diff --git a/nextflow.config b/nextflow.config
index d4d7468..53530ed 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -9,40 +9,49 @@
 // Global default params, used in configs
 params {
     // TODO nf-core: Specify your pipeline's command line flags
-    mode                       = "nanopore"
+
 
     // Input options
     input                     = null // location for the input samplesheet file
     classifier                = "kraken2"
     fasta                     = "test.fa"
     schema_ignore_params      = "fasta"
+    tracedir                  = "null"
 
     //rasusa subsampling options
+    skip_subsampling           = true
     depth_cut_off             = '50' // minimum coverage to subsample the reads is 50
+
     // assembly_qc: genomesize is used by confindr for spec
     subsampling_genomesize    = 5000000 // change name - de-group from reads reference genome size. Valid metric suffixes include Base (b), Kilo (k), Mega (m), Giga (g), Tera (t)
 
     //confindr options
+    skip_confindr              = false
     confindr_db               = "/mnt/cidgoh-object-storage/database/confindr/confindr_db" //database for confindr. The default database are only for detecting contamination in Escherichia, Listeria, and Salmonella. If you want to run ConFindr on any other genera, you need to build the database following the tutorial at https://olc-bioinformatics.github.io/ConFindr/install/.
 
-    //trimmer options
-
+    //QC options
+    skip_seqqc                = false
+    skip_trimming             = false
     trim_tool                 = "fastp"  // Select which trimming tool to use (fastp/trimmomatic/trimgalore)
     adapter_fasta             = "/mnt/cidgoh-object-storage/database/adaptors/test.fa" // location for adapator database (fasta file)
     save_trimmed_fail         = false //  Check if reads failed in the trimming process need to be saved (True/False, default: False)
-    save_merged               = false  // Check if merged reads need to be saved (True/False, default: True)
+    save_merged               = true  // Check if merged reads need to be saved (True/False, default: True)
 
 
     // MultiQC options
-    multiqc_config             = null
-    multiqc_title              = null
-    multiqc_logo               = null
     max_multiqc_email_size     = '25.MB'
-    multiqc_methods_description = null
+    multiqc_title              = "BACPAQ"
+    multiqc_config             = "null"
+    multiqc_logo               = "null"
+    multiqc_methods_description= "null"
+
+
 
     // Nanopore QC options
-    // skip_nanocomp           = false
-    // skip_pycoqc             = false
+    skip_nanocomp           = false
+    skip_pycoqc             = false
+    skip_porechop           = false
+
 
     // PycoQC options
     // Path to nanopore summary file to be used by PycoQC
@@ -71,14 +80,14 @@ params {
     medaka_model               = "r941_min_fast_g507"
 
     // Taxonomy module options
+
+    // Dehosting options
+    skip_dehosting             = false
     skip_combinekreports       = false
     skip_kreport2krona         = false
     skip_bracken               = false
     skip_kraken2               = false
     skip_combinebrackenoutputs = false
-    skip_dehosting             = false
-    skip_subsampling           = false
-    skip_confindr              = false
 
     // kraken2 options
     // Path to Kraken2 database used for querying reads during taxonomic classification
@@ -97,11 +106,12 @@ params {
     // Boolean for whether to save the output as a SAM file
     sam_format                 = true
 
-    // Dehosting options
     // Aligner used for dehosting ('minimap2' or 'bwa')
     dehosting_aligner          = 'minimap2'
+
     // Path to (human) reference genome used for dehosting
     host_genome                = "/mnt/cidgoh-object-storage/database/reference_genomes/human/GRCh38.p14/GCF_000001405.40/GCF_000001405.40_GRCh38.p14_genomic.fna"
+
     // ID/name for reference genome
     host_genome_id             = 'GRCh38'
 
@@ -170,12 +180,12 @@ params {
 
     // pipeline options
     skip_QC                    = false
-    skip_raw_qc                = false
     skip_taxonomy_qc           = false
     skip_assembly              = false
     skip_assembly_qc           = false
     skip_rmlst                 = false
 
+
     // Max resource options
     // Defaults only, expecting to be overwritten
     max_memory                 = '128.GB'
@@ -183,7 +193,14 @@ params {
     max_time                   = '240.h'
 
     /* Annotation options */
+    skip_annotation            = false
     skip_gene_annotation       = false
+    skip_abricate_summary      = false
+    amrfinderplus_db           = null
+    skip_resfinder             = false
+    skip_virsorter2            = false
+    skip_crispr_analysis       = false
+
 
