diff --git a/nextflow_schema.json b/nextflow_schema.json
index ee0a623e..e6726202 100644
--- a/nextflow_schema.json
+++ b/nextflow_schema.json
@@ -5,6 +5,81 @@
     "description": "Nextflow rnafusion analysis pipeline, part of the nf-core community.",
     "type": "object",
     "$defs": {
+        "input_output_options": {
+            "title": "Input/output options",
+            "type": "object",
+            "fa_icon": "fas fa-terminal",
+            "description": "Define where the pipeline should find input data and save output data.",
+            "required": [
+                "outdir",
+                "tools",
+                "genomes_base"
+            ],
+            "properties": {
+                "input": {
+                    "type": "string",
+                    "format": "file-path",
+                    "mimetype": "text/csv",
+                    "schema": "assets/schema_input.json",
+                    "exists": true,
+                    "pattern": "^\\S+\\.(csv|yaml|yml|json)$",
+                    "description": "Path to samplesheet file containing information about the samples in the experiment.",
+                    "help_text": "You will need to create a design file with information about the samples in your experiment before running the pipeline. Use this parameter to specify its location. It has to be a comma-separated file with 3 columns, and a header row. See [usage docs](https://nf-co.re/rnafusion/usage#samplesheet-input).",
+                    "fa_icon": "fas fa-file-csv"
+                },
+                "outdir": {
+                    "type": "string",
+                    "format": "directory-path",
+                    "description": "The output directory where the results will be saved. You have to use absolute paths to storage on Cloud infrastructure.",
+                    "fa_icon": "fas fa-folder-open"
+                },
+                "tools": {
+                    "type": "string",
+                    "description": "Comma-delimited list of tools to run",
+                    "fa_icon": "far fa-file-code",
+                    "help_text": "Comma-delimited list of tools to run.",
+                    "pattern": "^((arriba|ctatsplicing|fusioncatcher|starfusion|stringtie|fusionreport|fastp|salmon|fusioninspector|all)?,?)*(?<!,)$"
+                },
+                "tools_cutoff": {
+                    "type": "integer",
+                    "minimum": 1,
+                    "default": 1,
+                    "fa_icon": "far fa-file-code",
+                    "description": "Discard fusions identified by less than INT tools"
+                },
+                "arriba_fusions": {
+                    "type": "string",
+                    "format": "file-path",
+                    "exists": true,
+                    "pattern": "\\S+\\.tsv$",
+                    "fa_icon": "far fa-file-code",
+                    "description": "Path to arriba output"
+                },
+                "fusioncatcher_fusions": {
+                    "type": "string",
+                    "format": "file-path",
+                    "exists": true,
+                    "pattern": "\\S+\\.txt$",
+                    "fa_icon": "far fa-file-code",
+                    "description": "Path to fusioncatcher output"
+                },
+                "starfusion_fusions": {
+                    "type": "string",
+                    "format": "file-path",
+                    "exists": true,
+                    "pattern": "\\S+\\.tsv$",
+                    "fa_icon": "far fa-file-code",
+                    "description": "Path to starfusion output"
+                },
+                "fusioncatcher_limitSjdbInsertNsj": {
+                    "type": "integer",
+                    "fa_icon": "far fa-file-code",
+                    "description": "Use limitSjdbInsertNsj with int for fusioncatcher",
+                    "default": 2000000,
+                    "minimum": 1
+                }
+            }
+        },
         "skip_steps": {
             "title": "Skip steps",
             "type": "object",
@@ -29,56 +104,110 @@
             },
             "fa_icon": "fas fa-fast-forward"
         },
-        "input_output_options": {
-            "title": "Input/output options",
+        "read_trimming_options": {
+            "title": "Read trimming options",
             "type": "object",
-            "fa_icon": "fas fa-terminal",
-            "description": "Define where the pipeline should find input data and save output data.",
-            "required": ["outdir", "genomes_base", "tools"],
+            "fa_icon": "fas fa-cut",
+            "description": "Options to adjust read trimming criteria.",
             "properties": {
-                "input": {
+                "trim_tail": {
+                    "type": "integer",
+                    "description": "The amount of bases to trim at the tail of each read, none will be trimmed by default",
+                    "minimum": 0,
+                    "fa_icon": "fas fa-cut"
+                },
+                "trim_tail_fusioncatcher": {
+                    "type": "integer",
+                    "description": "The amount of bases to trim at the tail of each read for fusioncatcher, none will be trimmed by default",
