker = "quay.io/broadinstitute/viral-core:2.4.0"
   }
 
   Int disk_size = 375
@@ -303,7 +303,7 @@ task downsample_bams {
     Boolean      deduplicateAfter = false
 
     Int?         machine_mem_gb
-    String       docker = "quay.io/broadinstitute/viral-core:2.3.2"
+    String       docker = "quay.io/broadinstitute/viral-core:2.4.0"
   }
 
   Int disk_size = 750
@@ -367,7 +367,7 @@ task FastqToUBAM {
     String? sequencing_center
     String? additional_picard_options
 
-    String  docker = "quay.io/broadinstitute/viral-core:2.3.2"
+    String  docker = "quay.io/broadinstitute/viral-core:2.4.0"
   }
   Int disk_size = 375
   parameter_meta {
@@ -418,7 +418,7 @@ task read_depths {
     File      aligned_bam
 
     String    out_basename = basename(aligned_bam, '.bam')
-    String    docker = "quay.io/broadinstitute/viral-core:2.3.2"
+    String    docker = "quay.io/broadinstitute/viral-core:2.4.0"
   }
   Int disk_size = 200
   command <<<
diff --git a/pipes/WDL/tasks/tasks_reports.wdl b/pipes/WDL/tasks/tasks_reports.wdl
index 36205cb1b..146915b44 100644
--- a/pipes/WDL/tasks/tasks_reports.wdl
+++ b/pipes/WDL/tasks/tasks_reports.wdl
@@ -15,7 +15,7 @@ task alignment_metrics {
     Int    max_amplicons=500
 
     Int    machine_mem_gb=32
-    String docker = "quay.io/broadinstitute/viral-core:2.3.2"
+    String docker = "quay.io/broadinstitute/viral-core:2.4.0"
   }
 
   String out_basename = basename(aligned_bam, ".bam")
@@ -28,7 +28,12 @@ task alignment_metrics {
     echo "Requesting $MEM_MB MB of RAM for Java"
 
     # requisite Picard fasta indexing
-    cp "~{ref_fasta}" reference.fasta
+    python3<<CODE
+    import shutil
+    import util.file
+    with util.file.fastas_with_sanitized_ids("~{ref_fasta}", use_tmp=True) as sanitized_fastas:
+        shutil.copyfile(sanitized_fastas[0], 'reference.fasta')
+    CODE
     picard $XMX CreateSequenceDictionary -R reference.fasta
 
     if [ -s "~{ref_fasta}" ]; then
@@ -137,7 +142,7 @@ task plot_coverage {
     String? plotXLimits # of the form "min max" (ints, space between)
     String? plotYLimits # of the form "min max" (ints, space between)
 
-    String  docker = "quay.io/broadinstitute/viral-core:2.3.2"
+    String  docker = "quay.io/broadinstitute/viral-core:2.4.0"
   }
 
   Int disk_size = 375
@@ -284,7 +289,7 @@ task coverage_report {
     Array[File]  mapped_bam_idx # optional.. speeds it up if you provide it, otherwise we auto-index
     String       out_report_name = "coverage_report.txt"
 
-    String       docker = "quay.io/broadinstitute/viral-core:2.3.2"
+    String       docker = "quay.io/broadinstitute/viral-core:2.4.0"
   }
 
   Int disk_size = 375
@@ -351,7 +356,7 @@ task fastqc {
   input {
     File   reads_bam
 
-    String docker = "quay.io/broadinstitute/viral-core:2.3.2"
+    String docker = "quay.io/broadinstitute/viral-core:2.4.0"
   }
   parameter_meta {
     reads_bam:{ 
@@ -399,7 +404,7 @@ task align_and_count {
     Boolean keep_duplicates_when_filtering                    = false
 
     Int?   machine_mem_gb
-    String docker = "quay.io/broadinstitute/viral-core:2.3.2"
+    String docker = "quay.io/broadinstitute/viral-core:2.4.0"
   }
 
   String  reads_basename=basename(reads_bam, ".bam")
@@ -511,7 +516,7 @@ task align_and_count_summary {
 
     String       output_prefix = "count_summary"
 
-    String       docker = "quay.io/broadinstitute/viral-core:2.3.2"
+    String       docker = "quay.io/broadinstitute/viral-core:2.4.0"
   }
 
