From e06200a52c68076aee3d8c8fbd584bbbebac6a73 Mon Sep 17 00:00:00 2001
From: pruzanov <pruzanov@oicr.on.ca>
Date: Tue, 21 Jan 2025 13:13:51 -0500
Subject: [PATCH 1/6] Added vidarr_labels, minor changes

---
 README.md       |  8 ++++----
 dragenAlign.wdl | 22 ++++++++++++++++++++--
 2 files changed, 24 insertions(+), 6 deletions(-)

diff --git a/README.md b/README.md
index 6587745..493b96f 100644
--- a/README.md
+++ b/README.md
@@ -50,10 +50,10 @@ Parameter|Value|Default|Description
 
 Output | Type | Description | Labels
 ---|---|---|---
-`bam`|File|Output bam aligned to genome|
-`bamIndex`|File|Index for the aligned bam|
-`zippedOut`|File|Zip file containing the supporting .csv and .tab outputs from Dragen|
-`outputChimeric`|File?|Output chimeric junctions file, if available|
+`bam`|File|BAM file with alignments|vidarr_label: bam
+`bamIndex`|File|index of BAM file with alignments|vidarr_label: bamIndex
+`zippedOut`|File|Zipped .csv and .tab files (additional outputs)|vidarr_label: zippedOut
+`outputChimeric`|File?|Optional output file with chimeric junctions|vidarr_label: outputChimeric
 
 
 ## Commands
diff --git a/dragenAlign.wdl b/dragenAlign.wdl
index ebdbcb6..dadc2e2 100755
--- a/dragenAlign.wdl
+++ b/dragenAlign.wdl
@@ -31,7 +31,7 @@ workflow dragenAlign {
   }
   
   Map[String,String] dragenRef_by_genome = { 
-    "hg38": "/staging/data/references/hg38-p12.v9"
+    "hg38": "/.mounts/labs/gsiprojects/gsi/Dragen/reference/hg38fa.p12/"  # /staging/data/references/hg38-p12.v9
   }
 
   String dragenRef = dragenRef_by_genome[reference]
@@ -79,6 +79,24 @@ workflow dragenAlign {
         url: "https://developer.illumina.com/dragen"
       }
     ]
+    output_meta: {
+        bam: {
+            description: "BAM file with alignments",
+            vidarr_label: "bam"
+        },
+        bamIndex: {
+            description: "index of BAM file with alignments",
+            vidarr_label: "bamIndex"
+        },
+        zippedOut: {
+            description: "Zipped .csv and .tab files (additional outputs)",
+            vidarr_label: "zippedOut"
+        }
+        outputChimeric: {
+            description: "Optional output file with chimeric junctions",
+            vidarr_label: "outputChimeric"
+        }
+   }
   }
 
   output {
@@ -293,4 +311,4 @@ task runDragen {
       outputChimeric: "Output chimeric junctions file, if available"
     }
   }
-}
\ No newline at end of file
+}

From bc90d52ce4993963f3dc3e9453e38dbbff66c590 Mon Sep 17 00:00:00 2001
From: pruzanov <pruzanov@oicr.on.ca>
Date: Tue, 21 Jan 2025 14:25:09 -0500
Subject: [PATCH 2/6] Changes to references, adjusted paths

---
 dragenAlign.wdl | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/dragenAlign.wdl b/dragenAlign.wdl
index dadc2e2..adbaf5f 100755
--- a/dragenAlign.wdl
+++ b/dragenAlign.wdl
@@ -91,7 +91,7 @@ workflow dragenAlign {
         zippedOut: {
             description: "Zipped .csv and .tab files (additional outputs)",
             vidarr_label: "zippedOut"
-        }
+        },
         outputChimeric: {
             description: "Optional output file with chimeric junctions",
             vidarr_label: "outputChimeric"
@@ -246,8 +246,8 @@ task runDragen {
     String prefix
     Boolean isRNA
     Boolean adapterTrim
-    String adapter1File = "/staging/data/resources/ADAPTER1"
-    String adapter2File = "/staging/data/resources/ADAPTER2"
+    String adapter1File = "/.mounts/labs/gsiprojects/gsi/Dragen/resources/ADAPTER1"
+    String adapter2File = "/.mounts/labs/gsiprojects/gsi/Dragen/resources/ADAPTER2"
     Int jobMemory = 500
     Int timeout = 96
   }

From d81b21a7a6f1ab9a371ff839c7142f0f43090a1c Mon Sep 17 00:00:00 2001
From: pruzanov <pruzanov@oicr.on.ca>
Date: Mon, 10 Feb 2025 16:58:54 -0500
Subject: [PATCH 3/6] Switching to modularized scripts

---
 CHANGELOG.md                  |  40 ++++--
 README.md                     |  73 ++--------
 commands.txt                  |  62 +-------
 dragenAlign.wdl               | 259 ++++++++++++++++------------------
 vidarrtest-regression.json.in | 149 +++++++++++--------
 5 files changed, 262 insertions(+), 321 deletions(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 71fe162..a2eda89 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -1,16 +1,40 @@
-## 1.3.0 - 2024-06-25
+# Changelog
+All notable changes to this project will be documented in this file.
+
+The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
+and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
+
+## [Unreleased] - 2025-02-12
+### Changed
+- Regression testing adjusted, validates in Jenkins
+- default parameters adjusted according to [GBS-5046](https://jira.oicr.on.ca/browse/GBS-5046)
+- changed code that generates input list
+
+## [1.3.0] - 2024-06-25
+### Added
 [GRD-797](https://jira.oicr.on.ca/browse/GRD-797) - add vidarr labels to outputs (changes to medata only)
-## 1.2.2 - 2024-04-09
+
+## [1.2.2] - 2024-04-09
+### Changed
 - Updated to a reference built using hg38/p12
-## 1.2.1 - 2024-04-04
+
+## [1.2.1] - 2024-04-04
+### Changed
 - Changed names in vidarrbuild.json
-## 1.2.0 - 2024-03-26
-- Workflow requires an array of fastq files with read-groups as input. A single fastq-pair (or a single fastq file) must also be inputted as an array. 
-- runDragen task outputs a merged bam file
+
+## [1.2.0] - 2024-03-26
+### Added
 - Added new task makeCSV and headerFormat, and removed readGroupFormat task
+### Changed
+- Workflow requires an array of fastq files with read-groups as input. A single fastq-pair (or a single fastq file) must also be inputted as an array.
+- runDragen task outputs a merged bam file
 - Replaced mode parameter with isRNA parameter (false by default)
-## 1.1.0 - 2024-03-05
+
+## [1.1.0] - 2024-03-05
+### Changed
 - Changes the zippedOut output into a zipped directory. This ensures that extraction creates a new directory instead of tarbombing the working directory.
-## 1.0.0 - 2024-03-04
+
+## [1.0.0] - 2024-03-04
+### Added
 - Completes lane level alignments using Dragen
 - Supports whole transcriptome alignment
diff --git a/README.md b/README.md
index 493b96f..47c2d93 100644
--- a/README.md
+++ b/README.md
@@ -36,10 +36,14 @@ Parameter|Value|Default|Description
 #### Optional task parameters:
 Parameter|Value|Default|Description
 ---|---|---|---
-`headerFormat.jobMemory`|Int|1|Memory allocated for this job
-`headerFormat.timeout`|Int|5|Hours before task timeout
-`makeCSV.jobMemory`|Int|1|Memory allocated for this job
-`makeCSV.timeout`|Int|5|Hours before task timeout
+`extractInfoLine.parsingScript`|String|"$DRAGEN_SCRIPTS_ROOT/bin/composeList.py"|Script for parsing inputs into a line
+`extractInfoLine.timeout`|Int|4|Timeout for the job
+`extractInfoLine.jobMemory`|Int|4|Job allocated RAM
+`extractInfoLine.modules`|String|"dragen-scripts/0.1"|dependency modules
+`composeList.listWritingScript`|String|"$DRAGEN_SCRIPTS_ROOT/bin/writeFile.py"|Script for writing out list of inputs
+`composeList.jobMemory`|Int|4|Job allocated RAM
+`composeList.timeout`|Int|4|Timeout for the job
+`composeList.modules`|String|"dragen-scripts/0.1"|dependency modules
 `runDragen.adapter1File`|String|"/staging/data/resources/ADAPTER1"|Adapters to be trimmed from read 1
 `runDragen.adapter2File`|String|"/staging/data/resources/ADAPTER2"|Adapters to be trimmed from read 2
 `runDragen.jobMemory`|Int|500|Memory allocated for this job
@@ -63,64 +67,15 @@ This section lists command(s) run by dragenAlign workflow
  
 ### Ensures the read-group information is valid, and outputs a header for the input CSV.
  
-``` 
-     set -euo pipefail 
- 
-     headerString="Read1File,Read2File"
-     
-     # Split the string into an array of key-value pairs
-     IFS=, read -ra rgArray <<< ~{readGroupString}
- 
-     # Adds valid keys (for Dragen) to headerString
-     for field in "${rgArray[@]}"; do
-       tag=${field:0:5}
-       if [ "$tag" == "RGID=" ] || [ "$tag" == "RGLB=" ] || [ "$tag" == "RGPL=" ] || \
-          [ "$tag" == "RGPU=" ] || [ "$tag" == "RGSM=" ] || [ "$tag" == "RGCN=" ] || \
-          [ "$tag" == "RGDS=" ] || [ "$tag" == "RGDT=" ] || [ "$tag" == "RGPI=" ]
-       then
-         headerString+=",${field:0:4}"
-       else
-         # Redirect error message to stderr
-         echo "Invalid tag: '$tag'" >&2  
-         exit 1
-       fi
-     done
- 
-     # Ensures the required header information is present
-     if [ "$(echo "$headerString" | grep -c "RGID")" != 1 ] || \
-        [ "$(echo "$headerString" | grep -c "RGSM")" != 1 ] || \
-        [ "$(echo "$headerString" | grep -c "RGLB")" != 1 ] || \
-        [ "$(echo "$headerString" | grep -c "RGPU")" != 1 ]; then
-       echo "Missing required read-group information from header" >&2  
-       exit 1
-     fi
- 
-     echo "$headerString"
 ```
- 
-### Format input CSV file for Dragen.
- 
-``` 
-     set -euo pipefail 
-     
-     echo ~{csvHeader} > ~{csvResult}
- 
-     # Load arrays into bash variables
-     arrRead1s=(~{sep=" " read1s})
-     if ~{isPaired}; then arrRead2s=(~{sep=" " read2s}); fi
-     arrReadGroups=(~{sep=" " readGroups})
-     
-     # Iterate over the arrays concurrently
-     for (( i = 0; i < ~{arrayLength}; i++ ))
-     do
-       read1="${arrRead1s[i]}"
-       if ~{isPaired}; then read2="${arrRead2s[i]}"; else read2=""; fi
-       readGroup=$(echo "${arrReadGroups[i]}" | sed 's/RG..=//g')
-       echo "$read1,$read2,$readGroup" >> ~{csvResult}
-     done
+     python3 ~{parsingScript} -i ~{write_json(fastqInput)}
 ```
  
