diff --git a/.github/catalogue/docs/tools/dragen-somatic/4.2.4/dragen-somatic__4.2.4.md b/.github/catalogue/docs/tools/dragen-somatic/4.2.4/dragen-somatic__4.2.4.md
index 72446069..5d56b720 100644
--- a/.github/catalogue/docs/tools/dragen-somatic/4.2.4/dragen-somatic__4.2.4.md
+++ b/.github/catalogue/docs/tools/dragen-somatic/4.2.4/dragen-somatic__4.2.4.md
@@ -17,7 +17,7 @@ dragen-somatic 4.2.4 tool
 
   
 > ID: dragen-somatic--4.2.4  
-> md5sum: 833e6305bad43d281aec9ef3909e8e74
+> md5sum: 56c5a9a13a722e8593c4448039cba61d
 
 ### dragen-somatic v(4.2.4) documentation
   
@@ -1237,7 +1237,7 @@ Enables the multiallelic filter. The default is true.
 > ID: vc_enable_unequal_ntd
   
 **Optional:** `True`  
-**Type:** `['boolean', <cwl_utils.parser.cwl_v1_1.CommandInputEnumSchema object at 0x7f9ed06a1070>]`  
+**Type:** `['boolean', <cwl_utils.parser.cwl_v1_1.CommandInputEnumSchema object at 0x7f6f39b6ed50>]`  
 **Docs:**  
 Nucleotide (NTD) Error Bias Estimation is on by default and recommended as a replacement for the orientation bias filter.
 Both methods take account of strand-specific biases (systematic differences between F1R2 and F2R1 reads).
diff --git a/.github/catalogue/docs/tools/qualimap/2.2.2/qualimap__2.2.2.md b/.github/catalogue/docs/tools/qualimap/2.2.2/qualimap__2.2.2.md
index ccf7bfa3..19365059 100644
--- a/.github/catalogue/docs/tools/qualimap/2.2.2/qualimap__2.2.2.md
+++ b/.github/catalogue/docs/tools/qualimap/2.2.2/qualimap__2.2.2.md
@@ -17,7 +17,7 @@ qualimap 2.2.2 tool
 
   
 > ID: qualimap--2.2.2  
-> md5sum: f1abbae5449aa241845532350d577b55
+> md5sum: c6eae8729c871bc8bf5f3ae0ee64e0e4
 
 ### qualimap v(2.2.2) documentation
   
diff --git a/.github/catalogue/docs/workflows/dragen-somatic-pipeline/4.2.4/dragen-somatic-pipeline__4.2.4.md b/.github/catalogue/docs/workflows/dragen-somatic-pipeline/4.2.4/dragen-somatic-pipeline__4.2.4.md
index a4661e4a..e34bd260 100644
--- a/.github/catalogue/docs/workflows/dragen-somatic-pipeline/4.2.4/dragen-somatic-pipeline__4.2.4.md
+++ b/.github/catalogue/docs/workflows/dragen-somatic-pipeline/4.2.4/dragen-somatic-pipeline__4.2.4.md
@@ -19,7 +19,7 @@ dragen-somatic-pipeline 4.2.4 workflow
 
   
 > ID: dragen-somatic-pipeline--4.2.4  
-> md5sum: 6c7445d9a17ae6ffe6f411312383e87e
+> md5sum: d17f4493e61c1f6b0467067c6b1322dc
 
 ### dragen-somatic-pipeline v(4.2.4) documentation
   
@@ -1202,7 +1202,7 @@ Enables the multiallelic filter. The default is true.
 > ID: vc_enable_unequal_ntd
   
 **Optional:** `True`  
-**Type:** `['boolean', <cwl_utils.parser.cwl_v1_1.InputEnumSchema object at 0x7f097379ae10>]`  
+**Type:** `['boolean', <cwl_utils.parser.cwl_v1_1.InputEnumSchema object at 0x7eff40a2f2c0>]`  
 **Docs:**  
 Nucleotide (NTD) Error Bias Estimation is on by default and recommended as a replacement for the orientation bias filter.
 Both methods take account of strand-specific biases (systematic differences between F1R2 and F2R1 reads).
@@ -1660,7 +1660,7 @@ Bam file of the tumor sample
 