   Int disk_size = 100
@@ -693,7 +698,7 @@ task compare_two_genomes {
     File   genome_two
     String out_basename
 
-    String docker = "quay.io/broadinstitute/viral-assemble:2.3.2.0"
+    String docker = "quay.io/broadinstitute/viral-assemble:2.3.6.1"
   }
 
   Int disk_size = 50
diff --git a/pipes/WDL/tasks/tasks_sarscov2.wdl b/pipes/WDL/tasks/tasks_sarscov2.wdl
index 1d6b3341f..dfd188868 100644
--- a/pipes/WDL/tasks/tasks_sarscov2.wdl
+++ b/pipes/WDL/tasks/tasks_sarscov2.wdl
@@ -10,7 +10,7 @@ task pangolin_one_sample {
         Float?  max_ambig
         String? analysis_mode
         Boolean update_dbs_now=false
-        String  docker = "quay.io/staphb/pangolin:4.3.1-pdata-1.23.1"
+        String  docker = "quay.io/staphb/pangolin:4.3.1-pdata-1.30"
     }
     String basename = basename(genome_fasta, ".fasta")
     Int disk_size = 50
@@ -93,7 +93,7 @@ task pangolin_many_samples {
         String?      analysis_mode
         Boolean      update_dbs_now=false
         String       basename
-        String       docker = "quay.io/staphb/pangolin:4.3.1-pdata-1.23.1"
+        String       docker = "quay.io/staphb/pangolin:4.3.1-pdata-1.30"
     }
     Int disk_size = 100
     command <<<
diff --git a/pipes/WDL/tasks/tasks_taxon_filter.wdl b/pipes/WDL/tasks/tasks_taxon_filter.wdl
index 20f7336ad..9b1ff62fc 100644
--- a/pipes/WDL/tasks/tasks_taxon_filter.wdl
+++ b/pipes/WDL/tasks/tasks_taxon_filter.wdl
@@ -211,7 +211,7 @@ task merge_one_per_sample {
     Boolean      rmdup = false
 
     Int          machine_mem_gb = 7
-    String       docker = "quay.io/broadinstitute/viral-core:2.3.2"
+    String       docker = "quay.io/broadinstitute/viral-core:2.4.0"
   }
 
   Int disk_size = 750
diff --git a/pipes/WDL/tasks/tasks_terra.wdl b/pipes/WDL/tasks/tasks_terra.wdl
index 17771230a..a920ad548 100644
--- a/pipes/WDL/tasks/tasks_terra.wdl
+++ b/pipes/WDL/tasks/tasks_terra.wdl
@@ -391,7 +391,7 @@ task create_or_update_sample_tables {
     String  sample_table_name  = "sample"
     String  library_table_name = "library"
 
-    String  docker = "quay.io/broadinstitute/viral-core:2.3.2"
+    String  docker = "quay.io/broadinstitute/viral-core:2.4.0"
   }
 
   meta {
diff --git a/pipes/WDL/tasks/tasks_utils.wdl b/pipes/WDL/tasks/tasks_utils.wdl
index be138d8ea..a527d5607 100644
--- a/pipes/WDL/tasks/tasks_utils.wdl
+++ b/pipes/WDL/tasks/tasks_utils.wdl
@@ -103,7 +103,7 @@ task zcat {
         { if [ -f /sys/fs/cgroup/memory.peak ]; then cat /sys/fs/cgroup/memory.peak; elif [ -f /sys/fs/cgroup/memory/memory.peak ]; then cat /sys/fs/cgroup/memory/memory.peak; elif [ -f /sys/fs/cgroup/memory/memory.max_usage_in_bytes ]; then cat /sys/fs/cgroup/memory/memory.max_usage_in_bytes; else echo "0"; fi } > MEM_BYTES
     >>>
     runtime {
-        docker: "quay.io/broadinstitute/viral-core:2.3.2"
+        docker: "quay.io/broadinstitute/viral-core:2.4.0"
         memory: "1 GB"
         cpu:    cpus
         disks:  "local-disk " + disk_size + " LOCAL"
@@ -430,7 +430,7 @@ task tsv_join {
   runtime {
     memory: "~{machine_mem_gb} GB"
     cpu: 4
-    docker: "quay.io/broadinstitute/viral-core:2.3.2"
+    docker: "quay.io/broadinstitute/viral-core:2.4.0"
     disks:  "local-disk " + disk_size + " HDD"
     disk: disk_size + " GB" # TES
     dx_instance_type: "mem1_ssd1_v2_x4"
@@ -517,7 +517,7 @@ task tsv_stack {
   input {
     Array[File]+ input_tsvs
     String       out_basename
-    String       docker = "quay.io/broadinstitute/viral-core:2.3.2"
+    String       docker = "quay.io/broadinstitute/viral-core:2.4.0"
   }
 