+                    "minimum": 0,
+                    "fa_icon": "fas fa-cut"
+                },
+                "adapter_fasta": {
                     "type": "string",
                     "format": "file-path",
-                    "mimetype": "text/csv",
-                    "schema": "assets/schema_input.json",
                     "exists": true,
-                    "pattern": "^\\S+\\.(csv|yaml|yml|json)$",
-                    "description": "Path to samplesheet file containing information about the samples in the experiment.",
-                    "help_text": "You will need to create a design file with information about the samples in your experiment before running the pipeline. Use this parameter to specify its location. It has to be a comma-separated file with 3 columns, and a header row. See [usage docs](https://nf-co.re/rnafusion/usage#samplesheet-input).",
-                    "fa_icon": "fas fa-file-csv"
+                    "pattern": "\\S+\\.f(n|ast)?a$",
+                    "description": "Path to adapter fasta file: default: []",
+                    "fa_icon": "fas fa-cut"
                 },
-                "outdir": {
-                    "type": "string",
-                    "format": "directory-path",
-                    "description": "The output directory where the results will be saved. You have to use absolute paths to storage on Cloud infrastructure.",
-                    "fa_icon": "fas fa-folder-open"
+                "save_trimmed_fail": {
+                    "type": "boolean",
+                    "fa_icon": "far fa-times-circle",
+                    "description": "FASTP: Specify true to save files that failed to pass trimming thresholds"
                 },
-                "email": {
-                    "type": "string",
-                    "description": "Email address for completion summary.",
-                    "fa_icon": "fas fa-envelope",
-                    "help_text": "Set this parameter to your e-mail address to get a summary e-mail with details of the run sent to you when the workflow exits. If set in your user config file (`~/.nextflow/config`) then you don't need to specify this on the command line for every run.",
-                    "pattern": "^([a-zA-Z0-9_\\-\\.]+)@([a-zA-Z0-9_\\-\\.]+)\\.([a-zA-Z]{2,5})$"
+                "min_trimmed_reads": {
+                    "type": "integer",
+                    "default": 1,
+                    "fa_icon": "fas fa-search-minus",
+                    "description": "FASTP: Inputs with fewer than this reads will be filtered out of the \"reads\" output channel"
                 },
-                "multiqc_title": {
-                    "type": "string",
-                    "description": "MultiQC report title. Printed as page header, used for filename if not otherwise specified.",
-                    "fa_icon": "fas fa-file-signature"
+                "save_merged": {
+                    "type": "boolean",
+                    "fa_icon": "fas fa-download",
+                    "description": "FASTP: Specify true to save merged reads"
+                }
+            }
+        },
+        "alignment_options": {
+            "title": "Alignment options",
+            "type": "object",
+            "fa_icon": "fas fa-align-center",
+            "properties": {
+                "cram": {
+                    "type": "boolean",
+                    "description": "Option to compress BAM files to CRAM. Output CRAM files instead of BAM files.",
+                    "fa_icon": "fas fa-cut"
                 },
-                "cosmic_username": {
-                    "type": "string",
+                "star_limit_bam_sort_ram": {
+                    "type": "integer",
+                    "description": "The maximum amount of RAM to use for sorting the BAM file in STAR. Should by in bits. Setting this value to `0` will use the default amount of STAR.",
+                    "fa_icon": "fas fa-toolbox",
+                    "minimum": 0
+                },
+                "star_ignore_sjdbgtf": {
+                    "type": "boolean",
+                    "description": "Whether to ignore the GTF in STAR alignment",
+                    "hidden": true,
+                    "fa_icon": "fas fa-toolbox",
+                    "help_text": "Setting false will use GTF file for STAR alignment"
+                },
+                "read_length": {
+                    "type": "integer",
                     "fa_icon": "far fa-file-code",
-                    "description": "COSMIC username"
+                    "description": "The length of the reads provided to the pipeline. This is used for the '--sjdbOverhang' option of STAR as read_length - 1. Providing 1 to this option will disable overhang handling.",
+                    "default": 100,
+                    "minimum": 1
                 },
-                "cosmic_passwd": {
+                "seq_platform": {
                     "type": "string",
-                    "fa_icon": "far fa-file-code",
-                    "description": "COSMIC password"
+                    "description": "Sequencing platform, used to fill in read group PL tag in the BAM header",
+                    "fa_icon": "fas fa-toolbox",
+                    "help_text": "This will reported in the BAM header as PL."
