diff --git a/.dockstore.yml b/.dockstore.yml
index 7b5ff623..0c057d42 100644
--- a/.dockstore.yml
+++ b/.dockstore.yml
@@ -52,3 +52,15 @@ workflows:
       tags:
         - dragen-somatic-with-germline-pipeline/4.2.4
         - dragen-somatic-with-germline-pipeline/4.2.4__20240627054304
+  - name: rnasum-pipeline_1_0_0
+    subclass: CWL
+    primaryDescriptorPath: /.dockstore/rnasum-pipeline/1.0.0/rnasum-pipeline__1.0.0.packed.cwl.json
+    readMePath: 
+      /.github/catalogue/docs/workflows/rnasum-pipeline/1.0.0/rnasum-pipeline__1.0.0.md
+    authors:
+      - name: Alexis Lucattini
+        email: Alexis.Lucattini@umccr.org
+    filters:
+      tags:
+        - rnasum-pipeline/1.0.0
+        - rnasum-pipeline/1.0.0__20240627054519
diff --git a/.dockstore/rnasum-pipeline/1.0.0/rnasum-pipeline__1.0.0.packed.cwl.json b/.dockstore/rnasum-pipeline/1.0.0/rnasum-pipeline__1.0.0.packed.cwl.json
new file mode 100644
index 00000000..578b5903
--- /dev/null
+++ b/.dockstore/rnasum-pipeline/1.0.0/rnasum-pipeline__1.0.0.packed.cwl.json
@@ -0,0 +1,940 @@
+{
+  "$graph": [
+    {
+      "class": "CommandLineTool",
+      "id": "#rnasum__1.0.0.cwl",
+      "label": "rnasum v(1.0.0)",
+      "doc": "Documentation for rnasum v1.0.0\n",
+      "requirements": [
+        {
+          "class": "InlineJavascriptRequirement"
+        }
+      ],
+      "hints": [
+        {
+          "dockerPull": "ghcr.io/umccr/rnasum:1.0.0",
+          "class": "DockerRequirement"
+        },
+        {
+          "coresMin": 8,
+          "ramMin": 32000,
+          "class": "ResourceRequirement",
+          "https://platform.illumina.com/rdf/ica/resources:tier": "standard",
+          "https://platform.illumina.com/rdf/ica/resources:type": "standard",
+          "https://platform.illumina.com/rdf/ica/resources:size": "large"
+        }
+      ],
+      "baseCommand": [
+        "rnasum.R"
+      ],
+      "inputs": [
+        {
+          "label": "arriba directory",
+          "doc": "Location of the arriba outputs directory\n",
+          "type": [
+            "null",
+            "Directory"
+          ],
+          "inputBinding": {
+            "prefix": "--arriba_dir"
+          },
+          "id": "#rnasum__1.0.0.cwl/rnasum--1.0.0/arriba_dir"
+        },
+        {
+          "label": "arriba pdf",
+          "doc": "Location of the pdf output from arriba\n",
+          "type": [
+            "null",
+            "File"
+          ],
+          "inputBinding": {
+            "prefix": "--arriba_pdf"
+          },
+          "id": "#rnasum__1.0.0.cwl/rnasum--1.0.0/arriba_pdf"
+        },
+        {
+          "label": "arriba tsv",
+          "doc": "Location of the tsv output from arriba\n",
+          "type": [
+            "null",
+            "File"
+          ],
+          "inputBinding": {
+            "prefix": "--arriba_tsv"
+          },
+          "id": "#rnasum__1.0.0.cwl/rnasum--1.0.0/arriba_tsv"
+        },
+        {
+          "label": "batch rm",
+          "default": true,
+          "doc": "Remove batch-associated effects between datasets. Available options are: \"TRUE\" (default) and \"FALSE\"\n",
+          "type": [
+            "null",
+            "boolean"
+          ],
+          "inputBinding": {
+            "prefix": "--batch_rm"
+          },
+          "id": "#rnasum__1.0.0.cwl/rnasum--1.0.0/batch_rm"
+        },
+        {
+          "label": "cn gain",
+          "default": 95,
+          "doc": "CN threshold value to classify genes within gained regions.\n",
+          "type": [
+            "null",
+            "int"
+          ],
+          "inputBinding": {
+            "prefix": "--cn_gain"
+          },
+          "id": "#rnasum__1.0.0.cwl/rnasum--1.0.0/cn_gain"
+        },
+        {
+          "label": "cn loss",
+          "default": 5,
+          "doc": "CN threshold value to classify genes within lost regions.\n",
+          "type": [
+            "null",
+            "int"
+          ],
+          "inputBinding": {
+            "prefix": "--cn_loss"
+          },
+          "id": "#rnasum__1.0.0.cwl/rnasum--1.0.0/cn_loss"
+        },
+        {
+          "label": "dataset",
+          "default": "PANCAN",
+          "doc": "Reference dataset selection from https://github.com/umccr/RNAsum/blob/master/TCGA_projects_summary.md\n",
+          "type": "string",
+          "inputBinding": {
+            "prefix": "--dataset"
+          },
+          "id": "#rnasum__1.0.0.cwl/rnasum--1.0.0/dataset"
+        },
+        {
+          "label": "dataset name incl",
+          "doc": "Include dataset in the report and sample name.\n",
+          "type": [
+            "null",
+            "boolean"
+          ],
+          "inputBinding": {
+            "prefix": "--dataset_name_incl"
+          },
+          "id": "#rnasum__1.0.0.cwl/rnasum--1.0.0/dataset_name_incl"
+        },
+        {
+          "label": "dragen fusions",
+          "doc": "Location of the fusion output from Dragen RNA-seq pipeline\n",
+          "type": [
+            "null",
+            "File"
+          ],
+          "inputBinding": {
+            "prefix": "--dragen_fusions"
+          },
+          "id": "#rnasum__1.0.0.cwl/rnasum--1.0.0/dragen_fusions"
+        },
+        {
+          "label": "dragen mapping metrics",
+          "doc": "Location of the mapping metrics from Dragen RNA-seq pipeline\n",
+          "type": [
+            "null",
