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nf-core · Mar 14, 2024 · 3196720 · 3196720
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diff --git a/README.md b/README.md
@@ -41,16 +41,16 @@ website](https://nf-co.re/oncoanalyser/results).
 
 The following processes and tools can be run with oncoanalyser:
 
-* SNV and MNV calling (`SAGE`, `PAVE`)
-* SV calling (`SV Prep`, `GRIDSS`, `GRIPSS`, `PURPLE`, `LINX`)
-* CNV calling (`AMBER`, `COBALT`, `PURPLE`)
-* Transcript analysis (`Isofox`)
-* Oncoviral detection (`VIRUSBreakend`, `Virus Interpreter`)
-* HLA calling (`LILAC`)
-* HRD status prediction (`CHORD`)
-* Mutational signature fitting (`Sigs`)
-* Tissue of origin prediction (`CUPPA`)
-* Report generation (`ORANGE`, `linxreport`)
+- SNV and MNV calling (`SAGE`, `PAVE`)
+- SV calling (`SV Prep`, `GRIDSS`, `GRIPSS`, `PURPLE`, `LINX`)
+- CNV calling (`AMBER`, `COBALT`, `PURPLE`)
+- Transcript analysis (`Isofox`)
+- Oncoviral detection (`VIRUSBreakend`, `Virus Interpreter`)
+- HLA calling (`LILAC`)
+- HRD status prediction (`CHORD`)
+- Mutational signature fitting (`Sigs`)
+- Tissue of origin prediction (`CUPPA`)
+- Report generation (`ORANGE`, `linxreport`)
 
 ## Usage
 
@@ -109,9 +109,9 @@ of Melbourne Centre for Cancer Research](https://mdhs.unimelb.edu.au/centre-for-
 We thank the following organisations and people for their extensive assistance in the development of this pipeline,
 listed in alphabetical order:
 
-* [Hartwig Medical Foundation
+- [Hartwig Medical Foundation
   Australia](https://www.hartwigmedicalfoundation.nl/en/partnerships/hartwig-medical-foundation-australia/)
-* Oliver Hofmann
+- Oliver Hofmann
 
 ## Contributions and Support
 

diff --git a/modules/local/pave/germline/meta.yml b/modules/local/pave/germline/meta.yml
@@ -11,7 +11,7 @@ tools:
       description: Annotates small variant VCF with gene, transcript coding and protein effects.
       homepage: https://github.com/hartwigmedical/hmftools/tree/master/pave
       documentation: https://github.com/hartwigmedical/hmftools/tree/master/pave
-      licence: ['GPL v3']
+      licence: ["GPL v3"]
 input:
   - meta:
       type: map

diff --git a/modules/local/pave/somatic/meta.yml b/modules/local/pave/somatic/meta.yml
@@ -12,7 +12,7 @@ tools:
       description: Annotates small variant VCF with gene, transcript coding and protein effects.
       homepage: https://github.com/hartwigmedical/hmftools/tree/master/pave
       documentation: https://github.com/hartwigmedical/hmftools/tree/master/pave
-      licence: ['GPL v3']
+      licence: ["GPL v3"]
 input:
   - meta:
       type: map

diff --git a/modules/local/sage/append/meta.yml b/modules/local/sage/append/meta.yml
@@ -9,7 +9,7 @@ tools:
       description: A precise and highly sensitive somatic SNV, MNV and small INDEL caller.
       homepage: https://github.com/hartwigmedical/hmftools/tree/master/sage
       documentation: https://github.com/hartwigmedical/hmftools/tree/master/sage
-      licence: ['GPL v3']
+      licence: ["GPL v3"]
 input:
   - meta:
       type: map

diff --git a/modules/local/sage/germline/meta.yml b/modules/local/sage/germline/meta.yml
@@ -10,7 +10,7 @@ tools:
       description: A precise and highly sensitive somatic SNV, MNV and small INDEL caller.
       homepage: https://github.com/hartwigmedical/hmftools/tree/master/sage
       documentation: https://github.com/hartwigmedical/hmftools/tree/master/sage
-      licence: ['GPL v3']
+      licence: ["GPL v3"]
 input:
   - meta:
       type: map

diff --git a/modules/local/sage/somatic/meta.yml b/modules/local/sage/somatic/meta.yml
@@ -10,7 +10,7 @@ tools:
       description: A precise and highly sensitive somatic SNV, MNV and small INDEL caller.
       homepage: https://github.com/hartwigmedical/hmftools/tree/master/sage
       documentation: https://github.com/hartwigmedical/hmftools/tree/master/sage
-      licence: ['GPL v3']
+      licence: ["GPL v3"]
 input:
   - meta:
       type: map

diff --git a/nextflow_schema.json b/nextflow_schema.json
@@ -10,10 +10,7 @@
             "type": "object",
             "fa_icon": "fas fa-terminal",
             "description": "Define where the pipeline should find input data and save output data.",
-            "required": [
-                "input",
-                "outdir"
-            ],
+            "required": ["input", "outdir"],
             "properties": {
                 "input": {
                     "type": "string",
@@ -332,14 +329,7 @@
                     "description": "Method used to save pipeline results to output directory.",
                     "help_text": "The Nextflow `publishDir` option specifies which intermediate files should be saved to the output directory. This option tells the pipeline what method should be used to move these files. See [Nextflow docs](https://www.nextflow.io/docs/latest/process.html#publishdir) for details.",
                     "fa_icon": "fas fa-copy",
-                    "enum": [
-                        "symlink",
-                        "rellink",
-                        "link",
-                        "copy",
-                        "copyNoFollow",
-                        "move"
-                    ],
+                    "enum": ["symlink", "rellink", "link", "copy", "copyNoFollow", "move"],
                     "hidden": true
                 },
                 "email_on_fail": {