+                },
+                "seq_center": {
+                    "type": "string",
+                    "description": "Sequencing center, used to fill in read group CN tag in the BAM header",
+                    "fa_icon": "fas fa-toolbox",
+                    "help_text": "This will reported in the BAM header as CN"
+                }
+            }
+        },
+        "reference_genome_options": {
+            "title": "Reference genome options",
+            "type": "object",
+            "fa_icon": "fas fa-dna",
+            "description": "Reference genome related files and options required for the workflow.",
+            "properties": {
+                "references_only": {
+                    "type": "boolean",
+                    "description": "Skip running the analysis, only builds the references",
+                    "fa_icon": "fas fa-book"
                 },
                 "genomes_base": {
                     "type": "string",
                     "fa_icon": "far fa-file-code",
-                    "description": "Path to reference folder"
+                    "description": "Path to reference folder",
+                    "default": "s3://nf-core-awsmegatests/rnafusion/references"
                 },
                 "genomes_ignore": {
                     "type": "boolean",
@@ -88,20 +217,66 @@
                 "genome_gencode_version": {
                     "type": "integer",
                     "fa_icon": "far fa-file-code",
-                    "description": "gencode version"
+                    "description": "gencode version",
+                    "default": 46
                 },
-                "tools": {
+                "fasta": {
+                    "type": "string",
+                    "format": "file-path",
+                    "mimetype": "text/plain",
+                    "pattern": "^\\S+\\.fn?a(sta)?(\\.gz)?$",
+                    "description": "Path to FASTA genome file.",
+                    "fa_icon": "far fa-file-code"
+                },
+                "fai": {
+                    "type": "string",
+                    "format": "file-path",
+                    "mimetype": "text/plain",
+                    "pattern": "^\\S+\\.fn?ai(\\.gz)?$",
+                    "description": "Path to FASTA genome index file.",
+                    "fa_icon": "far fa-file-code"
+                },
+                "genome": {
+                    "type": "string",
+                    "description": "Name of iGenomes reference.",
+                    "fa_icon": "fas fa-book",
+                    "default": "GRCh38"
+                },
+                "gtf": {
+                    "type": "string",
+                    "format": "file-path",
+                    "pattern": "^\\S+\\.gtf?(\\.gz)?$",
+                    "description": "Path to GTF genome file.",
+                    "fa_icon": "far fa-file-code"
+                },
+                "refflat": {
+                    "type": "string",
+                    "format": "file-path",
+                    "pattern": "^\\S+\\.refflat?$",
+                    "description": "Path to GTF genome file.",
+                    "fa_icon": "far fa-file-code"
+                },
+                "rrna_intervals": {
+                    "type": "string",
+                    "format": "file-path",
+                    "pattern": "^\\S+\\.interval_list?$",
+                    "description": "Path to ribosomal interval list.",
+                    "fa_icon": "far fa-file-code"
+                },
+                "cosmic_username": {
                     "type": "string",
-                    "description": "Comma-delimited list of tools to run",
                     "fa_icon": "far fa-file-code",
-                    "pattern": "^((arriba|ctatsplicing|fusioncatcher|starfusion|stringtie|fusionreport|fastp|salmon|fusioninspector|all)?,?)*(?<!,)$"
+                    "description": "COSMIC username"
                 },
-                "read_length": {
-                    "type": "integer",
+                "cosmic_passwd": {
+                    "type": "string",
                     "fa_icon": "far fa-file-code",
-                    "description": "The length of the reads provided to the pipeline. This is used for the '--sjdbOverhang' option of STAR as read_length - 1. Providing 1 to this option will disable overhang handling.",
-                    "default": 100,
-                    "minimum": 1
+                    "description": "COSMIC password"
+                },
+                "no_cosmic": {
+                    "type": "boolean",
+                    "fa_icon": "far fa-file-code",
+                    "description": "Avoid using Cosmic DB (for example in clinical case applications where a paid license applies."