+            "File"
+          ],
+          "inputBinding": {
+            "prefix": "--dragen_mapping_metrics"
+          },
+          "id": "#rnasum__1.0.0.cwl/rnasum--1.0.0/dragen_mapping_metrics"
+        },
+        {
+          "label": "dragen transcriptome directory",
+          "doc": "Location of the results from Dragen RNA-seq pipeline\n",
+          "type": [
+            "null",
+            "Directory"
+          ],
+          "inputBinding": {
+            "prefix": "--dragen_wts_dir"
+          },
+          "id": "#rnasum__1.0.0.cwl/rnasum--1.0.0/dragen_wts_dir"
+        },
+        {
+          "label": "drugs",
+          "doc": "Include drug matching section in the report.\n",
+          "type": [
+            "null",
+            "boolean"
+          ],
+          "inputBinding": {
+            "prefix": "--drugs"
+          },
+          "id": "#rnasum__1.0.0.cwl/rnasum--1.0.0/drugs"
+        },
+        {
+          "label": "filter",
+          "default": true,
+          "doc": "Filtering out low expressed genes. Available options are: \"TRUE\" (default) and \"FALSE\"\n",
+          "type": [
+            "null",
+            "boolean"
+          ],
+          "inputBinding": {
+            "prefix": "--filter"
+          },
+          "id": "#rnasum__1.0.0.cwl/rnasum--1.0.0/filter"
+        },
+        {
+          "label": "immunogram",
+          "doc": "Include drug matching section in the report.\n",
+          "type": [
+            "null",
+            "boolean"
+          ],
+          "inputBinding": {
+            "prefix": "--immunogram"
+          },
+          "id": "#rnasum__1.0.0.cwl/rnasum--1.0.0/immunogram"
+        },
+        {
+          "label": "log",
+          "default": true,
+          "doc": "Log (base 2) transform data before normalisation. Available options are: \"TRUE\" (default) and \"FALSE\"\n",
+          "type": [
+            "null",
+            "boolean"
+          ],
+          "inputBinding": {
+            "prefix": "--log"
+          },
+          "id": "#rnasum__1.0.0.cwl/rnasum--1.0.0/log"
+        },
+        {
+          "label": "manta tsv",
+          "doc": "Location of the tsv output from manta\n",
+          "type": [
+            "null",
+            "File"
+          ],
+          "inputBinding": {
+            "prefix": "--manta_tsv"
+          },
+          "id": "#rnasum__1.0.0.cwl/rnasum--1.0.0/manta_tsv"
+        },
+        {
+          "label": "norm",
+          "default": "TMM",
+          "doc": "Normalisation method\n",
+          "type": [
+            "null",
+            "string"
+          ],
+          "inputBinding": {
+            "prefix": "--norm"
+          },
+          "id": "#rnasum__1.0.0.cwl/rnasum--1.0.0/norm"
+        },
+        {
+          "label": "PCGR splice vars",
+          "default": true,
+          "doc": "Include non-coding splice region variants reported in PCGR. Available options are: \"TRUE\" (default) and \"FALSE\"\n",
+          "type": [
+            "null",
+            "boolean"
+          ],
+          "inputBinding": {
+            "prefix": "--pcgr_splice_vars"
+          },
+          "id": "#rnasum__1.0.0.cwl/rnasum--1.0.0/pcgr_splice_vars"
+        },
+        {
+          "label": "pcgr tier",
+          "default": 4,
+          "doc": "Tier threshold for reporting variants reported in PCGR.\n",
+          "type": [
+            "null",
+            "int"
+          ],
+          "inputBinding": {
+            "prefix": "--pcgr_tier"
+          },
+          "id": "#rnasum__1.0.0.cwl/rnasum--1.0.0/pcgr_tier"
+        },
+        {
+          "label": "pcgr tiers tsv",
+          "doc": "Location of the tsv output from pcgr\n",
+          "type": [
+            "null",
+            "File"
+          ],
+          "inputBinding": {
+            "prefix": "--pcgr_tiers_tsv"
+          },
+          "id": "#rnasum__1.0.0.cwl/rnasum--1.0.0/pcgr_tiers_tsv"
+        },
+        {
+          "label": "project",
+          "doc": "Project name. This information is for annotation purposes only\n",
+          "type": [
+            "null",
+            "string"
+          ],
+          "inputBinding": {
+            "prefix": "--project"
+          },
+          "id": "#rnasum__1.0.0.cwl/rnasum--1.0.0/project"
+        },
+        {
+          "label": "purple gene tsv",
+          "doc": "Location of the tsv output from purple\n",
+          "type": [
+            "null",
+            "File"
+          ],
+          "inputBinding": {
+            "prefix": "--purple_gene_tsv"
+          },
+          "id": "#rnasum__1.0.0.cwl/rnasum--1.0.0/purple_gene_tsv"
+        },
+        {
+          "label": "report dir",
+          "doc": "Desired location for the outputs\n",
+          "type": "string",
+          "inputBinding": {
+            "prefix": "--report_dir",
+            "valueFrom": "$(runtime.outdir + \"/\" + self)"
+          },
+          "id": "#rnasum__1.0.0.cwl/rnasum--1.0.0/report_dir"
+        },
+        {
+          "label": "salmom",
+          "doc": "Location of the quantification output from salmon\n",
+          "type": [
+            "null",
+            "File"
+          ],
+          "inputBinding": {
+            "prefix": "--salmon"
+          },
+          "id": "#rnasum__1.0.0.cwl/rnasum--1.0.0/salmon"
+        },
+        {
+          "label": "sample name",