   
 **workflow name:** dragen-somatic-pipeline_prod-wf  
-**wfl version name:** 4.2.4--81f95bd  
+**wfl version name:** 4.2.4--a9cc9b5  
 
   
 
diff --git a/.github/catalogue/docs/workflows/dragen-somatic-with-germline-pipeline/4.2.4/dragen-somatic-with-germline-pipeline__4.2.4.md b/.github/catalogue/docs/workflows/dragen-somatic-with-germline-pipeline/4.2.4/dragen-somatic-with-germline-pipeline__4.2.4.md
index 44ef11ab..05aa378e 100644
--- a/.github/catalogue/docs/workflows/dragen-somatic-with-germline-pipeline/4.2.4/dragen-somatic-with-germline-pipeline__4.2.4.md
+++ b/.github/catalogue/docs/workflows/dragen-somatic-with-germline-pipeline/4.2.4/dragen-somatic-with-germline-pipeline__4.2.4.md
@@ -19,7 +19,7 @@ dragen-somatic-with-germline-pipeline 4.2.4 workflow
 
   
 > ID: dragen-somatic-with-germline-pipeline--4.2.4  
-> md5sum: d4b38cae611fe37681c02d03606ab3cd
+> md5sum: 2418c871a226483ee9bf79b9cbe66253
 
 ### dragen-somatic-with-germline-pipeline v(4.2.4) documentation
   
@@ -1483,7 +1483,7 @@ Enables the multiallelic filter. The default is true.
 > ID: vc_enable_unequal_ntd
   
 **Optional:** `True`  
-**Type:** `['boolean', <cwl_utils.parser.cwl_v1_1.InputEnumSchema object at 0x7f9813b124e0>]`  
+**Type:** `['boolean', <cwl_utils.parser.cwl_v1_1.InputEnumSchema object at 0x7f2edafa4ef0>]`  
 **Docs:**  
 Nucleotide (NTD) Error Bias Estimation is on by default and recommended as a replacement for the orientation bias filter.
 Both methods take account of strand-specific biases (systematic differences between F1R2 and F2R1 reads).
@@ -2029,7 +2029,7 @@ Bam file of the tumor sample
 
   
 **workflow name:** dragen-somatic-with-germline-pipeline_prod-wf  
-**wfl version name:** 4.2.4--81f95bd  
+**wfl version name:** 4.2.4--a9cc9b5  
 
   
 
diff --git a/.github/catalogue/docs/workflows/dragen-transcriptome-pipeline/3.9.3/dragen-transcriptome-pipeline__3.9.3.md b/.github/catalogue/docs/workflows/dragen-transcriptome-pipeline/3.9.3/dragen-transcriptome-pipeline__3.9.3.md
index c298401c..23ea2712 100644
--- a/.github/catalogue/docs/workflows/dragen-transcriptome-pipeline/3.9.3/dragen-transcriptome-pipeline__3.9.3.md
+++ b/.github/catalogue/docs/workflows/dragen-transcriptome-pipeline/3.9.3/dragen-transcriptome-pipeline__3.9.3.md
@@ -19,7 +19,7 @@ dragen-transcriptome-pipeline 3.9.3 workflow
 
   
 > ID: dragen-transcriptome-pipeline--3.9.3  
-> md5sum: b3855ac8040a148badc29bb04d92ba54
+> md5sum: f44f16964b77c3649db77f3230d0beef
 
 ### dragen-transcriptome-pipeline v(3.9.3) documentation
   
@@ -1124,7 +1124,7 @@ bash wfr.491f5fd1b5e74f6e87113d964675504e.launch.sh
 
   
 **workflow name:** dragen-transcriptome-pipeline_prod-wf  
-**wfl version name:** 3.9.3--0ac1f6a  
+**wfl version name:** 3.9.3--a9cc9b5  
 
   
 
diff --git a/.github/catalogue/docs/workflows/dragen-transcriptome-pipeline/4.0.3/dragen-transcriptome-pipeline__4.0.3.md b/.github/catalogue/docs/workflows/dragen-transcriptome-pipeline/4.0.3/dragen-transcriptome-pipeline__4.0.3.md
index b5d4dcdb..3ef579e5 100644
--- a/.github/catalogue/docs/workflows/dragen-transcriptome-pipeline/4.0.3/dragen-transcriptome-pipeline__4.0.3.md
+++ b/.github/catalogue/docs/workflows/dragen-transcriptome-pipeline/4.0.3/dragen-transcriptome-pipeline__4.0.3.md
@@ -19,7 +19,7 @@ dragen-transcriptome-pipeline 4.0.3 workflow
 