                 },
                 "arriba_ref_blacklist": {
                     "type": "string",
@@ -131,29 +306,6 @@
                     "fa_icon": "far fa-file-code",
                     "description": "Path to arriba reference protein domain"
                 },
-                "arriba_fusions": {
-                    "type": "string",
-                    "format": "file-path",
-                    "exists": true,
-                    "pattern": "\\S+\\.tsv$",
-                    "fa_icon": "far fa-file-code",
-                    "description": "Path to arriba output"
-                },
-                "fusioncatcher_fusions": {
-                    "type": "string",
-                    "format": "file-path",
-                    "exists": true,
-                    "pattern": "\\S+\\.txt$",
-                    "fa_icon": "far fa-file-code",
-                    "description": "Path to fusioncatcher output"
-                },
-                "fusioncatcher_limitSjdbInsertNsj": {
-                    "type": "integer",
-                    "fa_icon": "far fa-file-code",
-                    "description": "Use limitSjdbInsertNsj with int for fusioncatcher",
-                    "default": 2000000,
-                    "minimum": 1
-                },
                 "fusioncatcher_ref": {
                     "type": "string",
                     "format": "directory-path",
@@ -175,6 +327,14 @@
                     "fa_icon": "far fa-file-code",
                     "description": "Path to a fusion list file built with format GENE1--GENE2"
                 },
+                "whitelist": {
+                    "type": "string",
+                    "format": "file-path",
+                    "exists": true,
+                    "pattern": "\\S+\\.tsv$",
+                    "fa_icon": "far fa-file-code",
+                    "description": "Path to fusions to add to the input of fusioninspector"
+                },
                 "fusionreport_ref": {
                     "type": "string",
                     "format": "directory-path",
@@ -200,19 +360,17 @@
                     "fa_icon": "far fa-file-code",
                     "description": "Use QIAGEN instead of SANGER to download COSMIC database"
                 },
-                "salmon_index": {
+                "starindex_ref": {
                     "type": "string",
                     "format": "directory-path",
                     "fa_icon": "far fa-file-code",
-                    "description": "Path to salmon index"
+                    "description": "Path to starindex references"
                 },
-                "starfusion_fusions": {
+                "salmon_index": {
                     "type": "string",
-                    "format": "file-path",
-                    "exists": true,
-                    "pattern": "\\S+\\.tsv$",
+                    "format": "directory-path",
                     "fa_icon": "far fa-file-code",
-                    "description": "Path to starfusion output"
+                    "description": "Path to salmon index"
                 },
                 "starfusion_ref": {
                     "type": "string",
@@ -220,6 +378,14 @@
                     "fa_icon": "far fa-file-code",
                     "description": "Path to starfusion references"
                 },
+                "fusion_annot_lib": {
+                    "type": "string",
+                    "format": "file-path",
+                    "exists": true,
+                    "pattern": "\\S+\\.dat\\.gz$",
+                    "description": "Path to Fusion Annotation Library to be used in STARFUSION_BUILD.",
+                    "fa_icon": "far fa-file-code"
+                },
                 "ctatsplicing_cancer_introns": {
                     "type": "string",
                     "format": "file-path",
@@ -268,6 +434,20 @@
                     "help_text": "Provide a valid path pointing to the Dfam H3P database file. Leave as null if using the automatical filling with `--dfam_version` and `--species`.",
                     "fa_icon": "fas fa-link"
                 },
+                "species": {
+                    "type": "string",
+                    "description": "Which species dfam should automatically download, default: homo_sapiens.",
+                    "fa_icon": "far fa-file-code",
+                    "default": "homo_sapiens"
+                },
+                "dfam_version": {
+                    "type": [
+                        "number",
+                        "null"
+                    ],
+                    "description": "Version of dfam to use",
+                    "fa_icon": "fas fa-code-branch"
+                },
                 "pfam_file": {
                     "type": "string",
                     "format": "file-path",
@@ -276,6 +456,14 @@
                     "help_text": "Provide a valid path pointing to the Pfam database file. Leave as null if using the automatical filling with `--pfam_version`.",
                     "fa_icon": "fas fa-link"
                 },
+                "pfam_version": {
+                    "type": [
+                        "number",
+                        "null"
+                    ],
+                    "description": "Version of pfam to use",
+                    "fa_icon": "fas fa-code-branch"
+                },
                 "annot_filter_url": {
                     "type": "string",
                     "format": "uri",
@@ -284,168 +472,6 @@
                     "help_text": "Provide a valid HTTP/HTTPS URL pointing to the annotation filter rule file (typically a Perl module).",
                     "default": "https://data.broadinstitute.org/Trinity/CTAT_RESOURCE_LIB/AnnotFilterRule.pm",
                     "fa_icon": "fas fa-filter"
-                },
-                "starindex_ref": {
-                    "type": "string",
-                    "format": "directory-path",