+          "doc": "Desired sample name to be presented in the report\n",
+          "type": "string",
+          "inputBinding": {
+            "prefix": "--sample_name"
+          },
+          "id": "#rnasum__1.0.0.cwl/rnasum--1.0.0/sample_name"
+        },
+        {
+          "label": "sample source",
+          "doc": "Source of investigated sample (e.g. fresh frozen tissue, organoid).\nThis information is for annotation purposes only\n",
+          "type": [
+            "null",
+            "string"
+          ],
+          "inputBinding": {
+            "prefix": "--sample_source"
+          },
+          "id": "#rnasum__1.0.0.cwl/rnasum--1.0.0/sample_source"
+        },
+        {
+          "label": "save tables",
+          "default": true,
+          "doc": "Save interactive summary tables as HTML. Available options are: \"TRUE\" (default) and \"FALSE\"\n",
+          "type": [
+            "null",
+            "boolean"
+          ],
+          "inputBinding": {
+            "prefix": "--save_tables"
+          },
+          "id": "#rnasum__1.0.0.cwl/rnasum--1.0.0/save_tables"
+        },
+        {
+          "label": "scaling",
+          "default": "gene-wise",
+          "doc": "Apply \"gene-wise\" (default) or \"group-wise\" data scaling\n",
+          "type": [
+            "null",
+            "string"
+          ],
+          "inputBinding": {
+            "prefix": "--scaling"
+          },
+          "id": "#rnasum__1.0.0.cwl/rnasum--1.0.0/scaling"
+        },
+        {
+          "label": "subject id",
+          "doc": "Subject ID. If umccrise output is specified (flag --umccrise) then Subject ID\nis extracted from there and used to overwrite this argument.\n",
+          "type": [
+            "null",
+            "string"
+          ],
+          "inputBinding": {
+            "prefix": "--subject_id"
+          },
+          "id": "#rnasum__1.0.0.cwl/rnasum--1.0.0/subject_id"
+        },
+        {
+          "label": "top genes",
+          "default": 5,
+          "doc": "The number of top ranked genes to be presented.\n",
+          "type": [
+            "null",
+            "int"
+          ],
+          "inputBinding": {
+            "prefix": "--top_genes"
+          },
+          "id": "#rnasum__1.0.0.cwl/rnasum--1.0.0/top_genes"
+        },
+        {
+          "label": "transform",
+          "default": "CPM",
+          "doc": "Transformation method to be used when converting read counts\n",
+          "type": [
+            "null",
+            "string"
+          ],
+          "inputBinding": {
+            "prefix": "--transform"
+          },
+          "id": "#rnasum__1.0.0.cwl/rnasum--1.0.0/transform"
+        },
+        {
+          "label": "umccrise directory",
+          "doc": "The umccrise output directory\n",
+          "type": [
+            "null",
+            "Directory"
+          ],
+          "inputBinding": {
+            "prefix": "--umccrise"
+          },
+          "id": "#rnasum__1.0.0.cwl/rnasum--1.0.0/umccrise"
+        }
+      ],
+      "successCodes": [
+        0
+      ],
+      "https://schema.org/author": {
+        "class": "https://schema.org/Person",
+        "https://schema.org/name": "Sehrish Kanwal",
+        "https://schema.org/email": "sehrish.kanwal@umccr.org"
+      },
+      "outputs": [
+        {
+          "label": "rnasum html",
+          "doc": "The HTML report output of RNAsum\n",
+          "type": "File",
+          "outputBinding": {
+            "glob": "$(inputs.report_dir)/$(inputs.sample_name).RNAseq_report.html"
+          },
+          "id": "#rnasum__1.0.0.cwl/rnasum--1.0.0/rnasum_html"
+        },
+        {
+          "label": "RNAsum output directory",
+          "doc": "Output directory containing all outputs of the RNAsum run",
+          "type": "Directory",
+          "outputBinding": {
+            "glob": "$(inputs.report_dir)"
+          },
+          "id": "#rnasum__1.0.0.cwl/rnasum--1.0.0/rnasum_output_directory"
+        }
+      ]
+    },
+    {
+      "class": "Workflow",
+      "id": "#main",
+      "label": "rnasum-pipeline v(1.0.0)",
+      "doc": "Documentation for rnasum-pipeline v1.0.0\n",
+      "requirements": [
+        {
+          "class": "InlineJavascriptRequirement"
+        },
+        {
+          "class": "MultipleInputFeatureRequirement"
+        },
+        {
+          "class": "ScatterFeatureRequirement"
+        },
+        {
+          "class": "StepInputExpressionRequirement"
+        }
+      ],
+      "inputs": [
+        {
+          "label": "arriba directory",
+          "doc": "Location of the arriba outputs directory\n",
+          "type": [
+            "null",
+            "Directory"
+          ],
+          "id": "#main/arriba_dir"
+        },
+        {
+          "label": "arriba pdf",
+          "doc": "Location of the pdf output from arriba\n",
+          "type": [
+            "null",
+            "File"
+          ],
+          "id": "#main/arriba_pdf"
+        },
+        {
+          "label": "arriba tsv",
+          "doc": "Location of the tsv output from arriba\n",
+          "type": [
+            "null",
+            "File"
+          ],
+          "id": "#main/arriba_tsv"
+        },
+        {
+          "label": "batch rm",
+          "default": true,
+          "doc": "Remove batch-associated effects between datasets. Available options are: \"TRUE\" (default) and \"FALSE\"\n",
+          "type": [