   Int disk_size = 50
@@ -780,7 +780,7 @@ task filter_sequences_by_length {
         File   sequences_fasta
         Int    min_non_N = 1
 
-        String docker = "quay.io/broadinstitute/viral-core:2.3.2"
+        String docker = "quay.io/broadinstitute/viral-core:2.4.0"
         Int    disk_size = 750
     }
     parameter_meta {
diff --git a/pipes/WDL/workflows/augur_from_assemblies.wdl b/pipes/WDL/workflows/augur_from_assemblies.wdl
index e94ee5574..08c3ab87e 100644
--- a/pipes/WDL/workflows/augur_from_assemblies.wdl
+++ b/pipes/WDL/workflows/augur_from_assemblies.wdl
@@ -13,6 +13,7 @@ workflow augur_from_assemblies {
 
     input {
         Array[File]+   assembly_fastas
+        Array[File]?   contextual_genome_fastas
         Array[File]+   sample_metadata_tsvs
         File           ref_fasta
 
@@ -29,6 +30,10 @@ workflow augur_from_assemblies {
           description: "Set of assembled genomes to align and build trees. These must represent a single chromosome/segment of a genome only. Fastas may be one-sequence-per-individual or a concatenated multi-fasta (unaligned) or a mixture of the two. They may be compressed (gz, bz2, zst, lz4), uncompressed, or a mixture.",
           patterns: ["*.fasta", "*.fa", "*.fasta.gz", "*.fasta.zst"]
         }
+        contextual_genome_fastas: {
+          description: "Set of near-complete contextual genomes to include in tree build. Each fasta provided must represent a single chromosome/segment of a genome. Fastas may be one-sequence-per-individual or a concatenated multi-fasta (unaligned) or a mixture of the two. They may be compressed (gz, bz2, zst, lz4), uncompressed, or a mixture. ",
+          patterns: ["*.fasta", "*.fa", "*.fasta.gz", "*.fasta.zst"]
+        }
         sample_metadata_tsvs: {
             description: "Tab-separated metadata file that contain binning variables and values. Must contain all samples: output will be filtered to the IDs present in this file.",
             patterns: ["*.txt", "*.tsv"]
@@ -54,7 +59,7 @@ workflow augur_from_assemblies {
 
     call utils.zcat {
         input:
-            infiles     = assembly_fastas,
+            infiles     = flatten([assembly_fastas, select_first([contextual_genome_fastas,[]])]),
             output_name = "all_samples_combined_assembly.fasta"
     }
     call utils.filter_sequences_by_length {
diff --git a/pipes/WDL/workflows/scaffold_and_refine_multitaxa.wdl b/pipes/WDL/workflows/scaffold_and_refine_multitaxa.wdl
index 89258cfe1..0af33b228 100644
--- a/pipes/WDL/workflows/scaffold_and_refine_multitaxa.wdl
+++ b/pipes/WDL/workflows/scaffold_and_refine_multitaxa.wdl
@@ -150,21 +150,32 @@ workflow scaffold_and_refine_multitaxa {
             "sample":              '{"entityType":"sample","entityName":"' + sample_id + '"}'
         }
 
-        scatter(h in assembly_header) {
-            String stat_by_taxon = stats_by_taxon[h]
+        if(assembly_length_unambiguous > min_scaffold_unambig) {
+            scatter(h in assembly_header) {
+                String stat_by_taxon = stats_by_taxon[h]
+            }
         }
     }
 
