update viral-core 2.3.0 -> 2.3.1

.github/workflows/build.yml

@@ -69,7 +69,7 @@ jobs:
       - name: install python
         uses: actions/setup-python@v5
         with:
-          python-version: '3.8'
+          python-version: '3.10'
       - name: install system dependencies
         run: |
           sudo apt-get update
@@ -168,7 +168,7 @@ jobs:
       - name: install python
         uses: actions/setup-python@v5
         with: 
-          python-version: '3.8'
+          python-version: '3.10'
       - name: install docs dependencies
         shell: bash
         run: |
@@ -339,7 +339,7 @@ jobs:
       - name: install python
         uses: actions/setup-python@v5
         with: 
-          python-version: '3.8'
+          python-version: '3.10'
       - name: install java
         uses: actions/setup-java@v4
         with:

github_actions_ci/tests-cromwell.sh

@@ -7,28 +7,31 @@ cp -r test workflows/
 cd workflows
 
 for workflow in ../pipes/WDL/workflows/*.wdl; do
-	workflow_name=$(basename $workflow .wdl)
-	input_json="test/input/WDL/cromwell-local/test_inputs-$workflow_name-local.json"
-	if [ -f $input_json ]; then
-		date
-		echo "Executing $workflow_name using Cromwell on local instance"
-		# the "cat" is to allow a pipe failure (otherwise it halts because of set -e)
-		java -Dconfig.file=../pipes/cromwell/cromwell.local-github_actions.conf \
-			-jar cromwell.jar run \
-			$workflow_name.wdl \
-			-i $input_json | tee cromwell.out
-		if [ ${PIPESTATUS[0]} -gt 0 ]; then
-			echo "error running $workflow_name"
-			error_logs=$(grep stderr cromwell.out | perl -lape 's/.*\s(\S+)$/$1/g')
-			for log in $error_logs; do
-				echo "contents of stderr ($log):"
-				cat `dirname $log`/stderr | sed "s/^/[STDERR] /"
-				echo "contents of stdout ($log):"
-				cat `dirname $log`/stdout | sed "s/^/[STDOUT] /"
-			done
-			sync; sleep 20; exit 1
-		fi
+    workflow_name=$(basename $workflow .wdl)
+    input_json="test/input/WDL/cromwell-local/test_inputs-$workflow_name-local.json"
+    if [ -f $input_json ]; then
+        date
+        echo "Executing $workflow_name using Cromwell on local instance"
+        # the "cat" is to allow a pipe failure (otherwise it halts because of set -e)
+        java -Dconfig.file=../pipes/cromwell/cromwell.local-github_actions.conf \
+            -jar cromwell.jar run \
+            $workflow_name.wdl \
+            -i $input_json | tee cromwell.out
+        if [ ${PIPESTATUS[0]} -gt 0 ]; then
+            echo "error running $workflow_name"
+            error_logs=$(grep stderr cromwell.out | perl -lape 's/.*\s(\S+)$/$1/g')
+            for log in $error_logs; do
+                ls -lah $(dirname $log)
+
+                echo "contents of stderr ($log):"
+                cat `dirname $log`/stderr* | sed "s/^/[STDERR] /"
+                echo "contents of stdout ($log):"
+                cat `dirname $log`/stdout* | sed "s/^/[STDOUT] /"
+            done
+            sync; sleep 20; exit 1
+        fi
     fi
+    docker image prune --all --force # prune images from this workflow execution to save space before the next
 done
 
 cd -

github_actions_ci/tests-miniwdl.sh

@@ -56,6 +56,7 @@ for workflow in ../pipes/WDL/workflows/*.wdl; do
 			echo "$workflow_name FAILED"
 			exit 1
 		fi
+		docker image prune --all --force # prune images from this workflow execution to save space before the next
 	fi
 done
 

pipes/WDL/tasks/tasks_assembly.wdl

@@ -450,7 +450,7 @@ task align_reads {
     Boolean  skip_mark_dupes = false
 
     Int?     machine_mem_gb
-    String   docker = "quay.io/broadinstitute/viral-core:2.3.0"
+    String   docker = "quay.io/broadinstitute/viral-core:2.3.1"
 
     String   sample_name = basename(basename(basename(reads_unmapped_bam, ".bam"), ".taxfilt"), ".clean")
   }
@@ -847,7 +847,7 @@ task run_discordance {
       String out_basename = "run"
       Int    min_coverage = 4
 
-      String docker = "quay.io/broadinstitute/viral-core:2.3.0"
+      String docker = "quay.io/broadinstitute/viral-core:2.3.1"
     }
     parameter_meta {
       reads_aligned_bam: {

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:2.3.0"
+    String       docker = "quay.io/broadinstitute/viral-core:2.3.1"
   }
 