 
     // AMR options
@@ -199,7 +216,6 @@ params {
     disinfinder_db              = "/scratch/group_share/tmp/database/disinfinder_db"
     resfinder_species           = "ecoli"
 
-
     // gene annotation options
     skip_gene_annotation       = false
     skip_prokka                = false
diff --git a/nextflow_schema.json b/nextflow_schema.json
index 4bd730c..37a7cd5 100644
--- a/nextflow_schema.json
+++ b/nextflow_schema.json
@@ -9,7 +9,7 @@
       "title": "Input/output options",
       "type": "object",
       "fa_icon": "fas fa-terminal",
-      "description": "Define where the pipeline should find input data and save output data.",
+      "description": "Define where the pipeline should find input data and save output data",
       "required": ["input", "outdir"],
       "properties": {
         "input": {
@@ -20,13 +20,15 @@
           "schema": "assets/schema_input.json",
           "description": "Path to comma-separated 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/seqqc/usage#samplesheet-input).",
-          "fa_icon": "fas fa-file-csv"
+          "fa_icon": "fas fa-file-csv",
+          "default": "samplesheet.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"
+          "fa_icon": "fas fa-folder-open",
+          "default": "results"
         },
         "email": {
           "type": "string",
@@ -35,391 +37,558 @@
           "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})$"
         },
-        "multiqc_title": {
+        "fasta": {
           "type": "string",
-          "description": "MultiQC report title. Printed as page header, used for filename if not otherwise specified.",
-          "fa_icon": "fas fa-file-signature"
+          "default": "test.fa",
+          "hidden": true,
+          "format": "file-path",
+          "mimetype": "fasta"
         }
       }
     },
-    "sequencing_parameters": {
-      "title": "Sequencing parameters",
+    "workflow_parameters": {
+      "title": "Workflow parameters",
       "type": "object",
-      "description": "Define the parameters regarding the choice of sequencing type",
+      "description": "Define high level Workflow parameters",
       "default": "",
       "properties": {
-        "mode": {
-          "type": "string",
-          "default": "illumina",
-          "enum": ["illumina", "nanopore"],
-          "description": "Sequencing data type < illumina | nanopore >"
+        "skip_annotation": {
+          "type": "boolean",
+          "description": "Skip the entire annotation process"
         },
+        "skip_seqqc": {
+          "type": "boolean",
+          "description": "Skip seqqc workflow"
+        }
+      }
+    },
+    "nanopore_parameters": {
+      "title": "Nanopore parameters",
+      "type": "object",
+      "description": "Define the sequencing and QC parameters for Nanopore data",
+      "default": "",
+      "properties": {
         "nanopore_summary_file": {
           "type": "string",
-          "description": "File produced during basecalling, which contains high-level information on every read analysed by the basecaller (only required if mode = nanopore))"
+          "description": "File produced during basecalling, which contains high-level information on every read analysed by the basecaller (only required if mode = nanopore))",
+          "fa_icon": "fas fa-file-excel"
         },
         "nanopore_summary_file_id": {
           "type": "string",
           "default": "test",
-          "description": "User defined id for the nanopore summary file (only required if mode = nanopore))"
+          "description": "User defined id for the nanopore summary file (only required if mode = nanopore))",
+          "fa_icon": "fas fa-address-card"
+        },
+        "skip_porechop": {
+          "type": "boolean",
+          "description": "Skip porechop in Nanopore QC"
+        },
+        "skip_pycoqc": {
+          "type": "boolean",
+          "description": "Skip pycoqc in Nanopore QC"
+        },
+        "skip_nanocomp": {
+          "type": "boolean",
+          "description": "Skip nanocomp in Nanopore QC"
         }
-      },
-      "required": ["mode"]
+      }
     },
-    "raw_reads_qc_parameters": {
-      "title": "Raw Reads QC parameters",
+    "illumina_parameters": {
+      "title": "Illumina parameters",
       "type": "object",
-      "description": "Define the raw-reads QC parameters for Illumina data",
+      "description": "Define the QC parameters for llumina data",
       "default": "",
       "properties": {
-        "adapter_fasta": {
-          "type": "string",
-          "default": "https://object-arbutus.cloud.computecanada.ca/cidgohshare/database/adaptors/test.fa"
-        },
-        "skip_subsampling": {
+        "skip_QC": {