-### Align to reference using Dragen.
+### Compose a list of inputs for dragen:wq
+
+```
+    python3 ~{listWritingScript} -o ~{outputFileName} -l "~{sep=';' inputLines}"
+```
  
 ```
      set -euo pipefail
diff --git a/commands.txt b/commands.txt
index c402710..b53586e 100644
--- a/commands.txt
+++ b/commands.txt
@@ -3,66 +3,14 @@ This section lists command(s) run by dragenAlign workflow
 
 * Running dragenAlign
 
-=== Ensures the read-group information is valid, and outputs a header for the input CSV ===.
 
-``` 
-    set -euo pipefail 
-
-    headerString="Read1File,Read2File"
-    
-    # Split the string into an array of key-value pairs
-    IFS=, read -ra rgArray <<< ~{readGroupString}
-
-    # Adds valid keys (for Dragen) to headerString
-    for field in "${rgArray[@]}"; do
-      tag=${field:0:5}
-      if [ "$tag" == "RGID=" ] || [ "$tag" == "RGLB=" ] || [ "$tag" == "RGPL=" ] || \
-         [ "$tag" == "RGPU=" ] || [ "$tag" == "RGSM=" ] || [ "$tag" == "RGCN=" ] || \
-         [ "$tag" == "RGDS=" ] || [ "$tag" == "RGDT=" ] || [ "$tag" == "RGPI=" ]
-      then
-        headerString+=",${field:0:4}"
-      else
-        # Redirect error message to stderr
-        echo "Invalid tag: '$tag'" >&2  
-        exit 1
-      fi
-    done
-
-    # Ensures the required header information is present
-    if [ "$(echo "$headerString" | grep -c "RGID")" != 1 ] || \
-       [ "$(echo "$headerString" | grep -c "RGSM")" != 1 ] || \
-       [ "$(echo "$headerString" | grep -c "RGLB")" != 1 ] || \
-       [ "$(echo "$headerString" | grep -c "RGPU")" != 1 ]; then
-      echo "Missing required read-group information from header" >&2  
-      exit 1
-    fi
-
-    echo "$headerString"
 ```
-
-=== Format input CSV file for Dragen ===.
-
-``` 
-    set -euo pipefail 
-    
-    echo ~{csvHeader} > ~{csvResult}
-
-    # Load arrays into bash variables
-    arrRead1s=(~{sep=" " read1s})
-    if ~{isPaired}; then arrRead2s=(~{sep=" " read2s}); fi
-    arrReadGroups=(~{sep=" " readGroups})
-    
-    # Iterate over the arrays concurrently
-    for (( i = 0; i < ~{arrayLength}; i++ ))
-    do
-      read1="${arrRead1s[i]}"
-      if ~{isPaired}; then read2="${arrRead2s[i]}"; else read2=""; fi
-      readGroup=$(echo "${arrReadGroups[i]}" | sed 's/RG..=//g')
-      echo "$read1,$read2,$readGroup" >> ~{csvResult}
-    done
+    python3 ~{parsingScript} -i ~{write_json(fastqInput)}
 ```
 
-=== Align to reference using Dragen ===.
+```
+   python3 ~{listWritingScript} -o ~{outputFileName} -l "~{sep=';' inputLines}"
+```
 
 ```
     set -euo pipefail
@@ -87,4 +35,4 @@ This section lists command(s) run by dragenAlign workflow
     mkdir ~{zipFileName}
     cp -t ~{zipFileName} $(ls | grep '~{prefix}.*.csv\|~{prefix}.*.tab' | tr '\n' ' ')
     zip -r ~{zipFileName}.zip ~{zipFileName}
-```
\ No newline at end of file
+```
diff --git a/dragenAlign.wdl b/dragenAlign.wdl
index adbaf5f..4501627 100755
--- a/dragenAlign.wdl
+++ b/dragenAlign.wdl
@@ -6,6 +6,11 @@ struct InputGroup {
   String readGroup
 }
 
+struct GenomeResources {
+    String referenceDirectory
+    String dragenVersion
+}
+
 workflow dragenAlign {
 
   input {
@@ -30,11 +35,15 @@ workflow dragenAlign {
     }
   }
   
-  Map[String,String] dragenRef_by_genome = { 
-    "hg38": "/.mounts/labs/gsiprojects/gsi/Dragen/reference/hg38fa.p12/"  # /staging/data/references/hg38-p12.v9
+  Map[String,GenomeResources] dragenRef_by_genome = { 
+    "hg38": {
+      "referenceDirectory": "/.mounts/labs/gsiprojects/gsi/Dragen/reference/hg38fa.p12/",  # /staging/data/references/hg38-p12.v9
+      "dragenVersion": "4.2.4"
+    }
   }
 
-  String dragenRef = dragenRef_by_genome[reference]
+  String dragenRef = dragenRef_by_genome[reference].referenceDirectory
+  String dragen_version = dragenRef_by_genome[ reference ].dragenVersion
   
   parameter_meta {
     inputGroups: "Array of fastq files to align using Dragen. Read-group information is required for fastq files, with the following fields being non-optional: RGID, RGSM, RGLB, RGPU. Each FASTQ file can only be referenced once."
@@ -44,26 +53,24 @@ workflow dragenAlign {
     isRNA: "Specifies whether to complete transcriptomic analysis, [false, genomic]"
   }
 
-  call headerFormat {
-    input:
-    readGroupString = readGroups[0],
-    prefix = outputFileNamePrefix
+  scatter(t in inputGroups) {
+    call extractInfoLine {
+      input:
+      fastqInput = object{fastqR1: t.fastqR1, fastqR2: t.fastqR2, readGroup: t.readGroup}
+    }
   }
 
-  call makeCSV {  
-    input: 
-    read1s = read1s,
-    read2s = read2s,
-    readGroups = readGroups,
-    isPaired = isPaired,
-    csvHeader = headerFormat.csvHeader,
-    prefix = outputFileNamePrefix
+  call composeList {
+    input:
+      inputLines = extractInfoLine.outputLine,
+      outputFileName = "dragen_inputs.csv"
   }
 
-  call runDragen  { 
+  call runDragen  {
     input: 
-    csv = makeCSV.outCSV,
+    csv = composeList.inputList,
     dragenRef = dragenRef,
+    dragenVersion = dragen_version,
     adapterTrim = adapterTrim,
     prefix = outputFileNamePrefix,
     isRNA = isRNA
@@ -108,146 +115,116 @@ workflow dragenAlign {
 
 }
 
-task headerFormat { 
-  input { 
-    String readGroupString
-    String prefix
-    Int jobMemory = 1
-    Int timeout = 5
-  }
+# =====================================================================
+# A scripted extraction of info from RG line to dragen-compliant string
+# =====================================================================
+task extractInfoLine {
+   input {
+       InputGroup fastqInput
+       String parsingScript = "$DRAGEN_SCRIPTS_ROOT/bin/composeList.py"
+       Int timeout = 4
+       Int jobMemory = 4
+       String modules = "dragen-scripts/0.1"
+   }
 
-  parameter_meta { 
-    readGroupString: "Read-group information of one of the fastq files" 
-    prefix: "Prefix for output files"
-    jobMemory: "Memory allocated for this job" 
-    timeout: "Hours before task timeout" 
-  } 
-  
-  command <<< 
-    set -euo pipefail 
+   parameter_meta {
+     fastqInput: "InputGroup struct entry with fastq files"
+     parsingScript: "Script for parsing inputs into a line"
+     timeout: "Timeout for the job"
+     jobMemory: "Job allocated RAM"
+     modules: "dependency modules"
+   }
 
-    headerString="Read1File,Read2File"
-    
-    # Split the string into an array of key-value pairs
-    IFS=, read -ra rgArray <<< ~{readGroupString}
-
-    # Adds valid keys (for Dragen) to headerString
-    for field in "${rgArray[@]}"; do
-      tag=${field:0:5}
-      if [ "$tag" == "RGID=" ] || [ "$tag" == "RGLB=" ] || [ "$tag" == "RGPL=" ] || \
-         [ "$tag" == "RGPU=" ] || [ "$tag" == "RGSM=" ] || [ "$tag" == "RGCN=" ] || \
-         [ "$tag" == "RGDS=" ] || [ "$tag" == "RGDT=" ] || [ "$tag" == "RGPI=" ]
-      then
-        headerString+=",${field:0:4}"
-      else
-        # Redirect error message to stderr
-        echo "Invalid tag: '$tag'" >&2  
-        exit 1
-      fi
-    done
-
-    # Ensures the required header information is present
-    if [ "$(echo "$headerString" | grep -c "RGID")" != 1 ] || \
-       [ "$(echo "$headerString" | grep -c "RGSM")" != 1 ] || \
-       [ "$(echo "$headerString" | grep -c "RGLB")" != 1 ] || \
-       [ "$(echo "$headerString" | grep -c "RGPU")" != 1 ]; then
-      echo "Missing required read-group information from header" >&2  
-      exit 1
-    fi
-
-    echo "$headerString"
-  >>> 
-
-  runtime { 
-    memory: "~{jobMemory} GB" 
-    timeout: "~{timeout}" 
-  } 
-
-  output { 
-    String csvHeader = read_string(stdout())
-  }
+   command <<<
+    python3 ~{parsingScript} -i ~{write_json(fastqInput)}
+   >>>
 