+            "null",
+            "boolean"
+          ],
+          "id": "#main/batch_rm"
+        },
+        {
+          "label": "cn gain",
+          "default": 95,
+          "doc": "CN threshold value to classify genes within gained regions.\n",
+          "type": [
+            "null",
+            "int"
+          ],
+          "id": "#main/cn_gain"
+        },
+        {
+          "label": "cn loss",
+          "default": 5,
+          "doc": "CN threshold value to classify genes within lost regions.\n",
+          "type": [
+            "null",
+            "int"
+          ],
+          "id": "#main/cn_loss"
+        },
+        {
+          "label": "dataset",
+          "default": "PANCAN",
+          "doc": "Reference dataset selection from https://github.com/umccr/RNAsum/blob/master/TCGA_projects_summary.md\n",
+          "type": "string",
+          "id": "#main/dataset"
+        },
+        {
+          "label": "dataset name incl",
+          "doc": "Include dataset in the report and sample name.\n",
+          "type": [
+            "null",
+            "boolean"
+          ],
+          "id": "#main/dataset_name_incl"
+        },
+        {
+          "label": "dragen fusions",
+          "doc": "Location of the fusion output from Dragen RNA-seq pipeline\n",
+          "type": [
+            "null",
+            "File"
+          ],
+          "id": "#main/dragen_fusions"
+        },
+        {
+          "label": "dragen mapping metrics",
+          "doc": "Location of the mapping metrics from Dragen RNA-seq pipeline\n",
+          "type": [
+            "null",
+            "File"
+          ],
+          "id": "#main/dragen_mapping_metrics"
+        },
+        {
+          "label": "dragen transcriptome directory",
+          "doc": "Location of the results from Dragen RNA-seq pipeline\n",
+          "type": [
+            "null",
+            "Directory"
+          ],
+          "id": "#main/dragen_wts_dir"
+        },
+        {
+          "label": "drugs",
+          "doc": "Include drug matching section in the report.\n",
+          "type": [
+            "null",
+            "boolean"
+          ],
+          "id": "#main/drugs"
+        },
+        {
+          "label": "filter",
+          "default": true,
+          "doc": "Filtering out low expressed genes. Available options are: \"TRUE\" (default) and \"FALSE\"\n",
+          "type": [
+            "null",
+            "boolean"
+          ],
+          "id": "#main/filter"
+        },
+        {
+          "label": "immunogram",
+          "doc": "Include drug matching section in the report.\n",
+          "type": [
+            "null",
+            "boolean"
+          ],
+          "id": "#main/immunogram"
+        },
+        {
+          "label": "log",
+          "default": true,
+          "doc": "Log (base 2) transform data before normalisation. Available options are: \"TRUE\" (default) and \"FALSE\"\n",
+          "type": [
+            "null",
+            "boolean"
+          ],
+          "id": "#main/log"
+        },
+        {
+          "label": "manta tsv",
+          "doc": "Location of the tsv output from manta\n",
+          "type": [
+            "null",
+            "File"
+          ],
+          "id": "#main/manta_tsv"
+        },
+        {
+          "label": "norm",
+          "default": "TMM",
+          "doc": "Normalisation method\n",
+          "type": [
+            "null",
+            "string"
+          ],
+          "id": "#main/norm"
+        },
+        {
+          "label": "PCGR splice vars",
+          "default": true,
+          "doc": "Include non-coding splice region variants reported in PCGR. Available options are: \"TRUE\" (default) and \"FALSE\"\n",
+          "type": [
+            "null",
+            "boolean"
+          ],
+          "id": "#main/pcgr_splice_vars"
+        },
+        {
+          "label": "pcgr tier",
+          "default": 4,
+          "doc": "Tier threshold for reporting variants reported in PCGR.\n",
+          "type": [
+            "null",
+            "int"
+          ],
+          "id": "#main/pcgr_tier"
+        },
+        {
+          "label": "pcgr tiers tsv",
+          "doc": "Location of the tsv output from pcgr\n",
+          "type": [
+            "null",
+            "File"
+          ],
+          "id": "#main/pcgr_tiers_tsv"
+        },
+        {
+          "label": "project",
+          "doc": "Project name. This information is for annotation purposes only\n",
+          "type": [
+            "null",
+            "string"
+          ],
+          "id": "#main/project"
+        },
+        {
+          "label": "purple gene tsv",
+          "doc": "Location of the tsv output from purple\n",
+          "type": [
+            "null",
+            "File"
+          ],
+          "id": "#main/purple_gene_tsv"
+        },
+        {
+          "label": "report dir",
+          "doc": "Desired location for the outputs\n",
+          "type": "string",
+          "id": "#main/report_dir"
+        },
+        {
+          "label": "salmom",
+          "doc": "Location of the quantification output from salmon\n",
+          "type": [
+            "null",
+            "File"
+          ],
+          "id": "#main/salmon"
+        },
+        {
+          "label": "sample name",
+          "doc": "Desired sample name to be presented in the report\n",
+          "type": "string",