           "type": "boolean",
-          "default": true
+          "description": "Skip the Quality control"
         },
         "skip_confindr": {
-          "type": "boolean"
+          "type": "boolean",
+          "description": "Skip Confindr in Illumina QC"
         },
-        "save_merged": {
+        "confindr_db": {
+          "type": "string",
+          "description": "Path to confindr database",
+          "format": "path"
+        },
+        "skip_trimming": {
           "type": "boolean",
-          "default": true
+          "description": "Skip adapter trimming in Illumina QC"
         },
         "trim_tool": {
           "type": "string",
           "default": "fastp",
-          "enum": ["fastp", "trimgalore", "trimmomatic"]
-        },
-        "save_trimmed_fail": {
-          "type": "boolean"
+          "enum": ["fastp", "trimgalore", "trimmomatic"],
+          "description": "Specify the trimming tool"
         },
-        "depth_cut_off": {
+        "adapter_fasta": {
           "type": "string",
-          "default": "50,80"
+          "description": "Fasta file specifying Illumina adapters to be trimmed using FastP",
+          "fa_icon": "fas fa-file-alt",
+          "format": "path"
         },
-        "confindr_db": {
-          "type": "string",
-          "default": "/mnt/cidgoh-object-storage/database/confindr/confindr_db"
+        "save_merged": {
+          "type": "boolean",
+          "default": true,
+          "description": "Specify to save merged reads in Fastp"
         },
-        "skip_QC": {
-          "type": "boolean"
+        "save_trimmed_fail": {
+          "type": "boolean",
+          "description": "Specify to save failed reads in Fastp"
+        }
+      },
+      "fa_icon": "fas fa-microscope"
+    },
+    "subsampling_options": {
+      "title": "Subsampling Options",
+      "type": "object",
+      "description": "Define the parameters for subsampling (Illumina data)",
+      "default": "",
+      "properties": {
+        "skip_subsampling": {
+          "type": "boolean",
+          "default": true,
+          "description": "Specify to skip subsampling reads"
         },
-        "skip_raw_qc": {
-          "type": "boolean"
+        "depth_cut_off": {
+          "type": "string",
+          "default": "50",
+          "description": "Depth of coverage cutoff"
         },
         "subsampling_genomesize": {
           "type": "integer",
-          "default": 5000000
+          "default": 5000000,
+          "description": "Genome size of the species"
         }
       }
     },
     "taxonomy_qc_parameters": {
       "title": "Taxonomy QC parameters",
       "type": "object",
-      "description": "Define the taxonomy-based QC parameters for illumina and nanopore data",
+      "description": "Define the parameters for taxonomy-based QC",
       "default": "",
       "properties": {
+        "skip_taxonomy_qc": {
+          "type": "boolean",
+          "description": "Skip the taxonomy based QC"
+        },
         "classifier": {
           "type": "string",
           "default": "kraken2",
-          "enum": ["kraken2", "centrifuge"]
-        },
-        "skip_combinekreports": {
-          "type": "boolean"
-        },
-        "skip_kreport2krona": {
-          "type": "boolean"
-        },
-        "skip_bracken": {
-          "type": "boolean"
+          "enum": ["kraken2", "centrifuge"],
+          "description": "Specify the classifier"
         },
         "skip_kraken2": {
-          "type": "boolean"
-        },
-        "skip_combinebrackenoutputs": {
-          "type": "boolean"
-        },
-        "skip_dehosting": {
-          "type": "boolean"
+          "type": "boolean",
+          "description": "Skip Kraken2 classification"
         },
         "kraken2_db": {
           "type": "string",
-          "default": "/mnt/cidgoh-object-storage/database/minikraken2/minikraken2_v2_8GB_201904_UPDATE"
+          "description": "Path to Kraken2 database",
+          "format": "path"
         },
         "classified_reads": {
           "type": "boolean",
-          "default": true
+          "default": true,
+          "description": "Specify to save classified reads in Kraken2"
         },
         "unclassified_reads": {
           "type": "boolean",
-          "default": true
+          "default": true,
+          "description": "Specify to save unclassified reads in Kraken2"
+        },
+        "skip_kreport2krona": {
+          "type": "boolean",
+          "description": "Skip converting kraken2 report to Krona format"
+        },
+        "skip_combinekreports": {
+          "type": "boolean",
+          "description": "Skip combining kraken2 reports from all samples"
         },
         "centrifuge_db": {