-  meta { 
-    output_meta: {
-    csvHeader: {
-        description: "Formatted header for the csv input of Dragen",
-        vidarr_label: "csvHeader"
-    }
+   runtime {
+     timeout: "~{timeout}"
+     modules: "~{modules}"
+     memory:  "~{jobMemory} GB"
+   }
+
+   output {
+     String outputLine = read_string(stdout())
+   }
+
+   meta {
+     output_meta: {
+       outputLine: "Output line to use in a list of fastq files in dragen-compliant format"
+     }
+   }
 }
-  } 
-} 
-
-task makeCSV { 
-  input { 
-    Array[File] read1s
-    Array[File]? read2s
-    Array[String] readGroups
-    Boolean isPaired
-    String csvHeader
-    String prefix
-    Int jobMemory = 1
-    Int timeout = 5
-  }
 
-  parameter_meta { 
-    read1s: "Array of read 1 fastq files" 
-    read2s: "Array of read 2 fastq files. May be empty." 
-    readGroups: "Array of read-group information to be added into the bam file header" 
-    isPaired: "Identifies if paired-end sequencing, [true, paired]"
-    csvHeader: "Formatted header for the csv input of Dragen" 
-    prefix: "Prefix for output files"
-    jobMemory: "Memory allocated for this job" 
-    timeout: "Hours before task timeout" 
-  } 
-  
-  String csvResult = "~{prefix}_dragenInput.csv"
-  Int arrayLength = length(read1s)
+# =====================================================================
+#  Compose a dragen-compliant list of inputs to use with snv caller
+# =====================================================================
+task composeList {
+   input  {
+      Array[String] inputLines
+      String listWritingScript = "$DRAGEN_SCRIPTS_ROOT/bin/writeFile.py"
+      String outputFileName
+      Int jobMemory = 4
+      Int timeout = 4
+      String modules = "dragen-scripts/0.1"
+   }
 
-  command <<< 
-    set -euo pipefail 
-    
-    echo ~{csvHeader} > ~{csvResult}
+   parameter_meta {
+     inputLines: "Array of input lines to print"
+     listWritingScript: "Script for writing out list of inputs"
+     outputFileName: "Name of an output file, list of inputs"
+     jobMemory: "Job allocated RAM"
+     timeout: "Timeout for the job"
+     modules: "dependency modules"
+   }
 
-    # Load arrays into bash variables
-    arrRead1s=(~{sep=" " read1s})
-    if ~{isPaired}; then arrRead2s=(~{sep=" " read2s}); fi
-    arrReadGroups=(~{sep=" " readGroups})
-    
-    # Iterate over the arrays concurrently
-    for (( i = 0; i < ~{arrayLength}; i++ ))
-    do
-      read1="${arrRead1s[i]}"
-      if ~{isPaired}; then read2="${arrRead2s[i]}"; else read2=""; fi
-      readGroup=$(echo "${arrReadGroups[i]}" | sed 's/RG..=//g')
-      echo "$read1,$read2,$readGroup" >> ~{csvResult}
-    done
-  >>> 
-
-  runtime { 
-    memory: "~{jobMemory} GB" 
-    timeout: "~{timeout}" 
-  } 
-
-  output { 
-    File outCSV = "~{csvResult}"
-  }
+   command<<<
+   python3 ~{listWritingScript} -o ~{outputFileName} -l "~{sep=';' inputLines}"
+   >>>
+
+
+   runtime {
+      timeout: "~{timeout}"
+      modules: "~{modules}"
+      memory:  "~{jobMemory} GB"
+   }
 
-  meta { 
-    output_meta: { 
-      outCSV: "Formatted csv input for Dragen, containing fastq files and read-group information" 
-    } 
-  } 
+   output {
+     File inputList = "~{outputFileName}"
+   }
+
+   meta {
+     output_meta: {
+       inputList: "Output file to use with dragen SNV caller"
+     }
+   }
 }
 
+
+# ================================================================
+# Main task for generating SNV calls in somatic mode (DRAGEN mode)
+#
+# we need CSV files with a header and data lines organized as:
+#
+# RGID Read Group
+# RGSM Sample ID
+# RGLB Library
+# Lane Flow cell lane
+# Read1File - Full path to a valid FASTQ input file
+# Read2File - Full path to a valid FASTQ input file. Required for paired-end input. If not using paired-end input, leave empty.
+# Each FASTQ file can only be referenced once in the CSV list.
+# All values in the Read2File column must be reference valid files or must all be empty.
+# ================================================================
 task runDragen {
   input {
     File csv
     String dragenRef
+    String dragenVersion
     String prefix
     Boolean isRNA
     Boolean adapterTrim
-    String adapter1File = "/.mounts/labs/gsiprojects/gsi/Dragen/resources/ADAPTER1"
-    String adapter2File = "/.mounts/labs/gsiprojects/gsi/Dragen/resources/ADAPTER2"
+    String adapter1File = "/staging/data/resources/ADAPTER1"
+    String adapter2File = "/staging/data/resources/ADAPTER2"
     Int jobMemory = 500
     Int timeout = 96
   }
@@ -255,6 +232,7 @@ task runDragen {
   parameter_meta {
     csv: "Formatted csv input for Dragen, containing fastq files and read-group information"
     dragenRef: "The reference genome to align the sample with by Dragen"
+    dragenVersion: "Expected version of dragen software on the DRAGEN node"
     prefix: "Prefix for output files"
     isRNA: "True/False, whether to complete transcriptomic analysis"
     adapterTrim: "True/False for adapter trimming"
@@ -293,6 +271,7 @@ task runDragen {
 
   runtime {
     timeout: "~{timeout}"
+    dragen_version: "~{dragenVersion}"
     backend: "DRAGEN"
   }
   