   
 > ID: dragen-transcriptome-pipeline--4.0.3  
-> md5sum: d67c5240620328cde6e35aae5d106a72
+> md5sum: a8e084fa69cfe37d9841e7a711905a92
 
 ### dragen-transcriptome-pipeline v(4.0.3) documentation
   
@@ -591,7 +591,7 @@ The output directory containing all transcriptome output files
 
   
 **workflow name:** dragen-transcriptome-pipeline_prod-wf  
-**wfl version name:** 4.0.3--0ac1f6a  
+**wfl version name:** 4.0.3--a9cc9b5  
 
   
 
diff --git a/.github/catalogue/docs/workflows/dragen-transcriptome-pipeline/4.2.4/dragen-transcriptome-pipeline__4.2.4.md b/.github/catalogue/docs/workflows/dragen-transcriptome-pipeline/4.2.4/dragen-transcriptome-pipeline__4.2.4.md
index 60a701d9..6bc6d82e 100644
--- a/.github/catalogue/docs/workflows/dragen-transcriptome-pipeline/4.2.4/dragen-transcriptome-pipeline__4.2.4.md
+++ b/.github/catalogue/docs/workflows/dragen-transcriptome-pipeline/4.2.4/dragen-transcriptome-pipeline__4.2.4.md
@@ -19,7 +19,7 @@ dragen-transcriptome-pipeline 4.2.4 workflow
 
   
 > ID: dragen-transcriptome-pipeline--4.2.4  
-> md5sum: b63aaf8d3b9fc4800cdd1fbd26a55772
+> md5sum: c142f00004a02ac7d7247c0767ee9ff2
 
 ### dragen-transcriptome-pipeline v(4.2.4) documentation
   
@@ -740,7 +740,7 @@ The output directory containing all transcriptome output files
 
   
 **workflow name:** dragen-transcriptome-pipeline_prod-wf  
-**wfl version name:** 4.2.4--0ac1f6a  
+**wfl version name:** 4.2.4--a9cc9b5  
 
   
 
diff --git a/.github/catalogue/docs/workflows/dragen-wts-qc-pipeline/3.9.3/dragen-wts-qc-pipeline__3.9.3.md b/.github/catalogue/docs/workflows/dragen-wts-qc-pipeline/3.9.3/dragen-wts-qc-pipeline__3.9.3.md
index 81847a8b..5c6d4c63 100644
--- a/.github/catalogue/docs/workflows/dragen-wts-qc-pipeline/3.9.3/dragen-wts-qc-pipeline__3.9.3.md
+++ b/.github/catalogue/docs/workflows/dragen-wts-qc-pipeline/3.9.3/dragen-wts-qc-pipeline__3.9.3.md
@@ -19,7 +19,7 @@ dragen-wts-qc-pipeline 3.9.3 workflow
 
   
 > ID: dragen-wts-qc-pipeline--3.9.3  
-> md5sum: 20cdbee2575c25ec84a6f9852a6b409c
+> md5sum: cea1b3bdcffd8af6374837267ae886ab
 
 ### dragen-wts-qc-pipeline v(3.9.3) documentation
   
diff --git a/.github/catalogue/docs/workflows/dragen-wts-qc-pipeline/4.0.3/dragen-wts-qc-pipeline__4.0.3.md b/.github/catalogue/docs/workflows/dragen-wts-qc-pipeline/4.0.3/dragen-wts-qc-pipeline__4.0.3.md
index d50c70da..1a49c1f7 100644
--- a/.github/catalogue/docs/workflows/dragen-wts-qc-pipeline/4.0.3/dragen-wts-qc-pipeline__4.0.3.md
+++ b/.github/catalogue/docs/workflows/dragen-wts-qc-pipeline/4.0.3/dragen-wts-qc-pipeline__4.0.3.md
@@ -19,7 +19,7 @@ dragen-wts-qc-pipeline 4.0.3 workflow
 
   
 > ID: dragen-wts-qc-pipeline--4.0.3  
-> md5sum: d80801b9105b2843d6c9d46881419942
+> md5sum: d70578e8f6acfbea4aa0862645d0985f
 