-                    "fa_icon": "far fa-file-code",
-                    "description": "Path to starindex references"
-                },
-                "tools_cutoff": {
-                    "type": "integer",
-                    "minimum": 1,
-                    "default": 1,
-                    "fa_icon": "far fa-file-code",
-                    "description": "Discard fusions identified by less than INT tools"
-                },
-                "whitelist": {
-                    "type": "string",
-                    "format": "file-path",
-                    "exists": true,
-                    "pattern": "\\S+\\.tsv$",
-                    "fa_icon": "far fa-file-code",
-                    "description": "Path to fusions to add to the input of fusioninspector"
-                }
-            }
-        },
-        "read_trimming_options": {
-            "title": "Read trimming options",
-            "type": "object",
-            "fa_icon": "fas fa-cut",
-            "description": "Options to adjust read trimming criteria.",
-            "properties": {
-                "trim_tail": {
-                    "type": "integer",
-                    "description": "The amount of bases to trim at the tail of each read, none will be trimmed by default",
-                    "minimum": 0,
-                    "fa_icon": "fas fa-cut"
-                },
-                "trim_tail_fusioncatcher": {
-                    "type": "integer",
-                    "description": "The amount of bases to trim at the tail of each read for fusioncatcher, none will be trimmed by default",
-                    "minimum": 0,
-                    "fa_icon": "fas fa-cut"
-                },
-                "adapter_fasta": {
-                    "type": "string",
-                    "format": "file-path",
-                    "exists": true,
-                    "pattern": "\\S+\\.f(n|ast)?a$",
-                    "description": "Path to adapter fasta file: default: []",
-                    "fa_icon": "fas fa-cut"
-                },
-                "save_trimmed_fail": {
-                    "type": "boolean",
-                    "fa_icon": "far fa-times-circle",
-                    "description": "FASTP: Specify true to save files that failed to pass trimming thresholds"
-                },
-                "min_trimmed_reads": {
-                    "type": "integer",
-                    "default": 1,
-                    "fa_icon": "fas fa-search-minus",
-                    "description": "FASTP: Inputs with fewer than this reads will be filtered out of the \"reads\" output channel"
-                },
-                "save_merged": {
-                    "type": "boolean",
-                    "fa_icon": "fas fa-download",
-                    "description": "FASTP: Specify true to save merged reads"
-                }
-            }
-        },
-        "compression_options": {
-            "title": "Alignment compression options",
-            "type": "object",
-            "fa_icon": "fas fa-cut",
-            "description": "Option to compress BAM files to CRAM.",
-            "properties": {
-                "cram": {
-                    "type": "boolean",
-                    "description": "Output CRAM files instead of BAM files.",
-                    "fa_icon": "fas fa-cut"
-                }
-            }
-        },
-        "reference_genome_options": {
-            "title": "Reference genome options",
-            "type": "object",
-            "fa_icon": "fas fa-dna",
-            "description": "Reference genome related files and options required for the workflow.",
-            "properties": {
-                "references_only": {
-                    "type": "boolean",
-                    "description": "Skip running the analysis, only builds the references",
-                    "fa_icon": "fas fa-book"
-                },
-                "fasta": {
-                    "type": "string",
-                    "format": "file-path",
-                    "mimetype": "text/plain",
-                    "pattern": "^\\S+\\.fn?a(sta)?(\\.gz)?$",
-                    "description": "Path to FASTA genome file.",
-                    "fa_icon": "far fa-file-code"
-                },
-                "fai": {
-                    "type": "string",
-                    "format": "file-path",
-                    "mimetype": "text/plain",
-                    "pattern": "^\\S+\\.fn?ai(\\.gz)?$",
-                    "description": "Path to FASTA genome index file.",
-                    "fa_icon": "far fa-file-code"
-                },
-                "genome": {
-                    "type": "string",
-                    "description": "Name of iGenomes reference.",
-                    "fa_icon": "fas fa-book"
-                },
-                "gtf": {
-                    "type": "string",
-                    "format": "file-path",
-                    "pattern": "^\\S+\\.gtf?(\\.gz)?$",
-                    "description": "Path to GTF genome file.",
-                    "fa_icon": "far fa-file-code"
-                },
-                "refflat": {
-                    "type": "string",
-                    "format": "file-path",
-                    "pattern": "^\\S+\\.refflat?$",
-                    "description": "Path to GTF genome file.",
-                    "fa_icon": "far fa-file-code"
-                },
-                "rrna_intervals": {
-                    "type": "string",
-                    "format": "file-path",
-                    "pattern": "^\\S+\\.interval_list?$",
-                    "description": "Path to ribosomal interval list.",
-                    "fa_icon": "far fa-file-code"
-                },
-                "no_cosmic": {
-                    "type": "boolean",
-                    "fa_icon": "far fa-file-code",
-                    "description": "Avoid using Cosmic DB (for example in clinical case applications where a paid license applies."