diff --git a/vidarrtest-regression.json.in b/vidarrtest-regression.json.in
index 5f23d32..bf8d0b3 100644
--- a/vidarrtest-regression.json.in
+++ b/vidarrtest-regression.json.in
@@ -27,17 +27,21 @@
                         },
                         "type": "EXTERNAL"
                     },
-                    "readGroup": "RGID=121005_h804_0096_AD0V4NACXX-NoIndex_6,RGLB=PCSI0022C,RGPL=ILLUMINA,RGPU=121005_h804_0096_AD0V4NACXX-NoIndex_6,RGSM=PCSI0022C"
+                    "readGroup": "ID:121005_h804_0096_AD0V4NACXX-NoIndex_6 LB:PCSI0022C PL:ILLUMINA PU:121005_h804_0096_AD0V4NACXX-NoIndex_6 SM:PCSI0022C CM:OICR"
                 }
             ],
             "dragenAlign.outputFileNamePrefix": "121005_h804_0096_AD0V4NACXX_PCSI0022C_NoIndex_L006_001", 
             "dragenAlign.reference": "hg38", 
             "dragenAlign.adapterTrim": false, 
             "dragenAlign.isRNA": false,
-            "dragenAlign.headerFormat.jobMemory": null, 
-            "dragenAlign.headerFormat.timeout": null, 
-            "dragenAlign.makeCSV.jobMemory": null, 
-            "dragenAlign.makeCSV.timeout": null, 
+            "dragenAlign.extractInfoLine.jobMemory": null,
+            "dragenAlign.extractInfoLine.modules": null,
+            "dragenAlign.extractInfoLine.parsingScript": null,
+            "dragenAlign.extractInfoLine.timeout": null,
+            "dragenAlign.composeList.jobMemory": null,
+            "dragenAlign.composeList.listWritingScript": null,
+            "dragenAlign.composeList.modules": null,
+            "dragenAlign.composeList.timeout": null,
             "dragenAlign.runDragen.adapter1File": null, 
             "dragenAlign.runDragen.adapter2File": null, 
             "dragenAlign.runDragen.jobMemory": null, 
@@ -87,7 +91,7 @@
             {
                 "metrics_calculate": "@CHECKOUT@/tests/calculate.sh",
                 "metrics_compare": "@CHECKOUT@/tests/compare.sh",
-                "output_metrics": "/.mounts/labs/gsi/testdata/dragenAlign/1.2.2/output_metrics/PCSI0022C_notrim_bam.metrics",
+                "output_metrics": "/.mounts/labs/gsi/testdata/dragenAlign/1.4.0/output_metrics/PCSI0022C_notrim_bam.metrics",
                 "type": "script"
             }
         ]
@@ -120,17 +124,21 @@
                         },
                         "type": "EXTERNAL"
                     },
-                    "readGroup": "RGID=121005_h804_0096_AD0V4NACXX-NoIndex_6,RGLB=PCSI0022C,RGPL=ILLUMINA,RGPU=121005_h804_0096_AD0V4NACXX-NoIndex_6,RGSM=PCSI0022C"
+                    "readGroup": "ID:121005_h804_0096_AD0V4NACXX-NoIndex_6 LB:PCSI0022C PL:ILLUMINA PU:121005_h804_0096_AD0V4NACXX-NoIndex_6 SM:PCSI0022C CM:OICR"
                 }
             ],
             "dragenAlign.outputFileNamePrefix": "121005_h804_0096_AD0V4NACXX_PCSI0022C_NoIndex_L006_001", 
             "dragenAlign.reference": "hg38", 
             "dragenAlign.adapterTrim": null, 
             "dragenAlign.isRNA": false,
-            "dragenAlign.headerFormat.jobMemory": null, 
-            "dragenAlign.headerFormat.timeout": null, 
-            "dragenAlign.makeCSV.jobMemory": null, 
-            "dragenAlign.makeCSV.timeout": null,
+            "dragenAlign.extractInfoLine.jobMemory": null,
+            "dragenAlign.extractInfoLine.modules": null,
+            "dragenAlign.extractInfoLine.parsingScript": null,
+            "dragenAlign.extractInfoLine.timeout": null,
+            "dragenAlign.composeList.jobMemory": null,
+            "dragenAlign.composeList.listWritingScript": null,
+            "dragenAlign.composeList.modules": null,
+            "dragenAlign.composeList.timeout": null,
             "dragenAlign.runDragen.adapter1File": null, 
             "dragenAlign.runDragen.adapter2File": null, 
             "dragenAlign.runDragen.jobMemory": null, 
@@ -202,17 +210,21 @@
                         "type": "EXTERNAL"
                     },
                     "fastqR2": null,
-                    "readGroup": "RGID=121005_h804_0096_AD0V4NACXX-NoIndex_6,RGLB=PCSI0022C,RGPL=ILLUMINA,RGPU=121005_h804_0096_AD0V4NACXX-NoIndex_6,RGSM=PCSI0022C"
+                    "readGroup": "ID:121005_h804_0096_AD0V4NACXX-NoIndex_6 LB:PCSI0022C PL:ILLUMINA PU:121005_h804_0096_AD0V4NACXX-NoIndex_6 SM:PCSI0022C CM:OICR"
                 }
             ],
             "dragenAlign.outputFileNamePrefix": "121005_h804_0096_AD0V4NACXX_PCSI0022C_NoIndex_L006_001", 
             "dragenAlign.reference": "hg38", 
             "dragenAlign.adapterTrim": null, 
             "dragenAlign.isRNA": false,
-            "dragenAlign.headerFormat.jobMemory": null, 
-            "dragenAlign.headerFormat.timeout": null, 
-            "dragenAlign.makeCSV.jobMemory": null, 
-            "dragenAlign.makeCSV.timeout": null,
+            "dragenAlign.extractInfoLine.jobMemory": null,
+            "dragenAlign.extractInfoLine.modules": null,
+            "dragenAlign.extractInfoLine.parsingScript": null,
+            "dragenAlign.extractInfoLine.timeout": null,
+            "dragenAlign.composeList.jobMemory": null,
+            "dragenAlign.composeList.listWritingScript": null,
+            "dragenAlign.composeList.modules": null,
+            "dragenAlign.composeList.timeout": null,            
             "dragenAlign.runDragen.adapter1File": null, 
             "dragenAlign.runDragen.adapter2File": null, 
             "dragenAlign.runDragen.jobMemory": null, 
@@ -262,7 +274,7 @@
             {
                 "metrics_calculate": "@CHECKOUT@/tests/calculate.sh",
                 "metrics_compare": "@CHECKOUT@/tests/compare.sh",
-                "output_metrics": "/.mounts/labs/gsi/testdata/dragenAlign/1.2.2/output_metrics/PCSI0022C_trim_bam_se.metrics",
+                "output_metrics": "/.mounts/labs/gsi/testdata/dragenAlign/1.4.0/output_metrics/PCSI0022C_trim_bam_se.metrics",
                 "type": "script"
             }
         ]
@@ -284,18 +296,21 @@
                         "type": "EXTERNAL"
                     },
                     "fastqR2": null,
-                    "readGroup": "RGID=121005_h804_0096_AD0V4NACXX-NoIndex_6,RGLB=PCSI0022C,RGPL=ILLUMINA,RGPU=121005_h804_0096_AD0V4NACXX-NoIndex_6,RGSM=PCSI0022C"
+                    "readGroup": "ID:121005_h804_0096_AD0V4NACXX-NoIndex_6 LB:PCSI0022C PL:ILLUMINA PU:121005_h804_0096_AD0V4NACXX-NoIndex_6 SM:PCSI0022C CM:OICR"
                 }
             ],
             "dragenAlign.outputFileNamePrefix": "121005_h804_0096_AD0V4NACXX_PCSI0022C_NoIndex_L006_001", 
             "dragenAlign.reference": "hg38", 
             "dragenAlign.adapterTrim": false, 
-            "dragenAlign.rgInfo": "ID=121005_h804_0096_AD0V4NACXX-NoIndex_6,LB=PCSI0022C,PL=ILLUMINA,PU=121005_h804_0096_AD0V4NACXX-NoIndex_6,SM=PCSI0022C", 
             "dragenAlign.isRNA": false,
-            "dragenAlign.headerFormat.jobMemory": null, 
-            "dragenAlign.headerFormat.timeout": null, 
-            "dragenAlign.makeCSV.jobMemory": null, 
-            "dragenAlign.makeCSV.timeout": null,
+            "dragenAlign.extractInfoLine.jobMemory": null,
+            "dragenAlign.extractInfoLine.modules": null,
+            "dragenAlign.extractInfoLine.parsingScript": null,
+            "dragenAlign.extractInfoLine.timeout": null,
+            "dragenAlign.composeList.jobMemory": null,
+            "dragenAlign.composeList.listWritingScript": null,
+            "dragenAlign.composeList.modules": null,
+            "dragenAlign.composeList.timeout": null,            
             "dragenAlign.runDragen.adapter1File": null, 
             "dragenAlign.runDragen.adapter2File": null, 
             "dragenAlign.runDragen.jobMemory": null, 
@@ -345,7 +360,7 @@
             {
                 "metrics_calculate": "@CHECKOUT@/tests/calculate.sh",
                 "metrics_compare": "@CHECKOUT@/tests/compare.sh",
-                "output_metrics": "/.mounts/labs/gsi/testdata/dragenAlign/1.2.2/output_metrics/PCSI0022C_notrim_bam_se.metrics",
+                "output_metrics": "/.mounts/labs/gsi/testdata/dragenAlign/1.4.0/output_metrics/PCSI0022C_notrim_bam_se.metrics",
                 "type": "script"
             }
         ]
@@ -378,17 +393,21 @@
                         },
                         "type": "EXTERNAL"
                     },
-                    "readGroup": "RGID=121005_h804_0096_AD0V4NACXX_4_NoIndex,RGPL=Illumina,RGPU=121005_h804_0096_AD0V4NACXX_4_NoIndex,RGLB=K562_1,RGSM=K562_1test"
+                    "readGroup": "ID:121005_h804_0096_AD0V4NACXX_4_NoIndex PL:Illumina PU:121005_h804_0096_AD0V4NACXX_4_NoIndex LB:K562_1 SM:K562_1test CM:OICR"
                 }
             ],
             "dragenAlign.outputFileNamePrefix": "K562", 
             "dragenAlign.reference": "hg38", 
             "dragenAlign.adapterTrim": false, 
             "dragenAlign.isRNA": true,
-            "dragenAlign.headerFormat.jobMemory": null, 
-            "dragenAlign.headerFormat.timeout": null, 
-            "dragenAlign.makeCSV.jobMemory": null, 
-            "dragenAlign.makeCSV.timeout": null,
+            "dragenAlign.extractInfoLine.jobMemory": null,
+            "dragenAlign.extractInfoLine.modules": null,
+            "dragenAlign.extractInfoLine.parsingScript": null,
+            "dragenAlign.extractInfoLine.timeout": null,
+            "dragenAlign.composeList.jobMemory": null,
+            "dragenAlign.composeList.listWritingScript": null,
+            "dragenAlign.composeList.modules": null,
+            "dragenAlign.composeList.timeout": null,            
             "dragenAlign.runDragen.adapter1File": null, 
             "dragenAlign.runDragen.adapter2File": null, 
             "dragenAlign.runDragen.jobMemory": null, 
@@ -438,7 +457,7 @@
             {
                 "metrics_calculate": "@CHECKOUT@/tests/calculate.sh",
                 "metrics_compare": "@CHECKOUT@/tests/compare.sh",
-                "output_metrics": "/.mounts/labs/gsi/testdata/dragenAlign/1.2.2/output_metrics/K562_notrim_wt_bam.metrics",