+          "id": "#main/sample_name"
+        },
+        {
+          "label": "sample source",
+          "doc": "Source of investigated sample (e.g. fresh frozen tissue, organoid).\nThis information is for annotation purposes only\n",
+          "type": [
+            "null",
+            "string"
+          ],
+          "id": "#main/sample_source"
+        },
+        {
+          "label": "save tables",
+          "default": true,
+          "doc": "Save interactive summary tables as HTML. Available options are: \"TRUE\" (default) and \"FALSE\"\n",
+          "type": [
+            "null",
+            "boolean"
+          ],
+          "id": "#main/save_tables"
+        },
+        {
+          "label": "scaling",
+          "default": "gene-wise",
+          "doc": "Apply \"gene-wise\" (default) or \"group-wise\" data scaling\n",
+          "type": [
+            "null",
+            "string"
+          ],
+          "id": "#main/scaling"
+        },
+        {
+          "label": "subject id",
+          "doc": "Subject ID. If umccrise output is specified (flag --umccrise) then Subject ID\nis extracted from there and used to overwrite this argument.\n",
+          "type": [
+            "null",
+            "string"
+          ],
+          "id": "#main/subject_id"
+        },
+        {
+          "label": "top genes",
+          "default": 5,
+          "doc": "The number of top ranked genes to be presented.\n",
+          "type": [
+            "null",
+            "int"
+          ],
+          "id": "#main/top_genes"
+        },
+        {
+          "label": "transform",
+          "default": "CPM",
+          "doc": "Transformation method to be used when converting read counts\n",
+          "type": [
+            "null",
+            "string"
+          ],
+          "id": "#main/transform"
+        },
+        {
+          "label": "umccrise directory",
+          "doc": "The umccrise output directory\n",
+          "type": [
+            "null",
+            "Directory"
+          ],
+          "id": "#main/umccrise"
+        }
+      ],
+      "steps": [
+        {
+          "label": "run rnasum step",
+          "doc": "Run the rnasum pipeline\n",
+          "in": [
+            {
+              "source": "#main/arriba_dir",
+              "id": "#main/run_rnasum_step/arriba_dir"
+            },
+            {
+              "source": "#main/arriba_pdf",
+              "id": "#main/run_rnasum_step/arriba_pdf"
+            },
+            {
+              "source": "#main/arriba_tsv",
+              "id": "#main/run_rnasum_step/arriba_tsv"
+            },
+            {
+              "source": "#main/batch_rm",
+              "id": "#main/run_rnasum_step/batch_rm"
+            },
+            {
+              "source": "#main/cn_gain",
+              "id": "#main/run_rnasum_step/cn_gain"
+            },
+            {
+              "source": "#main/cn_loss",
+              "id": "#main/run_rnasum_step/cn_loss"
+            },
+            {
+              "source": "#main/dataset",
+              "id": "#main/run_rnasum_step/dataset"
+            },
+            {
+              "source": "#main/dataset_name_incl",
+              "id": "#main/run_rnasum_step/dataset_name_incl"
+            },
+            {
+              "source": "#main/dragen_fusions",
+              "id": "#main/run_rnasum_step/dragen_fusions"
+            },
+            {
+              "source": "#main/dragen_mapping_metrics",
+              "id": "#main/run_rnasum_step/dragen_mapping_metrics"
+            },
+            {
+              "source": "#main/dragen_wts_dir",
+              "id": "#main/run_rnasum_step/dragen_wts_dir"
+            },
+            {
+              "source": "#main/drugs",
+              "id": "#main/run_rnasum_step/drugs"
+            },
+            {
+              "source": "#main/filter",
+              "id": "#main/run_rnasum_step/filter"
+            },
+            {
+              "source": "#main/immunogram",
+              "id": "#main/run_rnasum_step/immunogram"
+            },
+            {
+              "source": "#main/log",
+              "id": "#main/run_rnasum_step/log"
+            },
+            {
+              "source": "#main/manta_tsv",
+              "id": "#main/run_rnasum_step/manta_tsv"
+            },
+            {
+              "source": "#main/norm",
+              "id": "#main/run_rnasum_step/norm"
+            },
+            {
+              "source": "#main/pcgr_splice_vars",
+              "id": "#main/run_rnasum_step/pcgr_splice_vars"
+            },
+            {
+              "source": "#main/pcgr_tier",
+              "id": "#main/run_rnasum_step/pcgr_tier"
+            },
+            {
+              "source": "#main/pcgr_tiers_tsv",
+              "id": "#main/run_rnasum_step/pcgr_tiers_tsv"
+            },
+            {
+              "source": "#main/project",
+              "id": "#main/run_rnasum_step/project"
+            },
+            {
+              "source": "#main/purple_gene_tsv",
+              "id": "#main/run_rnasum_step/purple_gene_tsv"
+            },
+            {
+              "source": "#main/report_dir",
+              "id": "#main/run_rnasum_step/report_dir"
+            },
+            {
+              "source": "#main/salmon",
+              "id": "#main/run_rnasum_step/salmon"
+            },
+            {
+              "source": "#main/sample_name",