-                },
-                "fusion_annot_lib": {
-                    "type": "string",
-                    "format": "file-path",
-                    "exists": true,
-                    "pattern": "\\S+\\.dat\\.gz$",
-                    "description": "Path to Fusion Annotation Library to be used in STARFUSION_BUILD.",
-                    "fa_icon": "far fa-file-code"
-                },
-                "species": {
-                    "type": "string",
-                    "description": "Which species dfam should automatically download, default: homo_sapiens.",
-                    "fa_icon": "far fa-file-code",
-                    "default": "homo_sapiens"
-                },
-                "dfam_version": {
-                    "type": ["number", "null"],
-                    "description": "Version of dfam to use",
-                    "fa_icon": "fas fa-code-branch"
-                },
-                "pfam_version": {
-                    "type": ["number", "null"],
-                    "description": "Version of pfam to use",
-                    "fa_icon": "fas fa-code-branch"
                 }
             }
         },
@@ -516,9 +542,23 @@
                     "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": {
+                    "type": "string",
+                    "description": "Email address for completion summary.",
+                    "fa_icon": "fas fa-envelope",
+                    "help_text": "Set this parameter to your e-mail address to get a summary e-mail with details of the run sent to you when the workflow exits. If set in your user config file (`~/.nextflow/config`) then you don't need to specify this on the command line for every run.",
+                    "pattern": "^([a-zA-Z0-9_\\-\\.]+)@([a-zA-Z0-9_\\-\\.]+)\\.([a-zA-Z]{2,5})$"
+                },
                 "email_on_fail": {
                     "type": "string",
                     "description": "Email address for completion summary, only when pipeline fails.",
@@ -554,6 +594,11 @@
                     "help_text": "Incoming hook URL for messaging service. Currently, MS Teams and Slack are supported.",
                     "hidden": true
                 },
+                "multiqc_title": {
+                    "type": "string",
+                    "description": "MultiQC report title. Printed as page header, used for filename if not otherwise specified.",
+                    "fa_icon": "fas fa-file-signature"
+                },
                 "multiqc_config": {
                     "type": "string",
                     "format": "file-path",
@@ -591,47 +636,22 @@
                     "fa_icon": "far calendar",
                     "description": "Suffix to add to the trace report filename. Default is the date and time in the format yyyy-MM-dd_HH-mm-ss.",
                     "hidden": true
-                },
-                "seq_center": {
-                    "type": "string",
-                    "description": "Sequencing center, used to fill in read group CN tag in the BAM header",
-                    "fa_icon": "fas fa-toolbox",
-                    "help_text": "This will reported in the BAM header as CN"
-                },
-                "seq_platform": {
-                    "type": "string",
-                    "description": "Sequencing platform, used to fill in read group PL tag in the BAM header",
-                    "fa_icon": "fas fa-toolbox",
-                    "help_text": "This will reported in the BAM header as PL."
-                },
-                "star_ignore_sjdbgtf": {
-                    "type": "boolean",
-                    "description": "Whether to ignore the GTF in STAR alignment",
-                    "hidden": true,
-                    "fa_icon": "fas fa-toolbox",
-                    "help_text": "Setting false will use GTF file for STAR alignment"
-                },
-                "star_limit_bam_sort_ram": {
-                    "type": "integer",
-                    "description": "The maximum amount of RAM to use for sorting the BAM file in STAR. Should by in bits. Setting this value to `0` will use the default amount of STAR.",
-                    "fa_icon": "fas fa-toolbox",
-                    "minimum": 0
                 }
             }
         }
     },
     "allOf": [
         {
-            "$ref": "#/$defs/skip_steps"
+            "$ref": "#/$defs/input_output_options"
         },
         {
-            "$ref": "#/$defs/input_output_options"
+            "$ref": "#/$defs/skip_steps"
         },
         {
             "$ref": "#/$defs/read_trimming_options"
         },
         {
-            "$ref": "#/$defs/compression_options"
+            "$ref": "#/$defs/alignment_options"
         },
         {
             "$ref": "#/$defs/reference_genome_options"
@@ -643,4 +663,4 @@
             "$ref": "#/$defs/generic_options"
         }
     ]
-}
+}
\ No newline at end of file