+                "output_metrics": "/.mounts/labs/gsi/testdata/dragenAlign/1.4.0/output_metrics/K562_notrim_wt_bam.metrics",
                 "type": "script"
             }
         ]
@@ -471,17 +490,21 @@
                         },
                         "type": "EXTERNAL"
                     },
-                    "readGroup": "RGID=121005_h804_0096_AD0V4NACXX_4_NoIndex,RGPL=Illumina,RGPU=121005_h804_0096_AD0V4NACXX_4_NoIndex,RGLB=K562_1,RGSM=K562_1test"
+                    "readGroup": "ID:121005_h804_0096_AD0V4NACXX_4_NoIndex PL:Illumina PU:121005_h804_0096_AD0V4NACXX_4_NoIndex LB:K562_1 SM:K562_1test CM:OICR"
                 }
             ],
             "dragenAlign.outputFileNamePrefix": "K562", 
             "dragenAlign.reference": "hg38", 
             "dragenAlign.adapterTrim": null, 
             "dragenAlign.isRNA": true,
-            "dragenAlign.headerFormat.jobMemory": null, 
-            "dragenAlign.headerFormat.timeout": null, 
-            "dragenAlign.makeCSV.jobMemory": null, 
-            "dragenAlign.makeCSV.timeout": null,
+            "dragenAlign.extractInfoLine.jobMemory": null,
+            "dragenAlign.extractInfoLine.modules": null,
+            "dragenAlign.extractInfoLine.parsingScript": null,
+            "dragenAlign.extractInfoLine.timeout": null,
+            "dragenAlign.composeList.jobMemory": null,
+            "dragenAlign.composeList.listWritingScript": null,
+            "dragenAlign.composeList.modules": null,
+            "dragenAlign.composeList.timeout": null,            
             "dragenAlign.runDragen.adapter1File": null, 
             "dragenAlign.runDragen.adapter2File": null, 
             "dragenAlign.runDragen.jobMemory": null, 
@@ -531,7 +554,7 @@
             {
                 "metrics_calculate": "@CHECKOUT@/tests/calculate.sh",
                 "metrics_compare": "@CHECKOUT@/tests/compare.sh",
-                "output_metrics": "/.mounts/labs/gsi/testdata/dragenAlign/1.2.2/output_metrics/K562_trim_wt_bam.metrics",
+                "output_metrics": "/.mounts/labs/gsi/testdata/dragenAlign/1.4.0/output_metrics/K562_trim_wt_bam.metrics",
                 "type": "script"
             }
         ]
@@ -553,17 +576,21 @@
                         "type": "EXTERNAL"
                     },
                     "fastqR2": null,
-                    "readGroup": "RGID=121005_h804_0096_AD0V4NACXX_4_NoIndex,RGPL=Illumina,RGPU=121005_h804_0096_AD0V4NACXX_4_NoIndex,RGLB=K562_1,RGSM=K562_1test"
+                    "readGroup": "ID:121005_h804_0096_AD0V4NACXX_4_NoIndex PL:Illumina PU:121005_h804_0096_AD0V4NACXX_4_NoIndex LB:K562_1 SM:K562_1test CM:OICR"
                 }
             ],
             "dragenAlign.outputFileNamePrefix": "K562", 
             "dragenAlign.reference": "hg38", 
             "dragenAlign.adapterTrim": false, 
             "dragenAlign.isRNA": true,
-            "dragenAlign.headerFormat.jobMemory": null, 
-            "dragenAlign.headerFormat.timeout": null, 
-            "dragenAlign.makeCSV.jobMemory": null, 
-            "dragenAlign.makeCSV.timeout": null,
+            "dragenAlign.extractInfoLine.jobMemory": null,
+            "dragenAlign.extractInfoLine.modules": null,
+            "dragenAlign.extractInfoLine.parsingScript": null,
+            "dragenAlign.extractInfoLine.timeout": null,
+            "dragenAlign.composeList.jobMemory": null,
+            "dragenAlign.composeList.listWritingScript": null,
+            "dragenAlign.composeList.modules": null,
+            "dragenAlign.composeList.timeout": null,            
             "dragenAlign.runDragen.adapter1File": null, 
             "dragenAlign.runDragen.adapter2File": null, 
             "dragenAlign.runDragen.jobMemory": null, 
@@ -613,7 +640,7 @@
             {
                 "metrics_calculate": "@CHECKOUT@/tests/calculate.sh",
                 "metrics_compare": "@CHECKOUT@/tests/compare.sh",
-                "output_metrics": "/.mounts/labs/gsi/testdata/dragenAlign/1.2.2/output_metrics/K562_notrim_wt_bam_se.metrics",
+                "output_metrics": "/.mounts/labs/gsi/testdata/dragenAlign/1.4.0/output_metrics/K562_notrim_wt_bam_se.metrics",
                 "type": "script"
             }
         ]
@@ -635,7 +662,7 @@
                         "type": "EXTERNAL"
                     },
                     "fastqR2": null,
-                    "readGroup": "RGID=VENHPV_0260_02_LB02-01_240304_A00469_0642_BHWVM7DSX7_3_TCCGCGAA-GCCTCTAT,RGLB=VENHPV_A00469_0642_WT,RGPL=ILLUMINA,RGPU=VENHPV_0260_02_LB02-01_240304_A00469_0642_BHWVM7DSX7_3_TCCGCGAA-GCCTCTAT,RGSM=VENHPV_TEST"
+                    "readGroup": "ID:VENHPV_0260_02_LB02-01_240304_A00469_0642_BHWVM7DSX7_3_TCCGCGAA-GCCTCTAT LB:VENHPV_A00469_0642_WT PL:ILLUMINA PU:VENHPV_0260_02_LB02-01_240304_A00469_0642_BHWVM7DSX7_3_TCCGCGAA-GCCTCTAT SM:VENHPV_TEST CM:OICR"
                 },
                 {
                     "fastqR1": {
@@ -651,17 +678,21 @@
                         "type": "EXTERNAL"
                     },
                     "fastqR2": null,
-                    "readGroup": "RGID=VENHPV_0260_02_LB02-01_240223_A00469_0636_BHWTVJDSX7_1_TCCGCGAA-GCCTCTAT,RGLB=VENHPV_A00469_0636_WT,RGPL=ILLUMINA,RGPU=VENHPV_0260_02_LB02-01_240223_A00469_0636_BHWTVJDSX7_1_TCCGCGAA-GCCTCTAT,RGSM=VENHPV_TEST"
+                    "readGroup": "ID:VENHPV_0260_02_LB02-01_240223_A00469_0636_BHWTVJDSX7_1_TCCGCGAA-GCCTCTAT LB:VENHPV_A00469_0636_WT PL:ILLUMINA PU:VENHPV_0260_02_LB02-01_240223_A00469_0636_BHWTVJDSX7_1_TCCGCGAA-GCCTCTAT SM:VENHPV_TEST CM:OICR"
                 }
             ],
             "dragenAlign.outputFileNamePrefix": "VENHPV_0260_02_LB02-01", 
             "dragenAlign.reference": "hg38", 
             "dragenAlign.adapterTrim": false, 
             "dragenAlign.isRNA": true,
-            "dragenAlign.headerFormat.jobMemory": null, 
-            "dragenAlign.headerFormat.timeout": null, 
-            "dragenAlign.makeCSV.jobMemory": null, 
-            "dragenAlign.makeCSV.timeout": null,
+            "dragenAlign.extractInfoLine.jobMemory": null,
+            "dragenAlign.extractInfoLine.modules": null,
+            "dragenAlign.extractInfoLine.parsingScript": null,
+            "dragenAlign.extractInfoLine.timeout": null,
+            "dragenAlign.composeList.jobMemory": null,
+            "dragenAlign.composeList.listWritingScript": null,
+            "dragenAlign.composeList.modules": null,
+            "dragenAlign.composeList.timeout": null,
             "dragenAlign.runDragen.adapter1File": null, 
             "dragenAlign.runDragen.adapter2File": null, 
             "dragenAlign.runDragen.jobMemory": null, 
@@ -711,7 +742,7 @@
             {
                 "metrics_calculate": "@CHECKOUT@/tests/calculate.sh",
                 "metrics_compare": "@CHECKOUT@/tests/compare.sh",
-                "output_metrics": "/.mounts/labs/gsi/testdata/dragenAlign/1.2.2/output_metrics/VENHPV_notrim_wt_bam_se.metrics",
+                "output_metrics": "/.mounts/labs/gsi/testdata/dragenAlign/1.4.0/output_metrics/VENHPV_notrim_wt_bam_se.metrics",
                 "type": "script"
             }
         ]
@@ -744,7 +775,7 @@
                         },
                         "type": "EXTERNAL"
                     },
-                    "readGroup": "RGID=VENHPV_0260_02_LB02-01_240304_A00469_0642_BHWVM7DSX7_3_TCCGCGAA-GCCTCTAT,RGLB=VENHPV_A00469_0642_WT,RGPL=ILLUMINA,RGPU=VENHPV_0260_02_LB02-01_240304_A00469_0642_BHWVM7DSX7_3_TCCGCGAA-GCCTCTAT,RGSM=VENHPV_TEST"
+                    "readGroup": "ID:VENHPV_0260_02_LB02-01_240304_A00469_0642_BHWVM7DSX7_3_TCCGCGAA-GCCTCTAT LB:VENHPV_A00469_0642_WT PL:ILLUMINA PU:VENHPV_0260_02_LB02-01_240304_A00469_0642_BHWVM7DSX7_3_TCCGCGAA-GCCTCTAT SM:VENHPV_TEST CM:OICR"
                 },
                 {
                     "fastqR1": {
@@ -771,17 +802,21 @@
                         },
                         "type": "EXTERNAL"
                     },
-                    "readGroup": "RGID=VENHPV_0260_02_LB02-01_240223_A00469_0636_BHWTVJDSX7_1_TCCGCGAA-GCCTCTAT,RGLB=VENHPV_A00469_0636_WT,RGPL=ILLUMINA,RGPU=VENHPV_0260_02_LB02-01_240223_A00469_0636_BHWTVJDSX7_1_TCCGCGAA-GCCTCTAT,RGSM=VENHPV_TEST"
+                    "readGroup": "ID:VENHPV_0260_02_LB02-01_240223_A00469_0636_BHWTVJDSX7_1_TCCGCGAA-GCCTCTAT LB:VENHPV_A00469_0636_WT PL:ILLUMINA PU:VENHPV_0260_02_LB02-01_240223_A00469_0636_BHWTVJDSX7_1_TCCGCGAA-GCCTCTAT SM:VENHPV_TEST CM:OICR"
                 }
             ],
             "dragenAlign.outputFileNamePrefix": "VENHPV_0260_02_LB02-01", 
             "dragenAlign.reference": "hg38",
             "dragenAlign.adapterTrim": true,
             "dragenAlign.isRNA": true,
-            "dragenAlign.headerFormat.jobMemory": null, 
-            "dragenAlign.headerFormat.timeout": null, 
-            "dragenAlign.makeCSV.jobMemory": null, 
-            "dragenAlign.makeCSV.timeout": null,
+            "dragenAlign.extractInfoLine.jobMemory": null,
+            "dragenAlign.extractInfoLine.modules": null,
+            "dragenAlign.extractInfoLine.parsingScript": null,
+            "dragenAlign.extractInfoLine.timeout": null,
+            "dragenAlign.composeList.jobMemory": null,
+            "dragenAlign.composeList.listWritingScript": null,
+            "dragenAlign.composeList.modules": null,
+            "dragenAlign.composeList.timeout": null,            
             "dragenAlign.runDragen.adapter1File": null, 
             "dragenAlign.runDragen.adapter2File": null, 
             "dragenAlign.runDragen.jobMemory": null, 
@@ -831,9 +866,9 @@
             {
                 "metrics_calculate": "@CHECKOUT@/tests/calculate.sh",
                 "metrics_compare": "@CHECKOUT@/tests/compare.sh",
-                "output_metrics": "/.mounts/labs/gsi/testdata/dragenAlign/1.2.2/output_metrics/VENHPV_trim_wt_bam.metrics",
+                "output_metrics": "/.mounts/labs/gsi/testdata/dragenAlign/1.4.0/output_metrics/VENHPV_trim_wt_bam.metrics",
                 "type": "script"
             }
         ]
     }
-]
\ No newline at end of file
+]