   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:2.3.0"
+    String  docker = "quay.io/broadinstitute/viral-core:2.3.1"
   }
 
   parameter_meta {

pipes/WDL/tasks/tasks_interhost.wdl

@@ -351,7 +351,7 @@ task index_ref {
     File?  novocraft_license
 
     Int?   machine_mem_gb
-    String docker = "quay.io/broadinstitute/viral-core:2.3.0"
+    String docker = "quay.io/broadinstitute/viral-core:2.3.1"
   }
 
   Int disk_size = 100

pipes/WDL/tasks/tasks_ncbi.wdl

@@ -192,7 +192,7 @@ task structured_comments {
 
     File?  filter_to_ids
 
-    String docker = "quay.io/broadinstitute/viral-core:2.3.0"
+    String docker = "quay.io/broadinstitute/viral-core:2.3.1"
   }
   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:2.3.0"
+    String docker = "quay.io/broadinstitute/viral-core:2.3.1"
   }
   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:2.3.0"
+    String      docker="quay.io/broadinstitute/viral-core:2.3.1"
   }
   Int disk_size = 100
   parameter_meta {

pipes/WDL/tasks/tasks_nextstrain.wdl

@@ -280,7 +280,7 @@ task derived_cols {
         String?       lab_highlight_loc
         Array[File]   table_map = []
 
-        String        docker = "quay.io/broadinstitute/viral-core:2.3.0"
+        String        docker = "quay.io/broadinstitute/viral-core:2.3.1"
         Int           disk_size = 50
     }
     parameter_meta {
@@ -450,7 +450,7 @@ task nextstrain_build_subsample {
         File?  drop_list
 
         Int    machine_mem_gb = 50
-        String docker = "nextstrain/base:build-20230905T192825Z"
+        String docker = "docker.io/nextstrain/base:build-20240318T173028Z"
         String nextstrain_ncov_repo_commit = "30435fb9ec8de2f045167fb90adfec12f123e80a"
         Int    disk_size = 750
     }
@@ -594,7 +594,7 @@ task nextstrain_build_subsample {
 task nextstrain_ncov_defaults {
     input {
         String nextstrain_ncov_repo_commit = "30435fb9ec8de2f045167fb90adfec12f123e80a"
-        String docker                      = "nextstrain/base:build-20230905T192825Z"
+        String docker                      = "docker.io/nextstrain/base:build-20240318T173028Z"
         Int    disk_size = 50
     }
     command {
@@ -632,7 +632,7 @@ task nextstrain_deduplicate_sequences {
         Boolean error_on_seq_diff = false
 
         String nextstrain_ncov_repo_commit = "30435fb9ec8de2f045167fb90adfec12f123e80a"
-        String docker                      = "nextstrain/base:build-20230905T192825Z"
+        String docker                      = "docker.io/nextstrain/base:build-20240318T173028Z"
         Int disk_size = 750
     }
 
@@ -686,7 +686,7 @@ task nextstrain_ncov_sanitize_gisaid_data {
         String? prefix_to_strip
 
         String nextstrain_ncov_repo_commit = "30435fb9ec8de2f045167fb90adfec12f123e80a"
-        String docker                      = "nextstrain/base:build-20230905T192825Z"
+        String docker                      = "docker.io/nextstrain/base:build-20240318T173028Z"
         Int    disk_size = 750
     }
 
@@ -762,7 +762,7 @@ task filter_subsample_sequences {
         Array[String]? exclude_where
         Array[String]? include_where
 
-        String         docker = "nextstrain/base:build-20230905T192825Z"
+        String         docker = "docker.io/nextstrain/base:build-20240318T173028Z"
         Int            disk_size = 750
     }
     parameter_meta {
@@ -847,8 +847,8 @@ task filter_sequences_to_list {
         Array[File]? keep_list
 
         String       out_fname = sub(sub(basename(sequences, ".zst"), ".vcf", ".filtered.vcf"), ".fasta$", ".filtered.fasta")
-        # Prior docker image: "nextstrain/base:build-20211012T204409Z"
-        String       docker = "quay.io/broadinstitute/viral-core:2.3.0"
+        # Prior docker image: "nextstrain/base:build-20240318T173028Z"
+        String       docker = "quay.io/broadinstitute/viral-core:2.3.1"
         Int          disk_size = 750
     }
     parameter_meta {
@@ -1145,7 +1145,7 @@ task augur_mafft_align {
         Boolean fill_gaps = true
         Boolean remove_reference = true
 
-        String  docker = "nextstrain/base:build-20230905T192825Z"
+        String  docker = "docker.io/nextstrain/base:build-20240318T173028Z"
         Int     disk_size = 750
         Int     mem_size = 180
         Int     cpus = 64
@@ -1220,7 +1220,7 @@ task augur_mask_sites {
         File   sequences
         File?  mask_bed
 