 ### dragen-wts-qc-pipeline v(4.0.3) documentation
   
diff --git a/.github/catalogue/docs/workflows/dragen-wts-qc-pipeline/4.2.4/dragen-wts-qc-pipeline__4.2.4.md b/.github/catalogue/docs/workflows/dragen-wts-qc-pipeline/4.2.4/dragen-wts-qc-pipeline__4.2.4.md
index 37afe9d0..2a599337 100644
--- a/.github/catalogue/docs/workflows/dragen-wts-qc-pipeline/4.2.4/dragen-wts-qc-pipeline__4.2.4.md
+++ b/.github/catalogue/docs/workflows/dragen-wts-qc-pipeline/4.2.4/dragen-wts-qc-pipeline__4.2.4.md
@@ -19,7 +19,7 @@ dragen-wts-qc-pipeline 4.2.4 workflow
 
   
 > ID: dragen-wts-qc-pipeline--4.2.4  
-> md5sum: d4939a3d60c5347d0be5149f325e262f
+> md5sum: f37412bb676a8ea2ebbdcf6bc24b62a9
 
 ### dragen-wts-qc-pipeline v(4.2.4) documentation
   
diff --git a/.github/catalogue/images/runs/workflows/dragen-transcriptome-pipeline/3.9.3/Dragen-3.9.3-PTC-test__wfr.f75bddad9d4740d3873fce5ceb782bc7.svg b/.github/catalogue/images/runs/workflows/dragen-transcriptome-pipeline/3.9.3/Dragen-3.9.3-PTC-test__wfr.f75bddad9d4740d3873fce5ceb782bc7.svg
index 809e2887..27ef2d78 100644
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+++ b/.github/catalogue/images/runs/workflows/dragen-transcriptome-pipeline/3.9.3/Dragen-3.9.3-PTC-test__wfr.f75bddad9d4740d3873fce5ceb782bc7.svg
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 <!-- repeat_genotype_specs&#45;&gt;run_dragen_somatic_step -->
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+<!-- fastq_list_rows&#45;&gt;run_dragen_somatic_step -->
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-<!-- sv_output_contigs&#45;&gt;run_dragen_germline_step -->
+<!-- sv_output_contigs&#45;&gt;run_dragen_somatic_step -->
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+<!-- sv_output_contigs&#45;&gt;run_dragen_germline_step -->
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-<!-- sv_region&#45;&gt;run_dragen_germline_step -->
+<!-- sv_region&#45;&gt;run_dragen_somatic_step -->
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-<!-- sv_region&#45;&gt;run_dragen_somatic_step -->
+<!-- sv_region&#45;&gt;run_dragen_germline_step -->
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-<!-- sv_se_overlap_pair_evidence&#45;&gt;run_dragen_germline_step -->
+<!-- sv_se_overlap_pair_evidence&#45;&gt;run_dragen_somatic_step -->
 <g id="edge96" class="edge">
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-<!-- sv_se_overlap_pair_evidence&#45;&gt;run_dragen_somatic_step -->
+<!-- sv_se_overlap_pair_evidence&#45;&gt;run_dragen_germline_step -->
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-<!-- sv_tin_contam_tolerance&#45;&gt;run_dragen_germline_step -->
+<!-- sv_tin_contam_tolerance&#45;&gt;run_dragen_somatic_step -->
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-<!-- sv_tin_contam_tolerance&#45;&gt;run_dragen_somatic_step -->
+<!-- sv_tin_contam_tolerance&#45;&gt;run_dragen_germline_step -->
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 <title>vc_base_qual_threshold</title>
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-<!-- vc_base_qual_threshold&#45;&gt;run_dragen_germline_step -->
+<!-- vc_base_qual_threshold&#45;&gt;run_dragen_somatic_step -->
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-<!-- vc_base_qual_threshold&#45;&gt;run_dragen_somatic_step -->
+<!-- vc_base_qual_threshold&#45;&gt;run_dragen_germline_step -->
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-<!-- vc_decoy_contigs&#45;&gt;run_dragen_germline_step -->
+<!-- vc_decoy_contigs&#45;&gt;run_dragen_somatic_step -->