From fb531ccd001a41818c4e51e34330e4a91442773c Mon Sep 17 00:00:00 2001
From: pruzanov <pruzanov@oicr.on.ca>
Date: Tue, 11 Feb 2025 12:40:40 -0500
Subject: [PATCH 4/6] Switching to modified dragen scripts

---
 dragenAlign.wdl               | 4 ++--
 vidarrtest-regression.json.in | 2 +-
 2 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/dragenAlign.wdl b/dragenAlign.wdl
index 4501627..f1bea4d 100755
--- a/dragenAlign.wdl
+++ b/dragenAlign.wdl
@@ -124,7 +124,7 @@ task extractInfoLine {
        String parsingScript = "$DRAGEN_SCRIPTS_ROOT/bin/composeList.py"
        Int timeout = 4
        Int jobMemory = 4
-       String modules = "dragen-scripts/0.1"
+       String modules = "dragen-scripts/0.2"
    }
 
    parameter_meta {
@@ -166,7 +166,7 @@ task composeList {
       String outputFileName
       Int jobMemory = 4
       Int timeout = 4
-      String modules = "dragen-scripts/0.1"
+      String modules = "dragen-scripts/0.2"
    }
 
    parameter_meta {
diff --git a/vidarrtest-regression.json.in b/vidarrtest-regression.json.in
index bf8d0b3..f22c620 100644
--- a/vidarrtest-regression.json.in
+++ b/vidarrtest-regression.json.in
@@ -188,7 +188,7 @@
             {
                 "metrics_calculate": "@CHECKOUT@/tests/calculate.sh",
                 "metrics_compare": "@CHECKOUT@/tests/compare.sh",
-                "output_metrics": "/.mounts/labs/gsi/testdata/dragenAlign/1.2.2/output_metrics/PCSI0022C_trim_bam.metrics",
+                "output_metrics": "/.mounts/labs/gsi/testdata/dragenAlign/1.4.0/output_metrics/PCSI0022C_trim_bam.metrics",
                 "type": "script"
             }
         ]

From cc179a5346cdaa0e00247e3411dea9eacaa238f2 Mon Sep 17 00:00:00 2001
From: pruzanov <pruzanov@oicr.on.ca>
Date: Tue, 11 Feb 2025 20:22:31 -0500
Subject: [PATCH 5/6] Test with new version of scripts

---
 CHANGELOG.md                  |  2 +-
 tests/calculate.sh            |  4 ---
 vidarrtest-regression.json.in | 58 +++++++++++++++++------------------
 3 files changed, 30 insertions(+), 34 deletions(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index a2eda89..15b109a 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -4,7 +4,7 @@ All notable changes to this project will be documented in this file.
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
-## [Unreleased] - 2025-02-12
+## [1.4.0] - 2025-02-12
 ### Changed
 - Regression testing adjusted, validates in Jenkins
 - default parameters adjusted according to [GBS-5046](https://jira.oicr.on.ca/browse/GBS-5046)
diff --git a/tests/calculate.sh b/tests/calculate.sh
index cf67225..5be37b7 100755
--- a/tests/calculate.sh
+++ b/tests/calculate.sh
@@ -7,12 +7,8 @@ cd $1
 module load samtools/1.9 2>/dev/null
 
 ls | sort
-
 find -name *.zip -xtype f -exec unzip -l {} \; | awk '{print $4}' | sed -e '/^\(Name\|----\)$/d' -e '/^[[:space:]]*$/d' | sort
-
 find -name *.bam -xtype f -exec samtools view -H {} \; | grep '^@RG' | sort
-
 find -name *.bam -xtype f -exec samtools flagstat {} \; | sort
-
 find -name *.bam -xtype f -exec /bin/bash -c "samtools view {} | md5sum" \; | sort
 