           "type": "string",
-          "default": "/mnt/cidgoh-object-storage/database/centrifuge"
+          "format": "path",
+          "description": "Specify path to centrifuge database"
+        },
+        "save_aligned": {
+          "type": "boolean",
+          "default": true,
+          "description": "Specify to save aligned reads in centrifuge"
         },
         "save_unaligned": {
           "type": "boolean",
-          "default": true
+          "default": true,
+          "description": "Specify to save un-aligned reads in centrifuge"
         },
-        "save_aligned": {
+        "sam_format": {
           "type": "boolean",
-          "default": true
+          "default": true,
+          "description": "Specify to save sam format for centrifuge"
         },
-        "dehosting_aligner": {
-          "type": "string",
-          "default": "minimap2",
-          "enum": ["minimap2", "bwa"]
+        "skip_bracken": {
+          "type": "boolean",
+          "description": "Skip Bracken classification"
         },
-        "sam_format": {
+        "skip_combinebrackenoutputs": {
           "type": "boolean",
-          "default": true
+          "description": "Skip combining bracken reports from all samples"
         },
-        "bam_format": {
+        "skip_dehosting": {
           "type": "boolean",
-          "default": true
+          "description": "Skip de-hosting process"
         },
-        "bwa_sort_bam": {
+        "dehosting_aligner": {
           "type": "string",
-          "default": "sort"
+          "default": "minimap2",
+          "enum": ["minimap2", "bwa"],
+          "description": "Specify the aligner used for dehosting"
+        },
+        "bam_format": {
+          "type": "boolean",
+          "default": true,
+          "description": "Specify to save bam format Minimap2"
         },
         "cigar_paf_format": {
-          "type": "boolean"
+          "type": "boolean",
+          "description": "Specify to save cigar in paf format for Minimap2"
         },
         "cigar_bam": {
-          "type": "boolean"
+          "type": "boolean",
+          "description": "Specify to save cigar in bam format for Minimap2"
+        },
+        "bwa_sort_bam": {
+          "type": "string",
+          "default": "sort",
+          "description": "Specify to sort bam file for bwa"
         },
         "interleaved": {
-          "type": "boolean"
+          "type": "boolean",
+          "description": "Specify to save dehosted sequences in interleaved format"
         },
         "host_genome": {
           "type": "string",
-          "default": "/mnt/cidgoh-object-storage/database/reference_genomes/human/GRCh38.p14/GCF_000001405.40/GCF_000001405.40_GRCh38.p14_genomic.fna"
+          "description": "Specify the host genome file",
+          "format": "path",
+          "pattern": "^\\S+\\.fasta$"
         },
         "host_genome_id": {
           "type": "string",
-          "default": "GRCh38"
-        },
-        "skip_taxonomy_qc": {
-          "type": "boolean"
+          "default": "GRCh38",
+          "description": "Specify to sort bam file for bwa"
         }
       }
     },
+    "multiqc_options": {
+      "title": "MultiQC options",
+      "type": "object",
+      "description": "Define the parameters for MultiQC reporting",
+      "default": "",
+      "properties": {
+        "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",
+          "default": "BACPAQ"
+        },
+        "max_multiqc_email_size": {
+          "type": "string",
+          "description": "File size limit when attaching MultiQC reports to summary emails.",
+          "pattern": "^\\d+(\\.\\d+)?\\.?\\s*(K|M|G|T)?B$",
+          "default": "25.MB",
+          "fa_icon": "fas fa-file-upload",
+          "hidden": true
+        },
+        "multiqc_logo": {
+          "type": "string",
+          "description": "Custom logo file to supply to MultiQC. File name must also be set in the MultiQC config file",
+          "fa_icon": "fas fa-image",
+          "hidden": true
+        },
+        "multiqc_config": {
+          "type": "string",
+          "description": "Custom config file to supply to MultiQC.",
+          "fa_icon": "fas fa-cog",
+          "hidden": true
+        },
+        "multiqc_methods_description": {
+          "type": "string",
+          "description": "Custom MultiQC yaml file containing HTML including a methods description.",
+          "fa_icon": "fas fa-cog"
+        }
+      },
+      "fa_icon": "fas fa-tv",
+      "help_text": ""
+    },
     "assembly_parameters": {
       "title": "Assembly parameters",
       "type": "object",
-      "description": "Define the genome assembly parameters",