     ### summary stats
-    call utils.concatenate {
-      input:
-        infiles     = [write_tsv([assembly_header]), write_tsv(stat_by_taxon)],
-        output_name = "assembly_metadata-~{sample_id}.tsv"
+    if (length(select_all(stat_by_taxon)) > 0) {
+        call utils.concatenate as assembly_stats_non_empty {
+            input:
+                infiles     = [write_tsv([assembly_header]), write_tsv(select_all(stat_by_taxon))],
+                output_name = "assembly_metadata-~{sample_id}.tsv"
+        }
+    }
+    if (length(select_all(stat_by_taxon)) == 0) {
+        call utils.concatenate as assembly_stats_empty {
+            input:
+                infiles     = [write_tsv([assembly_header])],
+                output_name = "assembly_metadata-~{sample_id}.tsv"
+        }
     }
 
     output {
         Array[Map[String,String]] assembly_stats_by_taxon  = stats_by_taxon
-        File   assembly_stats_by_taxon_tsv                 = concatenate.combined
+        File   assembly_stats_by_taxon_tsv                 = select_first([assembly_stats_non_empty.combined, assembly_stats_empty.combined])
         String assembly_method                             = "viral-ngs/scaffold_and_refine_multitaxa"
 
         #String assembly_top_taxon_id               = select_references.top_matches_per_cluster_basenames[0]
diff --git a/requirements-modules.txt b/requirements-modules.txt
index 9221cd99c..c0cab07d4 100644
--- a/requirements-modules.txt
+++ b/requirements-modules.txt
@@ -1,12 +1,12 @@
-broadinstitute/viral-core=2.3.2
-broadinstitute/viral-assemble=2.3.2.0
+broadinstitute/viral-core=2.4.0
+broadinstitute/viral-assemble=2.3.6.1
 broadinstitute/viral-classify=2.2.4.2
-broadinstitute/viral-phylo=2.1.20.2
+broadinstitute/viral-phylo=2.3.6.0
 broadinstitute/py3-bio=0.1.2
 broadinstitute/beast-beagle-cuda=1.10.5pre
 broadinstitute/ncbi-tools=2.10.7.10
 broadinstitute/delphy=0.999
 nextstrain/base=build-20240318T173028Z
 andersenlabapps/ivar=1.3.1
-quay.io/staphb/pangolin=4.3.1-pdata-1.23.1
-nextstrain/nextclade=2.14.0
+quay.io/staphb/pangolin=4.3.1-pdata-1.30
+nextstrain/nextclade=3.9.1
diff --git a/test/input/WDL/miniwdl-local/test_inputs-genbank-local.json b/test/input/WDL/miniwdl-local/test_inputs-genbank-local.json
deleted file mode 100644
index 1c938870e..000000000
--- a/test/input/WDL/miniwdl-local/test_inputs-genbank-local.json
+++ /dev/null
@@ -1,21 +0,0 @@
-{
-  "genbank.molType": "cRNA",
-  "genbank.reference_accessions": ["KM821997.1", "KM821998.1"],
-  "genbank.coverage_table": "test/input/genbank/coverage_report-RUN1-workflow.txt",
-  "genbank.alignments_bams": [],
-  "genbank.sequencingTech": "Illumina MiSeq",
-  "genbank.biosample_attributes": "test/input/genbank/biosample-attributes-lasv.txt",
-  "genbank.prep_genbank.assembly_method": "placeholder assembly software",
-  "genbank.prep_genbank.assembly_method_version": "5.4.3.2.1",
-  "genbank.comment": "this is only a test -- DO NOT SUBMIT to NCBI",
-  "genbank.author_list": "Odia,Ikponmwosa, Ehaine,Philomena, Oguzie,Judith,U. Siddle,Katherine,J. Mehta,Samar, Barnes,Kayla,M. Winnicki,Sarah,M. Brehio,Patrick, Shah,Rickey,R. Chak,Bridget, Yozwiak,Nathan, Amao,Adebayo, Nosamiefan,Iguosadolo, Birren,Bruce,W. Park,Daniel,J. Folarin,Onikepe, Okokhere,Peter, Sabeti,Pardis,C. Happi,Christian,T.",
-  "genbank.author_sbt_defaults_yaml": "test/input/genbank/default_sbt_values.yaml",
-  "genbank.author_sbt_j2_template": "test/input/genbank/author_template.sbt.j2",
-  "genbank.assemblies_fasta": [
-    "test/input/LASV_NGA_2018_0026.fasta",
-    "test/input/LASV_NGA_2018_0097.fasta",
-    "test/input/LASV_NGA_2018_0541.fasta"
-  ],
-  "genbank.email_address": "viral-ngs@broadinstitute.org"
-}
-