diff --git a/vidarrtest-regression.json.in b/vidarrtest-regression.json.in
index f22c620..1f84780 100644
--- a/vidarrtest-regression.json.in
+++ b/vidarrtest-regression.json.in
@@ -27,7 +27,7 @@
                         },
                         "type": "EXTERNAL"
                     },
-                    "readGroup": "ID:121005_h804_0096_AD0V4NACXX-NoIndex_6 LB:PCSI0022C PL:ILLUMINA PU:121005_h804_0096_AD0V4NACXX-NoIndex_6 SM:PCSI0022C CM:OICR"
+                    "readGroup": "ID:121005_h804_0096_AD0V4NACXX_6_NoIndex LB:PCSI0022C PL:ILLUMINA PU:121005_h804_0096_AD0V4NACXX_6_NoIndex SM:PCSI0022C CN:OICR"
                 }
             ],
             "dragenAlign.outputFileNamePrefix": "121005_h804_0096_AD0V4NACXX_PCSI0022C_NoIndex_L006_001", 
@@ -36,10 +36,10 @@
             "dragenAlign.isRNA": false,
             "dragenAlign.extractInfoLine.jobMemory": null,
             "dragenAlign.extractInfoLine.modules": null,
-            "dragenAlign.extractInfoLine.parsingScript": null,
+            "dragenAlign.extractInfoLine.parsingScript": "/.mounts/labs/gsi/testdata/dragenSomatic/scripts/composeList.py",
             "dragenAlign.extractInfoLine.timeout": null,
             "dragenAlign.composeList.jobMemory": null,
-            "dragenAlign.composeList.listWritingScript": null,
+            "dragenAlign.composeList.listWritingScript": "/.mounts/labs/gsi/testdata/dragenSomatic/scripts/writeFile.py",
             "dragenAlign.composeList.modules": null,
             "dragenAlign.composeList.timeout": null,
             "dragenAlign.runDragen.adapter1File": null, 
@@ -124,7 +124,7 @@
                         },
                         "type": "EXTERNAL"
                     },
-                    "readGroup": "ID:121005_h804_0096_AD0V4NACXX-NoIndex_6 LB:PCSI0022C PL:ILLUMINA PU:121005_h804_0096_AD0V4NACXX-NoIndex_6 SM:PCSI0022C CM:OICR"
+                    "readGroup": "ID:121005_h804_0096_AD0V4NACXX_6_NoIndex LB:PCSI0022C PL:ILLUMINA PU:121005_h804_0096_AD0V4NACXX_6_NoIndex SM:PCSI0022C CN:OICR"
                 }
             ],
             "dragenAlign.outputFileNamePrefix": "121005_h804_0096_AD0V4NACXX_PCSI0022C_NoIndex_L006_001", 
@@ -133,10 +133,10 @@
             "dragenAlign.isRNA": false,
             "dragenAlign.extractInfoLine.jobMemory": null,
             "dragenAlign.extractInfoLine.modules": null,
-            "dragenAlign.extractInfoLine.parsingScript": null,
+            "dragenAlign.extractInfoLine.parsingScript": "/.mounts/labs/gsi/testdata/dragenSomatic/scripts/composeList.py",
             "dragenAlign.extractInfoLine.timeout": null,
             "dragenAlign.composeList.jobMemory": null,
-            "dragenAlign.composeList.listWritingScript": null,
+            "dragenAlign.composeList.listWritingScript": "/.mounts/labs/gsi/testdata/dragenSomatic/scripts/writeFile.py",
             "dragenAlign.composeList.modules": null,
             "dragenAlign.composeList.timeout": null,
             "dragenAlign.runDragen.adapter1File": null, 
@@ -210,7 +210,7 @@
                         "type": "EXTERNAL"
                     },
                     "fastqR2": null,
-                    "readGroup": "ID:121005_h804_0096_AD0V4NACXX-NoIndex_6 LB:PCSI0022C PL:ILLUMINA PU:121005_h804_0096_AD0V4NACXX-NoIndex_6 SM:PCSI0022C CM:OICR"
+                    "readGroup": "ID:121005_h804_0096_AD0V4NACXX_6_NoIndex LB:PCSI0022C PL:ILLUMINA PU:121005_h804_0096_AD0V4NACXX_6_NoIndex SM:PCSI0022C CN:OICR"
                 }
             ],
             "dragenAlign.outputFileNamePrefix": "121005_h804_0096_AD0V4NACXX_PCSI0022C_NoIndex_L006_001", 
@@ -219,10 +219,10 @@
             "dragenAlign.isRNA": false,
             "dragenAlign.extractInfoLine.jobMemory": null,
             "dragenAlign.extractInfoLine.modules": null,
-            "dragenAlign.extractInfoLine.parsingScript": null,
+            "dragenAlign.extractInfoLine.parsingScript": "/.mounts/labs/gsi/testdata/dragenSomatic/scripts/composeList.py",
             "dragenAlign.extractInfoLine.timeout": null,
             "dragenAlign.composeList.jobMemory": null,
-            "dragenAlign.composeList.listWritingScript": null,
+            "dragenAlign.composeList.listWritingScript": "/.mounts/labs/gsi/testdata/dragenSomatic/scripts/writeFile.py",
             "dragenAlign.composeList.modules": null,
             "dragenAlign.composeList.timeout": null,            
             "dragenAlign.runDragen.adapter1File": null, 
@@ -296,7 +296,7 @@
                         "type": "EXTERNAL"
                     },
                     "fastqR2": null,
-                    "readGroup": "ID:121005_h804_0096_AD0V4NACXX-NoIndex_6 LB:PCSI0022C PL:ILLUMINA PU:121005_h804_0096_AD0V4NACXX-NoIndex_6 SM:PCSI0022C CM:OICR"
+                    "readGroup": "ID:121005_h804_0096_AD0V4NACXX_6_NoIndex LB:PCSI0022C PL:ILLUMINA PU:121005_h804_0096_AD0V4NACXX_6_NoIndex SM:PCSI0022C CN:OICR"
                 }
             ],
             "dragenAlign.outputFileNamePrefix": "121005_h804_0096_AD0V4NACXX_PCSI0022C_NoIndex_L006_001", 
@@ -305,10 +305,10 @@
             "dragenAlign.isRNA": false,
             "dragenAlign.extractInfoLine.jobMemory": null,
             "dragenAlign.extractInfoLine.modules": null,
-            "dragenAlign.extractInfoLine.parsingScript": null,
+            "dragenAlign.extractInfoLine.parsingScript": "/.mounts/labs/gsi/testdata/dragenSomatic/scripts/composeList.py",
             "dragenAlign.extractInfoLine.timeout": null,
             "dragenAlign.composeList.jobMemory": null,
-            "dragenAlign.composeList.listWritingScript": null,
+            "dragenAlign.composeList.listWritingScript": "/.mounts/labs/gsi/testdata/dragenSomatic/scripts/writeFile.py",
             "dragenAlign.composeList.modules": null,
             "dragenAlign.composeList.timeout": null,            
             "dragenAlign.runDragen.adapter1File": null, 
@@ -393,7 +393,7 @@
                         },
                         "type": "EXTERNAL"
                     },
-                    "readGroup": "ID:121005_h804_0096_AD0V4NACXX_4_NoIndex PL:Illumina PU:121005_h804_0096_AD0V4NACXX_4_NoIndex LB:K562_1 SM:K562_1test CM:OICR"
+                    "readGroup": "ID:121005_h804_0096_AD0V4NACXX_4_NoIndex PL:Illumina PU:121005_h804_0096_AD0V4NACXX_4_NoIndex LB:K562_1 SM:K562_1test CN:OICR"
                 }
             ],
             "dragenAlign.outputFileNamePrefix": "K562", 
@@ -402,10 +402,10 @@
             "dragenAlign.isRNA": true,
             "dragenAlign.extractInfoLine.jobMemory": null,
             "dragenAlign.extractInfoLine.modules": null,
-            "dragenAlign.extractInfoLine.parsingScript": null,
+            "dragenAlign.extractInfoLine.parsingScript": "/.mounts/labs/gsi/testdata/dragenSomatic/scripts/composeList.py",
             "dragenAlign.extractInfoLine.timeout": null,
             "dragenAlign.composeList.jobMemory": null,
-            "dragenAlign.composeList.listWritingScript": null,
+            "dragenAlign.composeList.listWritingScript": "/.mounts/labs/gsi/testdata/dragenSomatic/scripts/writeFile.py",
             "dragenAlign.composeList.modules": null,
             "dragenAlign.composeList.timeout": null,            
             "dragenAlign.runDragen.adapter1File": null, 
@@ -490,7 +490,7 @@
                         },
                         "type": "EXTERNAL"
                     },
-                    "readGroup": "ID:121005_h804_0096_AD0V4NACXX_4_NoIndex PL:Illumina PU:121005_h804_0096_AD0V4NACXX_4_NoIndex LB:K562_1 SM:K562_1test CM:OICR"
+                    "readGroup": "ID:121005_h804_0096_AD0V4NACXX_4_NoIndex PL:Illumina PU:121005_h804_0096_AD0V4NACXX_4_NoIndex LB:K562_1 SM:K562_1test CN:OICR"
                 }
             ],
             "dragenAlign.outputFileNamePrefix": "K562", 
@@ -499,10 +499,10 @@
             "dragenAlign.isRNA": true,
             "dragenAlign.extractInfoLine.jobMemory": null,
             "dragenAlign.extractInfoLine.modules": null,
-            "dragenAlign.extractInfoLine.parsingScript": null,
+            "dragenAlign.extractInfoLine.parsingScript": "/.mounts/labs/gsi/testdata/dragenSomatic/scripts/composeList.py",
             "dragenAlign.extractInfoLine.timeout": null,
             "dragenAlign.composeList.jobMemory": null,
-            "dragenAlign.composeList.listWritingScript": null,
+            "dragenAlign.composeList.listWritingScript": "/.mounts/labs/gsi/testdata/dragenSomatic/scripts/writeFile.py",
             "dragenAlign.composeList.modules": null,
             "dragenAlign.composeList.timeout": null,            
             "dragenAlign.runDragen.adapter1File": null, 
@@ -576,7 +576,7 @@
                         "type": "EXTERNAL"
                     },
                     "fastqR2": null,
-                    "readGroup": "ID:121005_h804_0096_AD0V4NACXX_4_NoIndex PL:Illumina PU:121005_h804_0096_AD0V4NACXX_4_NoIndex LB:K562_1 SM:K562_1test CM:OICR"
+                    "readGroup": "ID:121005_h804_0096_AD0V4NACXX_4_NoIndex PL:Illumina PU:121005_h804_0096_AD0V4NACXX_4_NoIndex LB:K562_1 SM:K562_1test CN:OICR"
                 }
             ],
             "dragenAlign.outputFileNamePrefix": "K562", 
@@ -585,10 +585,10 @@
             "dragenAlign.isRNA": true,
             "dragenAlign.extractInfoLine.jobMemory": null,
             "dragenAlign.extractInfoLine.modules": null,
-            "dragenAlign.extractInfoLine.parsingScript": null,
+            "dragenAlign.extractInfoLine.parsingScript": "/.mounts/labs/gsi/testdata/dragenSomatic/scripts/composeList.py",
             "dragenAlign.extractInfoLine.timeout": null,
             "dragenAlign.composeList.jobMemory": null,
-            "dragenAlign.composeList.listWritingScript": null,
+            "dragenAlign.composeList.listWritingScript": "/.mounts/labs/gsi/testdata/dragenSomatic/scripts/writeFile.py",
             "dragenAlign.composeList.modules": null,
             "dragenAlign.composeList.timeout": null,            
             "dragenAlign.runDragen.adapter1File": null, 
@@ -662,7 +662,7 @@
                         "type": "EXTERNAL"
                     },
                     "fastqR2": null,
-                    "readGroup": "ID:VENHPV_0260_02_LB02-01_240304_A00469_0642_BHWVM7DSX7_3_TCCGCGAA-GCCTCTAT LB:VENHPV_A00469_0642_WT PL:ILLUMINA PU:VENHPV_0260_02_LB02-01_240304_A00469_0642_BHWVM7DSX7_3_TCCGCGAA-GCCTCTAT SM:VENHPV_TEST CM:OICR"
+                    "readGroup": "ID:VENHPV_0260_02_LB02-01_240304_A00469_0642_BHWVM7DSX7_3_TCCGCGAA-GCCTCTAT LB:VENHPV_A00469_0642_WT PL:ILLUMINA PU:VENHPV_0260_02_LB02-01_240304_A00469_0642_BHWVM7DSX7_3_TCCGCGAA-GCCTCTAT SM:VENHPV_TEST CN:OICR"
                 },
                 {
                     "fastqR1": {
@@ -678,7 +678,7 @@
                         "type": "EXTERNAL"
                     },
                     "fastqR2": null,
-                    "readGroup": "ID:VENHPV_0260_02_LB02-01_240223_A00469_0636_BHWTVJDSX7_1_TCCGCGAA-GCCTCTAT LB:VENHPV_A00469_0636_WT PL:ILLUMINA PU:VENHPV_0260_02_LB02-01_240223_A00469_0636_BHWTVJDSX7_1_TCCGCGAA-GCCTCTAT SM:VENHPV_TEST CM:OICR"
+                    "readGroup": "ID:VENHPV_0260_02_LB02-01_240223_A00469_0636_BHWTVJDSX7_1_TCCGCGAA-GCCTCTAT LB:VENHPV_A00469_0636_WT PL:ILLUMINA PU:VENHPV_0260_02_LB02-01_240223_A00469_0636_BHWTVJDSX7_1_TCCGCGAA-GCCTCTAT SM:VENHPV_TEST CN:OICR"
                 }
             ],
             "dragenAlign.outputFileNamePrefix": "VENHPV_0260_02_LB02-01", 
@@ -687,10 +687,10 @@
             "dragenAlign.isRNA": true,
             "dragenAlign.extractInfoLine.jobMemory": null,
             "dragenAlign.extractInfoLine.modules": null,
-            "dragenAlign.extractInfoLine.parsingScript": null,
+            "dragenAlign.extractInfoLine.parsingScript": "/.mounts/labs/gsi/testdata/dragenSomatic/scripts/composeList.py",
             "dragenAlign.extractInfoLine.timeout": null,
             "dragenAlign.composeList.jobMemory": null,
-            "dragenAlign.composeList.listWritingScript": null,
+            "dragenAlign.composeList.listWritingScript": "/.mounts/labs/gsi/testdata/dragenSomatic/scripts/writeFile.py",
             "dragenAlign.composeList.modules": null,
             "dragenAlign.composeList.timeout": null,
             "dragenAlign.runDragen.adapter1File": null, 
@@ -775,7 +775,7 @@
                         },
                         "type": "EXTERNAL"
                     },
-                    "readGroup": "ID:VENHPV_0260_02_LB02-01_240304_A00469_0642_BHWVM7DSX7_3_TCCGCGAA-GCCTCTAT LB:VENHPV_A00469_0642_WT PL:ILLUMINA PU:VENHPV_0260_02_LB02-01_240304_A00469_0642_BHWVM7DSX7_3_TCCGCGAA-GCCTCTAT SM:VENHPV_TEST CM:OICR"
+                    "readGroup": "ID:VENHPV_0260_02_LB02-01_240304_A00469_0642_BHWVM7DSX7_3_TCCGCGAA-GCCTCTAT LB:VENHPV_A00469_0642_WT PL:ILLUMINA PU:VENHPV_0260_02_LB02-01_240304_A00469_0642_BHWVM7DSX7_3_TCCGCGAA-GCCTCTAT SM:VENHPV_TEST CN:OICR"
                 },
                 {
                     "fastqR1": {
@@ -802,7 +802,7 @@
                         },
                         "type": "EXTERNAL"
                     },
-                    "readGroup": "ID:VENHPV_0260_02_LB02-01_240223_A00469_0636_BHWTVJDSX7_1_TCCGCGAA-GCCTCTAT LB:VENHPV_A00469_0636_WT PL:ILLUMINA PU:VENHPV_0260_02_LB02-01_240223_A00469_0636_BHWTVJDSX7_1_TCCGCGAA-GCCTCTAT SM:VENHPV_TEST CM:OICR"
+                    "readGroup": "ID:VENHPV_0260_02_LB02-01_240223_A00469_0636_BHWTVJDSX7_1_TCCGCGAA-GCCTCTAT LB:VENHPV_A00469_0636_WT PL:ILLUMINA PU:VENHPV_0260_02_LB02-01_240223_A00469_0636_BHWTVJDSX7_1_TCCGCGAA-GCCTCTAT SM:VENHPV_TEST CN:OICR"
                 }
             ],
             "dragenAlign.outputFileNamePrefix": "VENHPV_0260_02_LB02-01", 
@@ -811,10 +811,10 @@
             "dragenAlign.isRNA": true,
             "dragenAlign.extractInfoLine.jobMemory": null,
             "dragenAlign.extractInfoLine.modules": null,
-            "dragenAlign.extractInfoLine.parsingScript": null,
+            "dragenAlign.extractInfoLine.parsingScript": "/.mounts/labs/gsi/testdata/dragenSomatic/scripts/composeList.py",
             "dragenAlign.extractInfoLine.timeout": null,
             "dragenAlign.composeList.jobMemory": null,
-            "dragenAlign.composeList.listWritingScript": null,
+            "dragenAlign.composeList.listWritingScript": "/.mounts/labs/gsi/testdata/dragenSomatic/scripts/writeFile.py",
             "dragenAlign.composeList.modules": null,
             "dragenAlign.composeList.timeout": null,            
             "dragenAlign.runDragen.adapter1File": null, 

From b7fdad3280eb83fa2583bf4a8852ebdd0079b46f Mon Sep 17 00:00:00 2001
From: pruzanov <pruzanov@oicr.on.ca>
Date: Thu, 13 Feb 2025 11:30:27 -0500
Subject: [PATCH 6/6] Switch to the latest version of dragen scripts