+      "description": "Define the parameters for genome assembly",
       "default": "",
       "properties": {
+        "skip_assembly": {
+          "type": "boolean",
+          "description": "Skip genome assembly"
+        },
+        "sr_assembler": {
+          "type": "string",
+          "default": "spades",
+          "enum": ["skesa", "spades", "megahit"],
+          "description": "Specify short read assembler"
+        },
+        "assembly_genomesize": {
+          "type": "string",
+          "default": "\\'\\",
+          "description": "Specify expected genome size"
+        },
         "min_contig_len": {
           "type": "integer",
-          "default": 500
+          "default": 500,
+          "description": "Specify minimum contig length for assembly"
         },
         "min_contig_coverage": {
           "type": "integer",
-          "default": 2
+          "default": 2,
+          "description": "Specify minimum contig coverage for assembly"
         },
         "min_input_read_len": {
           "type": "integer",
-          "default": 1000
+          "default": 1000,
+          "description": "Specify minimum input read length for DragonFlye"
         },
         "min_input_quality": {
           "type": "integer",
-          "default": 0
+          "default": 0,
+          "description": "Minimum average sequence quality for DragonFlye"
         },
         "racon_rounds": {
           "type": "integer",
-          "default": 1
+          "default": 1,
+          "description": "Number of polishing rounds to conduct with Racon"
         },
         "medaka_rounds": {
           "type": "integer",
-          "default": 1
+          "default": 1,
+          "description": "Number of polishing rounds to conduct with Medaka (requires a model to be specified)"
         },
         "medaka_model": {
           "type": "string",
-          "default": "r941_min_fast_g507"
-        },
-        "sr_assembler": {
-          "type": "string",
-          "default": "spades",
-          "enum": ["skesa", "spades", "megahit"]
-        },
-        "skip_assembly": {
-          "type": "boolean"
-        },
-        "assembly_genomesize": {
-          "type": "string",
-          "default": "\\'\\"
+          "default": "r941_min_fast_g507",
+          "description": "Path to model to be used for Medaka"
         }
       }
     },
     "assembly_qc_parameters": {
       "title": "Assembly QC parameters",
       "type": "object",
-      "description": "",
+      "description": "Define the parameters for assembly QC",
       "default": "",
       "properties": {
-        "checkm_db": {
-          "type": "string"
+        "skip_assembly_qc": {
+          "type": "boolean",
+          "description": "Skip assembly QC"
+        },
+        "skip_quast": {
+          "type": "boolean",
+          "description": "Skip Quast"
         },
         "combine_quast": {
-          "type": "boolean"
+          "type": "boolean",
+          "description": "Specify to combine Quast output from different samples"
         },
-        "busco_lineage": {
+        "reference_genome_fasta": {
           "type": "string",
-          "default": "bacteria"
+          "description": "Specify reference genome FASTA file for QUAST"
         },
-        "busco_lineages_path": {
+        "reference_genome_gff": {
           "type": "string",
-          "default": "/mnt/cidgoh-object-storage/database/busco"
-        },
-        "busco_config": {
-          "type": "boolean"
+          "description": "Specify reference genome GFF file for QUAST"
         },
-        "skip_checkm": {
-          "type": "boolean"
+        "skip_checkM": {
+          "type": "boolean",
+          "description": "Skip CheckM"
         },
-        "skip_quast": {
-          "type": "boolean"
+        "checkm_db": {
+          "type": "string",
+          "description": "Specify CheckM database"
         },
         "skip_busco": {
-          "type": "boolean"
+          "type": "boolean",
+          "description": "Skip BUSCO"
         },
-        "reference_genome_fasta": {
-          "type": "string"
+        "busco_lineage": {
+          "type": "string",
+          "default": "bacteria",
+          "description": "Specify Busco lineage"
         },
-        "reference_genome_gff": {
-          "type": "string"
+        "busco_lineages_path": {
+          "type": "string",
+          "default": "/mnt/cidgoh-object-storage/database/busco",
+          "description": "Specify Busco lineage path"
         },
-        "skip_assembly_qc": {
-          "type": "boolean"
+        "busco_config": {
+          "type": "boolean",
+          "description": "Specify Busco configuration"
         },
         "skip_rmlst": {
-          "type": "boolean"