+              "id": "#main/run_rnasum_step/sample_name"
+            },
+            {
+              "source": "#main/sample_source",
+              "id": "#main/run_rnasum_step/sample_source"
+            },
+            {
+              "source": "#main/save_tables",
+              "id": "#main/run_rnasum_step/save_tables"
+            },
+            {
+              "source": "#main/scaling",
+              "id": "#main/run_rnasum_step/scaling"
+            },
+            {
+              "source": "#main/subject_id",
+              "id": "#main/run_rnasum_step/subject_id"
+            },
+            {
+              "source": "#main/top_genes",
+              "id": "#main/run_rnasum_step/top_genes"
+            },
+            {
+              "source": "#main/transform",
+              "id": "#main/run_rnasum_step/transform"
+            },
+            {
+              "source": "#main/umccrise",
+              "id": "#main/run_rnasum_step/umccrise"
+            }
+          ],
+          "out": [
+            {
+              "id": "#main/run_rnasum_step/rnasum_output_directory"
+            },
+            {
+              "id": "#main/run_rnasum_step/rnasum_html"
+            }
+          ],
+          "run": "#rnasum__1.0.0.cwl",
+          "id": "#main/run_rnasum_step"
+        }
+      ],
+      "outputs": [
+        {
+          "label": "rnasum html",
+          "doc": "The HTML report output of RNAsum\n",
+          "type": "File",
+          "outputSource": "#main/run_rnasum_step/rnasum_html",
+          "id": "#main/rnasum_html"
+        },
+        {
+          "label": "RNAsum output directory",
+          "doc": "Output directory containing all outputs of the RNAsum run",
+          "type": "Directory",
+          "outputSource": "#main/run_rnasum_step/rnasum_output_directory",
+          "id": "#main/rnasum_output_directory"
+        }
+      ],
+      "https://schema.org/author": {
+        "class": "https://schema.org/Person",
+        "https://schema.org/name": "Alexis Lucattini",
+        "https://schema.org/email": "Alexis.Lucattini@umccr.org",
+        "https://schema.org/identifier": "https://orcid.org/0000-0001-9754-647X"
+      }
+    }
+  ],
+  "cwlVersion": "v1.1",
+  "$schemas": [
+    "https://schema.org/version/latest/schemaorg-current-http.rdf"
+  ],
+  "$namespaces": {
+    "s": "https://schema.org/"
+  }
+}
\ No newline at end of file
diff --git a/.github/releases/rnasum-pipeline__1.0.0__20240627054519/workflow.svg b/.github/releases/rnasum-pipeline__1.0.0__20240627054519/workflow.svg
new file mode 100644
index 00000000..4d9e8869
--- /dev/null
+++ b/.github/releases/rnasum-pipeline__1.0.0__20240627054519/workflow.svg
@@ -0,0 +1,437 @@
+<?xml version="1.0" encoding="UTF-8" standalone="no"?>
+<!DOCTYPE svg PUBLIC "-//W3C//DTD SVG 1.1//EN"
+ "http://www.w3.org/Graphics/SVG/1.1/DTD/svg11.dtd">
+<!-- Generated by graphviz version 2.43.0 (0)
+ -->
+<!-- Title: G Pages: 1 -->
+<svg width="3617pt" height="1051pt"
+ viewBox="0.00 0.00 3617.00 1051.00" xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink">
+<g id="graph0" class="graph" transform="scale(1 1) rotate(0) translate(4 1047)">
+<title>G</title>
+<polygon fill="#eeeeee" stroke="transparent" points="-4,4 -4,-1047 3613,-1047 3613,4 -4,4"/>
+<g id="clust1" class="cluster">
+<title>cluster_inputs</title>
+<polygon fill="#eeeeee" stroke="black" stroke-dasharray="5,2" points="8,-677.95 8,-1008.23 3601,-1008.23 3601,-677.95 8,-677.95"/>
+<text text-anchor="middle" x="3534.5" y="-685.75" font-family="Times,serif" font-size="14.00">Workflow Inputs</text>
+</g>
+<g id="clust2" class="cluster">
+<title>cluster_outputs</title>
+<polygon fill="#eeeeee" stroke="black" stroke-dasharray="5,2" points="1605,-34.77 1605,-365.05 1947,-365.05 1947,-34.77 1605,-34.77"/>
+<text text-anchor="middle" x="1874.5" y="-42.57" font-family="Times,serif" font-size="14.00">Workflow Outputs</text>
+</g>
+<!-- arriba_dir -->
+<g id="node1" class="node">
+<title>arriba_dir</title>
+<polygon fill="#94ddf4" stroke="black" points="3505.5,-874.77 3505.5,-910.77 3592.5,-910.77 3592.5,-874.77 3505.5,-874.77"/>
+<text text-anchor="middle" x="3549" y="-889.07" font-family="Times,serif" font-size="14.00">arriba_dir</text>
+</g>
+<!-- run_rnasum_step -->
+<g id="node33" class="node">
+<title>run_rnasum_step</title>
+<ellipse fill="none" stroke="black" cx="1798" cy="-564.77" rx="90.98" ry="18"/>
+<text text-anchor="middle" x="1798" y="-561.07" font-family="Times,serif" font-size="14.00">run_rnasum_step</text>
+</g>
+<!-- arriba_dir&#45;&gt;run_rnasum_step -->
+<g id="edge1" class="edge">
+<title>arriba_dir&#45;&gt;run_rnasum_step</title>
+<path fill="none" stroke="black" d="M3535.04,-874.67C3525.27,-863.89 3511.26,-850.67 3496,-843.27 3206.25,-702.75 2200.07,-602.08 1889.81,-573.82"/>
+<polygon fill="black" stroke="black" points="1889.79,-570.3 1879.51,-572.88 1889.15,-577.27 1889.79,-570.3"/>
+</g>
+<!-- arriba_pdf -->
+<g id="node2" class="node">
+<title>arriba_pdf</title>
+<polygon fill="#94ddf4" stroke="black" points="3397,-874.77 3397,-910.77 3487,-910.77 3487,-874.77 3397,-874.77"/>
+<text text-anchor="middle" x="3442" y="-889.07" font-family="Times,serif" font-size="14.00">arriba_pdf</text>
+</g>
+<!-- arriba_pdf&#45;&gt;run_rnasum_step -->
+<g id="edge2" class="edge">
+<title>arriba_pdf&#45;&gt;run_rnasum_step</title>
