exposed parameters to nextflow schema

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'
 
@@ -170,20 +180,27 @@ 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'
     max_cpus                   = 16
     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