Demultiplexing of Illumina flowcells optionally with inline barcodes

.github/workflows/build.yml

@@ -130,8 +130,8 @@ jobs:
       - name: install java
         uses: actions/setup-java@v4
         with:
-          distribution: 'adopt'
-          java-version: '11'
+          distribution: 'temurin'
+          java-version: '17'
       - name: install cromwell+womtool+dxWDL
         shell: bash
         run: |
@@ -236,8 +236,8 @@ jobs:
       - name: install java
         uses: actions/setup-java@v4
         with:
-          distribution: 'adopt'
-          java-version: '11'
+          distribution: 'temurin'
+          java-version: '17'
       - name: install cromwell+womtool+dxWDL
         shell: bash
         run: |
@@ -365,8 +365,8 @@ jobs:
       - name: install java
         uses: actions/setup-java@v4
         with:
-          distribution: 'adopt'
-          java-version: '11'
+          distribution: 'temurin'
+          java-version: '17'
       - name: install miniwdl
         run: |
           pip3 install pyyaml dxpy

github_actions_ci/check-wdl-runtimes.sh

@@ -2,6 +2,29 @@
 # requires $MODULE_VERSIONS to be set to point to a text file with equal-sign-separated values
 # export MODULE_VERSIONS="./requirements-modules.txt" && ./github_actions_ci/check-wdl-runtimes.sh
 
+function absolute_path() {
+    local SOURCE="$1"
+    while [ -h "$SOURCE" ]; do # resolve $SOURCE until the file is no longer a symlink
+        DIR="$( cd -P "$( dirname "$SOURCE" )" && pwd )"
+        if [[ "$OSTYPE" == "darwin"* ]]; then
+            SOURCE="$(readlink "$SOURCE")"
+        else
+            SOURCE="$(readlink -f "$SOURCE")"
+        fi
+        [[ $SOURCE != /* ]] && SOURCE="$DIR/$SOURCE" # if $SOURCE was a relative symlink, we need to resolve it relative to the path where the symlink file was located
+    done
+    echo "$SOURCE"
+}
+SOURCE="${BASH_SOURCE[0]}"
+SCRIPT=$(absolute_path "$SOURCE")
+SCRIPT_DIRNAME="$(dirname "$SOURCE")"
+SCRIPTPATH="$(cd -P "$(echo "$SCRIPT_DIRNAME")" &> /dev/null && pwd)"
+SCRIPT="$SCRIPTPATH/$(basename "$SCRIPT")"
+REPO_PATH="$(realpath "$SCRIPTPATH/../")"
+
+# set MODULE_VERSIONS with default value of "$(realpath "$SCRIPTPATH/../requirements-modules.txt")", assumed to be located one level above this script
+MODULE_VERSIONS="${MODULE_VERSIONS:-"${REPO_PATH}/requirements-modules.txt"}"
+
 echo "Checking wdl container versions against ${MODULE_VERSIONS}"
 
 # this is the newer script that simply validates existing version strings

github_actions_ci/install-wdl.sh

@@ -12,8 +12,8 @@ fetch_jar_from_github () {
 	ln -s $_jar_fname $_tool_name.jar
 }
 
-fetch_jar_from_github broadinstitute cromwell womtool 87
-fetch_jar_from_github broadinstitute cromwell cromwell 87
+fetch_jar_from_github broadinstitute cromwell womtool 88
+fetch_jar_from_github broadinstitute cromwell cromwell 88
 fetch_jar_from_github dnanexus dxWDL dxWDL v1.50
 fetch_jar_from_github dnanexus dxCompiler dxCompiler 2.11.6
 

github_actions_ci/validate-wdl-womtool.sh

@@ -1,8 +1,17 @@
 #!/bin/bash
 set -e -o pipefail
 
-for workflow in pipes/WDL/workflows/*.wdl; do
-  echo -n "validating $workflow ... "
+# if WORKFLOW_TO_VALIDATE env var is set, validate only that workflow
+#   ex. WORKFLOW_TO_VALIDATE=demux_deplete ./github_actions_ci/validate-wdl-womtool.sh
+
+if [ -n "$WORKFLOW_TO_VALIDATE" ]; then
+  WF_GLOB_PATTERN="pipes/WDL/workflows/${WORKFLOW_TO_VALIDATE}.wdl"
+else
+  WF_GLOB_PATTERN='pipes/WDL/workflows/*.wdl'
+fi
+
+for workflow in ${WF_GLOB_PATTERN}; do
+  printf "validating $workflow ... "
   if $(hash -r  womtool &> /dev/null); then
     womtool validate $workflow
   else

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:2.4.3.1"
+      String   docker = "quay.io/broadinstitute/viral-assemble:2.5.1.0"
     }
     parameter_meta{
       reads_unmapped_bam: {
@@ -116,7 +116,7 @@ task select_references {
     Int?          skani_c
     Int?          skani_n
 
-    String        docker = "quay.io/broadinstitute/viral-assemble:2.4.3.1"
+    String        docker = "quay.io/broadinstitute/viral-assemble:2.5.1.0"
     Int           machine_mem_gb = 4
     Int           cpu = 2
     Int           disk_size = 100
@@ -208,7 +208,7 @@ task scaffold {
       Float?       scaffold_min_pct_contig_aligned
 
       Int?         machine_mem_gb
-      String       docker="quay.io/broadinstitute/viral-assemble:2.4.3.1"
+      String       docker="quay.io/broadinstitute/viral-assemble:2.5.1.0"
 
       # 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")
@@ -585,7 +585,7 @@ task align_reads {
     Boolean  skip_mark_dupes = false
 
     Int?     machine_mem_gb
-    String   docker = "quay.io/broadinstitute/viral-core:2.4.1"
+    String   docker = "quay.io/broadinstitute/viral-core:2.5.1"
 
     String   sample_name = basename(basename(basename(reads_unmapped_bam, ".bam"), ".taxfilt"), ".clean")
   }
@@ -722,7 +722,7 @@ task refine_assembly_with_aligned_reads {
       Int      min_coverage = 3
 
       Int      machine_mem_gb = 15
-      String   docker = "quay.io/broadinstitute/viral-assemble:2.4.3.1"
+      String   docker = "quay.io/broadinstitute/viral-assemble:2.5.1.0"
     }
 
     Int disk_size = 375
@@ -851,7 +851,7 @@ task run_discordance {
       String out_basename = "run"
       Int    min_coverage = 4
 
-      String docker = "quay.io/broadinstitute/viral-core:2.4.1"
+      String docker = "quay.io/broadinstitute/viral-core:2.5.1"
     }
     parameter_meta {
       reads_aligned_bam: {
@@ -1100,7 +1100,7 @@ task wgsim {
         Int?   random_seed
 
         Int    machine_mem_gb = 7
-        String docker = "quay.io/broadinstitute/viral-assemble:2.4.3.1"
+        String docker = "quay.io/broadinstitute/viral-assemble:2.5.1.0"
     }
 
     parameter_meta {