---
 README.md                     |  2 +-
 dragenAlign.wdl               |  8 ++++++--
 vidarrtest-regression.json.in | 36 +++++++++++++++++------------------
 3 files changed, 25 insertions(+), 21 deletions(-)

diff --git a/README.md b/README.md
index 47c2d93..d2e589a 100644
--- a/README.md
+++ b/README.md
@@ -7,7 +7,7 @@ This workflow will align sequence data (WG or WT) provided as fastq files to the
 ## Dependencies
 
 * [dragen](https://developer.illumina.com/dragen)
-
+* [gsi modules : dragen-scripts 0.3](https://gitlab.oicr.on.ca/ResearchIT/modulator)
 
 ## Usage
 
diff --git a/dragenAlign.wdl b/dragenAlign.wdl
index f1bea4d..6e40dd1 100755
--- a/dragenAlign.wdl
+++ b/dragenAlign.wdl
@@ -84,6 +84,10 @@ workflow dragenAlign {
       {
         name: "dragen",
         url: "https://developer.illumina.com/dragen"
+      },
+      {
+        name: "gsi modules : dragen-scripts/0.3",
+        url: "https://gitlab.oicr.on.ca/ResearchIT/modulator"
       }
     ]
     output_meta: {
@@ -124,7 +128,7 @@ task extractInfoLine {
        String parsingScript = "$DRAGEN_SCRIPTS_ROOT/bin/composeList.py"
        Int timeout = 4
        Int jobMemory = 4
-       String modules = "dragen-scripts/0.2"
+       String modules = "dragen-scripts/0.3"
    }
 
    parameter_meta {
@@ -166,7 +170,7 @@ task composeList {
       String outputFileName
       Int jobMemory = 4
       Int timeout = 4
-      String modules = "dragen-scripts/0.2"
+      String modules = "dragen-scripts/0.3"
    }
 
    parameter_meta {
diff --git a/vidarrtest-regression.json.in b/vidarrtest-regression.json.in
index 1f84780..cf5eb3f 100644
--- a/vidarrtest-regression.json.in
+++ b/vidarrtest-regression.json.in
@@ -36,10 +36,10 @@
             "dragenAlign.isRNA": false,
             "dragenAlign.extractInfoLine.jobMemory": null,
             "dragenAlign.extractInfoLine.modules": null,
-            "dragenAlign.extractInfoLine.parsingScript": "/.mounts/labs/gsi/testdata/dragenSomatic/scripts/composeList.py",
+            "dragenAlign.extractInfoLine.parsingScript": null,
             "dragenAlign.extractInfoLine.timeout": null,
             "dragenAlign.composeList.jobMemory": null,
-            "dragenAlign.composeList.listWritingScript": "/.mounts/labs/gsi/testdata/dragenSomatic/scripts/writeFile.py",
+            "dragenAlign.composeList.listWritingScript": null,
             "dragenAlign.composeList.modules": null,
             "dragenAlign.composeList.timeout": null,
             "dragenAlign.runDragen.adapter1File": null, 
@@ -133,10 +133,10 @@
             "dragenAlign.isRNA": false,
             "dragenAlign.extractInfoLine.jobMemory": null,
             "dragenAlign.extractInfoLine.modules": null,
-            "dragenAlign.extractInfoLine.parsingScript": "/.mounts/labs/gsi/testdata/dragenSomatic/scripts/composeList.py",
+            "dragenAlign.extractInfoLine.parsingScript": null,
             "dragenAlign.extractInfoLine.timeout": null,
             "dragenAlign.composeList.jobMemory": null,
-            "dragenAlign.composeList.listWritingScript": "/.mounts/labs/gsi/testdata/dragenSomatic/scripts/writeFile.py",
+            "dragenAlign.composeList.listWritingScript": null,
             "dragenAlign.composeList.modules": null,
             "dragenAlign.composeList.timeout": null,
             "dragenAlign.runDragen.adapter1File": null, 
@@ -219,10 +219,10 @@
             "dragenAlign.isRNA": false,
             "dragenAlign.extractInfoLine.jobMemory": null,
             "dragenAlign.extractInfoLine.modules": null,
-            "dragenAlign.extractInfoLine.parsingScript": "/.mounts/labs/gsi/testdata/dragenSomatic/scripts/composeList.py",
+            "dragenAlign.extractInfoLine.parsingScript": null,
             "dragenAlign.extractInfoLine.timeout": null,
             "dragenAlign.composeList.jobMemory": null,
-            "dragenAlign.composeList.listWritingScript": "/.mounts/labs/gsi/testdata/dragenSomatic/scripts/writeFile.py",
+            "dragenAlign.composeList.listWritingScript": null,
             "dragenAlign.composeList.modules": null,
             "dragenAlign.composeList.timeout": null,            
             "dragenAlign.runDragen.adapter1File": null, 
@@ -305,10 +305,10 @@
             "dragenAlign.isRNA": false,
             "dragenAlign.extractInfoLine.jobMemory": null,
             "dragenAlign.extractInfoLine.modules": null,
-            "dragenAlign.extractInfoLine.parsingScript": "/.mounts/labs/gsi/testdata/dragenSomatic/scripts/composeList.py",
+            "dragenAlign.extractInfoLine.parsingScript": null,
             "dragenAlign.extractInfoLine.timeout": null,
             "dragenAlign.composeList.jobMemory": null,
-            "dragenAlign.composeList.listWritingScript": "/.mounts/labs/gsi/testdata/dragenSomatic/scripts/writeFile.py",
+            "dragenAlign.composeList.listWritingScript": null,
             "dragenAlign.composeList.modules": null,
             "dragenAlign.composeList.timeout": null,            
             "dragenAlign.runDragen.adapter1File": null, 
@@ -402,10 +402,10 @@
             "dragenAlign.isRNA": true,
             "dragenAlign.extractInfoLine.jobMemory": null,
             "dragenAlign.extractInfoLine.modules": null,
-            "dragenAlign.extractInfoLine.parsingScript": "/.mounts/labs/gsi/testdata/dragenSomatic/scripts/composeList.py",
+            "dragenAlign.extractInfoLine.parsingScript": null,
             "dragenAlign.extractInfoLine.timeout": null,
             "dragenAlign.composeList.jobMemory": null,
-            "dragenAlign.composeList.listWritingScript": "/.mounts/labs/gsi/testdata/dragenSomatic/scripts/writeFile.py",
+            "dragenAlign.composeList.listWritingScript": null,
             "dragenAlign.composeList.modules": null,
             "dragenAlign.composeList.timeout": null,            
             "dragenAlign.runDragen.adapter1File": null, 
@@ -499,10 +499,10 @@
             "dragenAlign.isRNA": true,
             "dragenAlign.extractInfoLine.jobMemory": null,
             "dragenAlign.extractInfoLine.modules": null,
-            "dragenAlign.extractInfoLine.parsingScript": "/.mounts/labs/gsi/testdata/dragenSomatic/scripts/composeList.py",
+            "dragenAlign.extractInfoLine.parsingScript": null,
             "dragenAlign.extractInfoLine.timeout": null,
             "dragenAlign.composeList.jobMemory": null,
-            "dragenAlign.composeList.listWritingScript": "/.mounts/labs/gsi/testdata/dragenSomatic/scripts/writeFile.py",
+            "dragenAlign.composeList.listWritingScript": null,
             "dragenAlign.composeList.modules": null,
             "dragenAlign.composeList.timeout": null,            
             "dragenAlign.runDragen.adapter1File": null, 
@@ -585,10 +585,10 @@
             "dragenAlign.isRNA": true,
             "dragenAlign.extractInfoLine.jobMemory": null,
             "dragenAlign.extractInfoLine.modules": null,
-            "dragenAlign.extractInfoLine.parsingScript": "/.mounts/labs/gsi/testdata/dragenSomatic/scripts/composeList.py",
+            "dragenAlign.extractInfoLine.parsingScript": null,
             "dragenAlign.extractInfoLine.timeout": null,
             "dragenAlign.composeList.jobMemory": null,
-            "dragenAlign.composeList.listWritingScript": "/.mounts/labs/gsi/testdata/dragenSomatic/scripts/writeFile.py",
+            "dragenAlign.composeList.listWritingScript": null,
             "dragenAlign.composeList.modules": null,
             "dragenAlign.composeList.timeout": null,            
             "dragenAlign.runDragen.adapter1File": null, 
@@ -687,10 +687,10 @@
             "dragenAlign.isRNA": true,
             "dragenAlign.extractInfoLine.jobMemory": null,
             "dragenAlign.extractInfoLine.modules": null,
-            "dragenAlign.extractInfoLine.parsingScript": "/.mounts/labs/gsi/testdata/dragenSomatic/scripts/composeList.py",
+            "dragenAlign.extractInfoLine.parsingScript": null,
             "dragenAlign.extractInfoLine.timeout": null,
             "dragenAlign.composeList.jobMemory": null,
-            "dragenAlign.composeList.listWritingScript": "/.mounts/labs/gsi/testdata/dragenSomatic/scripts/writeFile.py",
+            "dragenAlign.composeList.listWritingScript": null,
             "dragenAlign.composeList.modules": null,
             "dragenAlign.composeList.timeout": null,
             "dragenAlign.runDragen.adapter1File": null, 
@@ -811,10 +811,10 @@
             "dragenAlign.isRNA": true,
             "dragenAlign.extractInfoLine.jobMemory": null,
             "dragenAlign.extractInfoLine.modules": null,
-            "dragenAlign.extractInfoLine.parsingScript": "/.mounts/labs/gsi/testdata/dragenSomatic/scripts/composeList.py",
+            "dragenAlign.extractInfoLine.parsingScript": null,
             "dragenAlign.extractInfoLine.timeout": null,
             "dragenAlign.composeList.jobMemory": null,
-            "dragenAlign.composeList.listWritingScript": "/.mounts/labs/gsi/testdata/dragenSomatic/scripts/writeFile.py",
+            "dragenAlign.composeList.listWritingScript": null,
             "dragenAlign.composeList.modules": null,
             "dragenAlign.composeList.timeout": null,            
             "dragenAlign.runDragen.adapter1File": null,