+<path fill="none" stroke="black" d="M3427.69,-874.72C3417.69,-863.98 3403.41,-850.76 3388,-843.27 3117.28,-711.73 2181.23,-605.54 1887.14,-574.78"/>
+<polygon fill="black" stroke="black" points="1887.27,-571.28 1876.96,-573.72 1886.54,-578.24 1887.27,-571.28"/>
+</g>
+<!-- arriba_tsv -->
+<g id="node3" class="node">
+<title>arriba_tsv</title>
+<polygon fill="#94ddf4" stroke="black" points="3289.5,-874.77 3289.5,-910.77 3378.5,-910.77 3378.5,-874.77 3289.5,-874.77"/>
+<text text-anchor="middle" x="3334" y="-889.07" font-family="Times,serif" font-size="14.00">arriba_tsv</text>
+</g>
+<!-- arriba_tsv&#45;&gt;run_rnasum_step -->
+<g id="edge3" class="edge">
+<title>arriba_tsv&#45;&gt;run_rnasum_step</title>
+<path fill="none" stroke="black" d="M3319.55,-874.31C3309.77,-863.67 3295.95,-850.73 3281,-843.27 2803.97,-605.11 2147.94,-570.24 1899.16,-565.95"/>
+<polygon fill="black" stroke="black" points="1899.11,-562.45 1889.05,-565.79 1899,-569.45 1899.11,-562.45"/>
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+<!-- batch_rm -->
+<g id="node4" class="node">
+<title>batch_rm</title>
+<polygon fill="#94ddf4" stroke="black" points="3188.5,-874.77 3188.5,-910.77 3271.5,-910.77 3271.5,-874.77 3188.5,-874.77"/>
+<text text-anchor="middle" x="3230" y="-889.07" font-family="Times,serif" font-size="14.00">batch_rm</text>
+</g>
+<!-- batch_rm&#45;&gt;run_rnasum_step -->
+<g id="edge4" class="edge">
+<title>batch_rm&#45;&gt;run_rnasum_step</title>
+<path fill="none" stroke="black" d="M3216.53,-874.36C3207.37,-863.74 3194.34,-850.81 3180,-843.27 2743.02,-613.45 2136.46,-573.52 1899.01,-566.91"/>
+<polygon fill="black" stroke="black" points="1898.76,-563.4 1888.67,-566.64 1898.57,-570.4 1898.76,-563.4"/>
+</g>
+<!-- cn_gain -->
+<g id="node5" class="node">
+<title>cn_gain</title>
+<polygon fill="#94ddf4" stroke="black" points="3099.5,-874.77 3099.5,-910.77 3170.5,-910.77 3170.5,-874.77 3099.5,-874.77"/>
+<text text-anchor="middle" x="3135" y="-889.07" font-family="Times,serif" font-size="14.00">cn_gain</text>
+</g>
+<!-- cn_gain&#45;&gt;run_rnasum_step -->
+<g id="edge5" class="edge">
+<title>cn_gain&#45;&gt;run_rnasum_step</title>
+<path fill="none" stroke="black" d="M3123.2,-874.41C3115.08,-863.81 3103.38,-850.88 3090,-843.27 2691.07,-616.34 2126.65,-574.62 1899,-567.22"/>
+<polygon fill="black" stroke="black" points="1898.85,-563.71 1888.74,-566.9 1898.63,-570.71 1898.85,-563.71"/>
+</g>
+<!-- cn_loss -->
+<g id="node6" class="node">
+<title>cn_loss</title>
+<polygon fill="#94ddf4" stroke="black" points="3013,-874.77 3013,-910.77 3081,-910.77 3081,-874.77 3013,-874.77"/>
+<text text-anchor="middle" x="3047" y="-889.07" font-family="Times,serif" font-size="14.00">cn_loss</text>
+</g>
+<!-- cn_loss&#45;&gt;run_rnasum_step -->
+<g id="edge6" class="edge">
+<title>cn_loss&#45;&gt;run_rnasum_step</title>
+<path fill="none" stroke="black" d="M3035.84,-874.47C3028.14,-863.89 3016.97,-850.96 3004,-843.27 2637.34,-625.57 2114.32,-578.63 1897.78,-568.53"/>
+<polygon fill="black" stroke="black" points="1897.85,-565.03 1887.7,-568.07 1897.53,-572.02 1897.85,-565.03"/>
+</g>
+<!-- dataset -->
+<g id="node7" class="node">
+<title>dataset</title>
+<polygon fill="#94ddf4" stroke="black" points="2925,-874.77 2925,-910.77 2995,-910.77 2995,-874.77 2925,-874.77"/>
+<text text-anchor="middle" x="2960" y="-889.07" font-family="Times,serif" font-size="14.00">dataset</text>
+</g>
+<!-- dataset&#45;&gt;run_rnasum_step -->
+<g id="edge7" class="edge">
+<title>dataset&#45;&gt;run_rnasum_step</title>
+<path fill="none" stroke="black" d="M2948.46,-874.55C2940.52,-864 2929.08,-851.08 2916,-843.27 2577.73,-641.12 2097.83,-585.75 1894.74,-570.98"/>
+<polygon fill="black" stroke="black" points="1894.92,-567.48 1884.69,-570.26 1894.42,-574.46 1894.92,-567.48"/>
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+<!-- dataset_name_incl -->
+<g id="node8" class="node">
+<title>dataset_name_incl</title>
+<polygon fill="#94ddf4" stroke="black" points="2759,-874.77 2759,-910.77 2907,-910.77 2907,-874.77 2759,-874.77"/>
+<text text-anchor="middle" x="2833" y="-889.07" font-family="Times,serif" font-size="14.00">dataset_name_incl</text>
+</g>
+<!-- dataset_name_incl&#45;&gt;run_rnasum_step -->
+<g id="edge8" class="edge">
+<title>dataset_name_incl&#45;&gt;run_rnasum_step</title>
+<path fill="none" stroke="black" d="M2807.32,-874.55C2791.35,-864.4 2770.08,-851.91 2750,-843.27 2433.42,-707.09 2029.83,-614.2 1868.89,-580.17"/>
+<polygon fill="black" stroke="black" points="1869.6,-576.74 1859.1,-578.11 1868.16,-583.59 1869.6,-576.74"/>
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+<!-- dragen_fusions -->
+<g id="node9" class="node">
+<title>dragen_fusions</title>
+<polygon fill="#94ddf4" stroke="black" points="2615.5,-874.77 2615.5,-910.77 2740.5,-910.77 2740.5,-874.77 2615.5,-874.77"/>
+<text text-anchor="middle" x="2678" y="-889.07" font-family="Times,serif" font-size="14.00">dragen_fusions</text>
+</g>
+<!-- dragen_fusions&#45;&gt;run_rnasum_step -->
+<g id="edge9" class="edge">
+<title>dragen_fusions&#45;&gt;run_rnasum_step</title>
+<path fill="none" stroke="black" d="M2656.25,-874.64C2642.66,-864.53 2624.48,-852.03 2607,-843.27 2343.88,-711.3 2003.14,-617.31 1862.78,-581.62"/>
+<polygon fill="black" stroke="black" points="1863.58,-578.21 1853.02,-579.15 1861.86,-585 1863.58,-578.21"/>
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+<!-- dragen_mapping_metrics -->
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+<title>dragen_mapping_metrics</title>