+          "type": "boolean",
+          "description": "Skip RMLST analysis"
         }
       }
     },
     "gene_annotation_parameters": {
       "title": "Gene annotation parameters",
       "type": "object",
-      "description": "",
+      "description": "Define the parameters for gene annotation",
       "default": "",
       "properties": {
         "skip_gene_annotation": {
-          "type": "boolean"
+          "type": "boolean",
+          "description": "Skip the gene annotation process"
         },
         "skip_prokka": {
-          "type": "boolean"
+          "type": "boolean",
+          "description": "Skip Prokka"
         },
         "skip_bakta": {
-          "type": "boolean"
+          "type": "boolean",
+          "description": "Skip Bakta"
         },
         "bakta_db": {
           "type": "string",
-          "default": "/mnt/cidgoh-object-storage/database/bakta/db/"
+          "description": "Specify database path for Bakta"
         },
         "prodigal_training_file": {
-          "type": "string"
+          "type": "string",
+          "description": "Specify prodigal training file"
         },
         "annotation_protein_file": {
-          "type": "string"
+          "type": "string",
+          "description": "Specify annotation protein file"
         }
       }
     },
     "pangenome_parameters": {
       "title": "Pangenome parameters",
       "type": "object",
-      "description": "",
+      "description": "Define the parameters for pangenome analysis",
       "default": "",
       "properties": {
         "skip_pangenome_analysis": {
-          "type": "boolean"
+          "type": "boolean",
+          "description": "Skip pangenome analysis"
         },
         "pangenome_input": {
           "type": "string",
-          "default": "bakta"
+          "default": "bakta",
+          "description": "Specify pangenome input",
+          "enum": ["bakta", "prokka"]
         },
         "skip_roary": {
-          "type": "boolean"
+          "type": "boolean",
+          "description": "Skip Roary"
         },
         "skip_pirate": {
-          "type": "boolean"
-        },
-        "skip_panaroo": {
-          "type": "boolean"
+          "type": "boolean",
+          "description": "Skip PIRATE"
         },
         "skip_peppan": {
-          "type": "boolean"
+          "type": "boolean",
+          "description": "Skip PEPPAN"
         },
-        "clean_mode": {
+        "reference_gff": {
           "type": "string",
-          "default": "moderate"
+          "description": "Specify reference GFF file for PEPPAN"
         },
-        "reference_gff": {
-          "type": "string"
+        "skip_panaroo": {
+          "type": "boolean",
+          "description": "Skip PANAROO"
+        },
+        "clean_mode": {
+          "type": "string",
+          "default": "moderate",
+          "description": "Specify stringency mode for PANAROO",
+          "enum": ["strict", "moderate", "sensitive"]
         }
       }
     },
     "plasmids_parameters": {
       "title": "Plasmids parameters",
       "type": "object",
-      "description": "",
+      "description": "Define the parameters for plasmid annotations",
       "default": "",
       "properties": {
         "skip_plasmid_analysis": {
-          "type": "boolean"
+          "type": "boolean",
+          "description": "Skip plasmid annotation"
         },
         "skip_plasmidfinder": {
-          "type": "boolean"
+          "type": "boolean",
+          "description": "Skip plasmidfinder"
         },
         "skip_mobsuite": {
-          "type": "boolean"
+          "type": "boolean",
+          "description": "Skip MOB-suite"
         }
       }
     },
     "phage_parameters": {
-      "title": "Phage parameters",
+      "title": "PHAGE parameters",
       "type": "object",
-      "description": "",
+      "description": "Define the parameters for PHAGE annotations",
       "default": "",
       "properties": {
         "skip_phage_annotation": {
-          "type": "boolean"
+          "type": "boolean",
+          "description": "Skip the PHAGE annotation process"
+        },
+        "skip_virsorter2": {
+          "type": "boolean",
+          "description": "Skip Virsorter in PHAGE annotation",
+          "hidden": true
         },
         "virsorter_db": {
-          "type": "string"
+          "type": "string",
+          "description": "Specify virsorte2 database path"
         },
         "virsorter_virus_grp": {
           "type": "string",
-          "default": "dsDNAphage,ssDNA"
+          "default": "dsDNAphage,ssDNA",
+          "description": "Specify vthe virus group for virsorter2"
         },
         "virsorter_min_len": {
           "type": "integer",