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-<!-- vc_decoy_contigs&#45;&gt;run_dragen_somatic_step -->
+<!-- vc_decoy_contigs&#45;&gt;run_dragen_germline_step -->
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-<!-- vc_enable_baf&#45;&gt;run_dragen_germline_step -->
+<!-- vc_enable_baf&#45;&gt;run_dragen_somatic_step -->
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+<!-- vc_enable_baf&#45;&gt;run_dragen_germline_step -->
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index 30f54a5e..2ebaa418 100644
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+<title>dragen_qc_step&#45;&gt;multiqc_output_directory</title>
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diff --git a/config/project.yaml b/config/project.yaml
index b0693c8c..184b4815 100644
--- a/config/project.yaml
+++ b/config/project.yaml
@@ -383,7 +383,7 @@ projects:
           - name: 4.2.4
             path: 4.2.4/dragen-somatic__4.2.4.cwl
             ica_workflow_version_name: 4.2.4
-            modification_time: 2024-07-30T09:09:59UTC
+            modification_time: 2024-08-03T06:26:49UTC
             run_instances: []
       - name: custom-create-umccr-dragen-refdata-tarball-from-illumina-tar
         path: custom-create-umccr-dragen-refdata-tarball-from-illumina-tar
@@ -577,7 +577,7 @@ projects:
           - name: 2.2.2
             path: 2.2.2/qualimap__2.2.2.cwl
             ica_workflow_version_name: 2.2.2
-            modification_time: 2024-07-31T02:10:31UTC
+            modification_time: 2024-08-03T06:27:12UTC
             run_instances: []
       - name: map_resource_requirements
         path: map_resource_requirements
@@ -736,7 +736,7 @@ projects:
           - name: 4.2.4
             path: 4.2.4/dragen-somatic-pipeline__4.2.4.cwl
             ica_workflow_version_name: 4.2.4
-            modification_time: 2024-07-30T09:26:21UTC
+            modification_time: 2024-08-03T06:42:17UTC
             run_instances: []
       - name: bcl-conversion
         path: bcl-conversion
@@ -768,7 +768,7 @@ projects:
           - name: 3.9.3
             path: 3.9.3/dragen-transcriptome-pipeline__3.9.3.cwl
             ica_workflow_version_name: 3.9.3
-            modification_time: 2024-07-31T02:26:02UTC
+            modification_time: 2024-08-03T06:42:23UTC
             run_instances:
               - wfr.784173de5b4342b797f04259ebd04df6
               - wfr.f75bddad9d4740d3873fce5ceb782bc7
@@ -776,12 +776,12 @@ projects:
           - name: 4.0.3
             path: 4.0.3/dragen-transcriptome-pipeline__4.0.3.cwl
             ica_workflow_version_name: 4.0.3
-            modification_time: 2024-07-31T02:26:04UTC
+            modification_time: 2024-08-03T06:42:26UTC
             run_instances: []
           - name: 4.2.4
             path: 4.2.4/dragen-transcriptome-pipeline__4.2.4.cwl
             ica_workflow_version_name: 4.2.4
-            modification_time: 2024-07-31T02:26:07UTC
+            modification_time: 2024-08-03T06:42:28UTC
             run_instances: []
       - name: dragen-alignment-pipeline
         path: dragen-alignment-pipeline
@@ -957,17 +957,17 @@ projects:
           - name: 3.9.3
             path: 3.9.3/dragen-wts-qc-pipeline__3.9.3.cwl
             ica_workflow_version_name: 3.9.3
-            modification_time: 2024-07-31T02:26:38UTC
+            modification_time: 2024-08-03T06:42:58UTC
             run_instances: []
           - name: 4.0.3
             path: 4.0.3/dragen-wts-qc-pipeline__4.0.3.cwl
             ica_workflow_version_name: 4.0.3
-            modification_time: 2024-07-31T02:26:40UTC