-        String docker = "nextstrain/base:build-20230905T192825Z"
+        String docker = "docker.io/nextstrain/base:build-20240318T173028Z"
         Int    disk_size = 750
     }
     parameter_meta {
@@ -1279,7 +1279,7 @@ task draft_augur_tree {
 
         Int     cpus = 64
         Int     machine_mem_gb = 32
-        String  docker = "nextstrain/base:build-20230905T192825Z"
+        String  docker = "docker.io/nextstrain/base:build-20240318T173028Z"
         Int     disk_size = 1250
     }
     parameter_meta {
@@ -1348,7 +1348,7 @@ task refine_augur_tree {
         String?  divergence_units = "mutations"
         File?    vcf_reference
 
-        String   docker = "nextstrain/base:build-20230905T192825Z"
+        String   docker = "docker.io/nextstrain/base:build-20240318T173028Z"
         Int      disk_size = 750
         Int      machine_mem_gb = 75
     }
@@ -1422,7 +1422,7 @@ task ancestral_traits {
         Float?        sampling_bias_correction
 
         Int           machine_mem_gb = 32
-        String        docker = "nextstrain/base:build-20230905T192825Z"
+        String        docker = "docker.io/nextstrain/base:build-20240318T173028Z"
         Int           disk_size = 750
     }
     String out_basename = basename(tree, '.nwk')
@@ -1475,7 +1475,7 @@ task ancestral_tree {
         File?    vcf_reference
         File?    output_vcf
 
-        String   docker = "nextstrain/base:build-20230905T192825Z"
+        String   docker = "docker.io/nextstrain/base:build-20240318T173028Z"
         Int      disk_size = 300
     }
     parameter_meta {
@@ -1536,7 +1536,7 @@ task translate_augur_tree {
         File?  vcf_reference_output
         File?  vcf_reference
 
-        String docker = "nextstrain/base:build-20230905T192825Z"
+        String docker = "docker.io/nextstrain/base:build-20240318T173028Z"
         Int    disk_size = 300
     }
     String out_basename = basename(tree, '.nwk')
@@ -1593,7 +1593,7 @@ task tip_frequencies {
         Boolean  include_internal_nodes = false
 
         Int      machine_mem_gb = 64
-        String   docker = "nextstrain/base:build-20230905T192825Z"
+        String   docker = "docker.io/nextstrain/base:build-20240318T173028Z"
         String   out_basename = basename(tree, '.nwk')
         Int      disk_size = 200
     }
@@ -1653,7 +1653,7 @@ task assign_clades_to_nodes {
         File ref_fasta
         File clades_tsv
 
-        String docker = "nextstrain/base:build-20230905T192825Z"
+        String docker = "docker.io/nextstrain/base:build-20240318T173028Z"
         Int    disk_size = 300
     }
     String out_basename = basename(basename(tree_nwk, ".nwk"), "_timetree")
@@ -1698,7 +1698,7 @@ task augur_import_beast {
         String? tip_date_delimiter
 
         Int     machine_mem_gb = 3
-        String  docker = "nextstrain/base:build-20230905T192825Z"
+        String  docker = "docker.io/nextstrain/base:build-20240318T173028Z"
         Int     disk_size = 150
     }
     String tree_basename = basename(beast_mcc_tree, ".tree")
@@ -1759,7 +1759,7 @@ task export_auspice_json {
         String out_basename = basename(basename(tree, ".nwk"), "_timetree")
 
         Int    machine_mem_gb = 64
-        String docker = "nextstrain/base:build-20230905T192825Z"
+        String docker = "docker.io/nextstrain/base:build-20240318T173028Z"
         Int    disk_size = 300
     }
 

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:2.3.0"
+    String  docker = "quay.io/broadinstitute/viral-core:2.3.1"
   }
   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:2.3.0"
+    String      docker = "quay.io/broadinstitute/viral-core:2.3.1"
   }
   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:2.3.0"
+      String       docker = "quay.io/broadinstitute/viral-core:2.3.1"
     }
 
     Int disk_size = 750
@@ -244,7 +244,7 @@ task rmdup_ubam {
     String  method = "mvicuna"
 
     Int     machine_mem_gb = 7
-    String  docker = "quay.io/broadinstitute/viral-core:2.3.0"
+    String  docker = "quay.io/broadinstitute/viral-core:2.3.1"
   }
 
   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:2.3.0"
+    String       docker = "quay.io/broadinstitute/viral-core:2.3.1"
   }
 
   Int disk_size = 750
@@ -367,7 +367,7 @@ task FastqToUBAM {
     String? sequencing_center
     String? additional_picard_options
 
-    String  docker = "quay.io/broadinstitute/viral-core:2.3.0"
+    String  docker = "quay.io/broadinstitute/viral-core:2.3.1"
   }
   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:2.3.0"
+    String    docker = "quay.io/broadinstitute/viral-core:2.3.1"
   }
   Int disk_size = 200
   command <<<