+<polygon fill="#94ddf4" stroke="black" points="2400.5,-874.77 2400.5,-910.77 2597.5,-910.77 2597.5,-874.77 2400.5,-874.77"/>
+<text text-anchor="middle" x="2499" y="-889.07" font-family="Times,serif" font-size="14.00">dragen_mapping_metrics</text>
+</g>
+<!-- dragen_mapping_metrics&#45;&gt;run_rnasum_step -->
+<g id="edge10" class="edge">
+<title>dragen_mapping_metrics&#45;&gt;run_rnasum_step</title>
+<path fill="none" stroke="black" d="M2462.3,-874.7C2343.3,-819.36 1968.46,-645.04 1840.95,-585.74"/>
+<polygon fill="black" stroke="black" points="1842.4,-582.55 1831.85,-581.51 1839.44,-588.9 1842.4,-582.55"/>
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+<!-- dragen_wts_dir -->
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+<title>dragen_wts_dir</title>
+<polygon fill="#94ddf4" stroke="black" points="2256,-874.77 2256,-910.77 2382,-910.77 2382,-874.77 2256,-874.77"/>
+<text text-anchor="middle" x="2319" y="-889.07" font-family="Times,serif" font-size="14.00">dragen_wts_dir</text>
+</g>
+<!-- dragen_wts_dir&#45;&gt;run_rnasum_step -->
+<g id="edge11" class="edge">
+<title>dragen_wts_dir&#45;&gt;run_rnasum_step</title>
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+<polygon fill="black" stroke="black" points="1835.43,-584.13 1825.05,-581.98 1831.82,-590.13 1835.43,-584.13"/>
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+<!-- drugs -->
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+<title>drugs</title>
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+<text text-anchor="middle" x="2209" y="-889.07" font-family="Times,serif" font-size="14.00">drugs</text>
+</g>
+<!-- drugs&#45;&gt;run_rnasum_step -->
+<g id="edge12" class="edge">
+<title>drugs&#45;&gt;run_rnasum_step</title>
+<path fill="none" stroke="black" d="M2197.35,-874.69C2190.3,-864.95 2180.8,-852.83 2171,-843.27 2059.02,-734.05 1902.82,-631.16 1833.53,-587.61"/>
+<polygon fill="black" stroke="black" points="1835.07,-584.44 1824.73,-582.11 1831.35,-590.38 1835.07,-584.44"/>
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+<title>filter</title>
+<polygon fill="#94ddf4" stroke="black" points="2108,-874.77 2108,-910.77 2162,-910.77 2162,-874.77 2108,-874.77"/>
+<text text-anchor="middle" x="2135" y="-889.07" font-family="Times,serif" font-size="14.00">filter</text>
+</g>
+<!-- filter&#45;&gt;run_rnasum_step -->
+<g id="edge13" class="edge">
+<title>filter&#45;&gt;run_rnasum_step</title>
+<path fill="none" stroke="black" d="M2123.41,-874.55C2116.69,-865 2107.83,-853.09 2099,-843.27 2007.02,-740.96 1882.05,-634.71 1826.57,-588.98"/>
+<polygon fill="black" stroke="black" points="1828.53,-586.06 1818.58,-582.42 1824.09,-591.47 1828.53,-586.06"/>
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+<!-- immunogram -->
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+<title>immunogram</title>
+<polygon fill="#94ddf4" stroke="black" points="1978,-874.77 1978,-910.77 2090,-910.77 2090,-874.77 1978,-874.77"/>
+<text text-anchor="middle" x="2034" y="-889.07" font-family="Times,serif" font-size="14.00">immunogram</text>
+</g>
+<!-- immunogram&#45;&gt;run_rnasum_step -->
+<g id="edge14" class="edge">
+<title>immunogram&#45;&gt;run_rnasum_step</title>
+<path fill="none" stroke="black" d="M2021.64,-874.7C1982.69,-820.9 1862.34,-654.64 1816.23,-590.95"/>
+<polygon fill="black" stroke="black" points="1818.93,-588.71 1810.23,-582.67 1813.26,-592.82 1818.93,-588.71"/>
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+<!-- log -->
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+<title>log</title>
+<polygon fill="#94ddf4" stroke="black" points="1906,-874.77 1906,-910.77 1960,-910.77 1960,-874.77 1906,-874.77"/>
+<text text-anchor="middle" x="1933" y="-889.07" font-family="Times,serif" font-size="14.00">log</text>
+</g>
+<!-- log&#45;&gt;run_rnasum_step -->
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+<title>pcgr_splice_vars&#45;&gt;run_rnasum_step</title>
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+<!-- pcgr_tier&#45;&gt;run_rnasum_step -->
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+<title>pcgr_tier&#45;&gt;run_rnasum_step</title>
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+<!-- pcgr_tiers_tsv -->
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+<!-- project&#45;&gt;run_rnasum_step -->
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+<!-- purple_gene_tsv -->
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+<!-- purple_gene_tsv&#45;&gt;run_rnasum_step -->
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+<title>purple_gene_tsv&#45;&gt;run_rnasum_step</title>
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+<!-- report_dir&#45;&gt;run_rnasum_step -->
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+<!-- salmon&#45;&gt;run_rnasum_step -->
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+<!-- sample_name -->
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+<title>sample_name</title>
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+<!-- sample_name&#45;&gt;run_rnasum_step -->
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+<title>sample_name&#45;&gt;run_rnasum_step</title>
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+<!-- sample_source&#45;&gt;run_rnasum_step -->
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+<!-- save_tables&#45;&gt;run_rnasum_step -->
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