+            modification_time: 2024-08-03T06:43:01UTC
             run_instances: []
           - name: 4.2.4
             path: 4.2.4/dragen-wts-qc-pipeline__4.2.4.cwl
             ica_workflow_version_name: 4.2.4
-            modification_time: 2024-07-31T02:26:42UTC
+            modification_time: 2024-08-03T06:43:03UTC
             run_instances: []
       - name: bclconvert-with-qc-pipeline
         path: bclconvert-with-qc-pipeline
@@ -1027,7 +1027,7 @@ projects:
           - name: 4.2.4
             path: 4.2.4/dragen-somatic-with-germline-pipeline__4.2.4.cwl
             ica_workflow_version_name: 4.2.4
-            modification_time: 2024-07-30T09:27:41UTC
+            modification_time: 2024-08-03T06:43:14UTC
             run_instances: []
       - name: illumina-interop-qc
         path: illumina-interop-qc
@@ -1910,6 +1910,11 @@ projects:
             ica_workflow_version_name: 4.2.4--81f95bd
             modification_time: 2024-07-30T23:30:36UTC
             run_instances: []
+          - name: 4.2.4
+            path: 4.2.4/dragen-somatic-pipeline__4.2.4.cwl
+            ica_workflow_version_name: 4.2.4--a9cc9b5
+            modification_time: 2024-08-03T06:43:26UTC
+            run_instances: []
       - name: bcl-conversion
         path: bcl-conversion
         ica_workflow_name: bcl-conversion_prod-wf
@@ -2425,6 +2430,21 @@ projects:
             ica_workflow_version_name: 4.2.4--0ac1f6a
             modification_time: 2024-07-31T02:27:17UTC
             run_instances: []
+          - name: 3.9.3
+            path: 3.9.3/dragen-transcriptome-pipeline__3.9.3.cwl
+            ica_workflow_version_name: 3.9.3--a9cc9b5
+            modification_time: 2024-08-03T06:43:35UTC
+            run_instances: []
+          - name: 4.0.3
+            path: 4.0.3/dragen-transcriptome-pipeline__4.0.3.cwl
+            ica_workflow_version_name: 4.0.3--a9cc9b5
+            modification_time: 2024-08-03T06:43:39UTC
+            run_instances: []
+          - name: 4.2.4
+            path: 4.2.4/dragen-transcriptome-pipeline__4.2.4.cwl
+            ica_workflow_version_name: 4.2.4--a9cc9b5
+            modification_time: 2024-08-03T06:43:42UTC
+            run_instances: []
       - name: dragen-germline-pipeline
         path: dragen-germline-pipeline
         ica_workflow_name: dragen-germline-pipeline_prod-wf
@@ -3730,6 +3750,11 @@ projects:
             ica_workflow_version_name: 4.2.4--81f95bd
             modification_time: 2024-07-30T23:31:16UTC
             run_instances: []
+          - name: 4.2.4
+            path: 4.2.4/dragen-somatic-with-germline-pipeline__4.2.4.cwl
+            ica_workflow_version_name: 4.2.4--a9cc9b5
+            modification_time: 2024-08-03T06:44:06UTC
+            run_instances: []
       - name: dragen-alignment-pipeline
         path: dragen-alignment-pipeline
         ica_workflow_name: dragen-alignment-pipeline_prod-wf
diff --git a/config/tool.yaml b/config/tool.yaml
index 41488bbe..688a9dc8 100644
--- a/config/tool.yaml
+++ b/config/tool.yaml
@@ -168,7 +168,7 @@ tools:
         md5sum: 8a976bbc29b602eca4a36fcde5a51e6d
       - name: 4.2.4
         path: 4.2.4/dragen-somatic__4.2.4.cwl
-        md5sum: 833e6305bad43d281aec9ef3909e8e74
+        md5sum: 56c5a9a13a722e8593c4448039cba61d
     categories: []
   - name: dragen-transcriptome
     path: dragen-transcriptome
@@ -500,7 +500,7 @@ tools:
     versions:
       - name: 2.2.2
         path: 2.2.2/qualimap__2.2.2.cwl
-        md5sum: f1abbae5449aa241845532350d577b55
+        md5sum: c6eae8729c871bc8bf5f3ae0ee64e0e4
     categories: []