-          "default": 5000
+          "default": 5000,
+          "description": "Specify minimum length for virsorter2"
         },
         "virsorter_min_score": {
           "type": "number",
-          "default": 0.4
+          "default": 0.4,
+          "description": "Specify minimum score for virsorter2"
         }
       }
     },
     "crispr_parameters": {
       "title": "CRISPR parameters",
       "type": "object",
-      "description": "",
+      "description": "Define the parameters for CRISPR annotations",
       "default": "",
       "properties": {
+        "skip_crispr_analysis": {
+          "type": "boolean",
+          "description": "Skip CRISPR analysis in annotation"
+        },
         "skip_cctyper": {
-          "type": "boolean"
+          "type": "boolean",
+          "description": "Skip cctyper annotation",
+          "hidden": true
         }
       }
     },
     "amr_parameters": {
       "title": "AMR parameters",
       "type": "object",
-      "description": "",
+      "description": "Define the parameters for AMR annotations",
       "default": "",
       "properties": {
         "amr_finderplus_db": {
@@ -467,6 +636,19 @@
           "type": "string",
           "default": "ecoli",
           "description": "Species in the sample, supported species can be seen at https://github.com/cadms/resfinder"
+        },
+        "skip_abricate_summary": {
+          "type": "boolean",
+          "description": "Skip summarizing abricate results across samples"
+        },
+        "amrfinderplus_db": {
+          "type": "string",
+          "format": "path",
+          "description": "Path to amrfinderplus database. If the path is not provided, the  database will be downloaded during the run"
+        },
+        "skip_resfinder": {
+          "type": "boolean",
+          "description": "Skip Resfinder in AMR annotation"
         }
       }
     },
@@ -602,14 +784,6 @@
           "fa_icon": "fas fa-remove-format",
           "hidden": true
         },
-        "max_multiqc_email_size": {
-          "type": "string",
-          "description": "File size limit when attaching MultiQC reports to summary emails.",
-          "pattern": "^\\d+(\\.\\d+)?\\.?\\s*(K|M|G|T)?B$",
-          "default": "25.MB",
-          "fa_icon": "fas fa-file-upload",
-          "hidden": true
-        },
         "monochrome_logs": {
           "type": "boolean",
           "description": "Do not use coloured log outputs.",
@@ -623,34 +797,16 @@
           "help_text": "Incoming hook URL for messaging service. Currently, MS Teams and Slack are supported.",
           "hidden": true
         },
-        "multiqc_config": {
-          "type": "string",
-          "description": "Custom config file to supply to MultiQC.",
-          "fa_icon": "fas fa-cog",
-          "hidden": true
-        },
-        "multiqc_logo": {
-          "type": "string",
-          "description": "Custom logo file to supply to MultiQC. File name must also be set in the MultiQC config file",
-          "fa_icon": "fas fa-image",
-          "hidden": true
-        },
-        "multiqc_methods_description": {
-          "type": "string",
-          "description": "Custom MultiQC yaml file containing HTML including a methods description.",
-          "fa_icon": "fas fa-cog"
-        },
         "tracedir": {
           "type": "string",
           "description": "Directory to keep pipeline Nextflow logs and reports.",
-          "default": "null/pipeline_info",
+          "default": "pipeline_info",
           "fa_icon": "fas fa-cogs",
           "hidden": true
         },
         "validate_params": {
           "type": "boolean",
           "description": "Boolean whether to validate parameters against the schema at runtime",
-          "default": true,
           "fa_icon": "fas fa-check-square",
           "hidden": true
         },
@@ -674,14 +830,23 @@
       "$ref": "#/definitions/input_output_options"
     },
     {
-      "$ref": "#/definitions/sequencing_parameters"
+      "$ref": "#/definitions/workflow_parameters"
+    },
+    {
+      "$ref": "#/definitions/nanopore_parameters"
+    },
+    {
+      "$ref": "#/definitions/illumina_parameters"
     },
     {
-      "$ref": "#/definitions/raw_reads_qc_parameters"
+      "$ref": "#/definitions/subsampling_options"
     },
     {
       "$ref": "#/definitions/taxonomy_qc_parameters"
     },
+    {
+      "$ref": "#/definitions/multiqc_options"
+    },
     {
       "$ref": "#/definitions/assembly_parameters"
     },
@@ -715,12 +880,5 @@
     {
       "$ref": "#/definitions/generic_options"
     }
-  ],
-  "properties": {
-    "fasta": {
-      "type": "string",
-      "default": "test.fa",
-      "hidden": true
-    }
-  }
+  ]
 }