   - name: map_resource_requirements
     path: map_resource_requirements
diff --git a/config/workflow.yaml b/config/workflow.yaml
index 197f542b..7bd9b622 100644
--- a/config/workflow.yaml
+++ b/config/workflow.yaml
@@ -70,7 +70,7 @@ workflows:
         md5sum: 1910e7cd9c56b6785b6afe977e72e3b6
       - name: 4.2.4
         path: 4.2.4/dragen-somatic-pipeline__4.2.4.cwl
-        md5sum: 6c7445d9a17ae6ffe6f411312383e87e
+        md5sum: d17f4493e61c1f6b0467067c6b1322dc
     categories:
       - dragen
       - variant-calling
@@ -85,13 +85,13 @@ workflows:
         md5sum: a9f114ec0ddf31225eea520fab8d2ce6
       - name: 3.9.3
         path: 3.9.3/dragen-transcriptome-pipeline__3.9.3.cwl
-        md5sum: b3855ac8040a148badc29bb04d92ba54
+        md5sum: f44f16964b77c3649db77f3230d0beef
       - name: 4.0.3
         path: 4.0.3/dragen-transcriptome-pipeline__4.0.3.cwl
-        md5sum: d67c5240620328cde6e35aae5d106a72
+        md5sum: a8e084fa69cfe37d9841e7a711905a92
       - name: 4.2.4
         path: 4.2.4/dragen-transcriptome-pipeline__4.2.4.cwl
-        md5sum: b63aaf8d3b9fc4800cdd1fbd26a55772
+        md5sum: c142f00004a02ac7d7247c0767ee9ff2
     categories: []
   - name: dragen-alignment-pipeline
     path: dragen-alignment-pipeline
@@ -210,13 +210,13 @@ workflows:
     versions:
       - name: 3.9.3
         path: 3.9.3/dragen-wts-qc-pipeline__3.9.3.cwl
-        md5sum: 20cdbee2575c25ec84a6f9852a6b409c
+        md5sum: cea1b3bdcffd8af6374837267ae886ab
       - name: 4.0.3
         path: 4.0.3/dragen-wts-qc-pipeline__4.0.3.cwl
-        md5sum: d80801b9105b2843d6c9d46881419942
+        md5sum: d70578e8f6acfbea4aa0862645d0985f
       - name: 4.2.4
         path: 4.2.4/dragen-wts-qc-pipeline__4.2.4.cwl
-        md5sum: d4939a3d60c5347d0be5149f325e262f
+        md5sum: f37412bb676a8ea2ebbdcf6bc24b62a9
     categories: []
   - name: tabix-workflow
     path: tabix-workflow
@@ -264,7 +264,7 @@ workflows:
         md5sum: 30b4219906569c20b5d8d4a7ec79ee67
       - name: 4.2.4
         path: 4.2.4/dragen-somatic-with-germline-pipeline__4.2.4.cwl
-        md5sum: d4b38cae611fe37681c02d03606ab3cd
+        md5sum: 2418c871a226483ee9bf79b9cbe66253
     categories: []
   - name: illumina-interop-qc
     path: illumina-interop-qc
diff --git a/tools/dragen-somatic/4.2.4/dragen-somatic__4.2.4.cwl b/tools/dragen-somatic/4.2.4/dragen-somatic__4.2.4.cwl
index c46fb036..1a8f3246 100644
--- a/tools/dragen-somatic/4.2.4/dragen-somatic__4.2.4.cwl
+++ b/tools/dragen-somatic/4.2.4/dragen-somatic__4.2.4.cwl
@@ -41,8 +41,8 @@ requirements:
   ResourceRequirement:
     tmpdirMin: |
       ${
-        /* 1 Tb */
-        return Math.pow(2, 20); 
+        /* 2 Tb */
+        return Math.pow(2, 21); 
       }
   SchemaDefRequirement:
     types:
diff --git a/tools/qualimap/2.2.2/qualimap__2.2.2.cwl b/tools/qualimap/2.2.2/qualimap__2.2.2.cwl
index 991d2e29..e66446fb 100644
--- a/tools/qualimap/2.2.2/qualimap__2.2.2.cwl
+++ b/tools/qualimap/2.2.2/qualimap__2.2.2.cwl
@@ -50,8 +50,13 @@ requirements:
           set -euo pipefail
           
           # Set java opts
+          # Use /scratch if the directory is available
           # Note :- means if TMPDIR is set to "" or undefined use /tmp
-          export JAVA_OPTS="-Djava.io.tmpdir=\${TMPDIR:-/tmp}"
+          if [[ -d "/scratch" ]]; then
+            export JAVA_OPTS="-Djava.io.tmpdir=/scratch"
+          else
+            export JAVA_OPTS="-Djava.io.tmpdir=\${TMPDIR:-/tmp}"
+          fi
           
           # Run qualimap
           qualimap rnaseq --paired "\${@}"