Update schema and change default String values to null instead of false

main.nf

@@ -464,10 +464,10 @@ Channel.from( peptide_molecules )
   .into { ch_peptide_molecules; ch_peptide_molecules_for_compare }
 
 // Parse sketch value and style parameters
-sketch_num_hashes = params.sketch_num_hashes
-sketch_num_hashes_log2 = params.sketch_num_hashes_log2
-sketch_scaled = params.sketch_scaled
-sketch_scaled_log2 = params.sketch_scaled_log2
+sketch_num_hashes = params.sketch_num_hashes ? params.sketch_num_hashes : false
+sketch_num_hashes_log2 = params.sketch_num_hashes_log2 ? params.sketch_num_hashes_log2 : false
+sketch_scaled = params.sketch_scaled ? params.sketch_scaled : false
+sketch_scaled_log2 = params.sketch_scaled_log2 ? params.sketch_scaled_log2 : false
 have_sketch_value = params.sketch_num_hashes || params.sketch_num_hashes_log2 || params.sketch_scaled || params.sketch_scaled_log2
 
 if (!have_sketch_value && !params.split_kmer) {

nextflow.config

@@ -9,18 +9,18 @@
 params {
   // Pipeline Options
   // Many different input modalities can be provided at once
-  read_pairs = false
-  read_singles = false
-  csv_pairs = false
-  csv_singles = false
-  fastas = false
-  protein_fastas = false
-  sra = false
+  read_pairs = null
+  read_singles = null
+  csv_pairs = null
+  csv_singles = null
+  fastas = null
+  protein_fastas = null
+  sra = null
 
-  input = false
+  input = null
 
   // Parsing 10x bam files
-  tenx_tgz = false
+  tenx_tgz = null
   tenx_tags = "CB,CR,CY,XC,UB,UR,UY,AN,TR,XM,XB,RG,GN,GX,TX,NH,HI,AS,nM,RE,MM,pa,xf,fb,fr,fq,fx"
   tenx_cell_barcode_pattern = '(CB|XC):Z:([ACGT]+)(\\-1)?'
   tenx_molecular_barcode_pattern = '(UB|XB|XM):Z:([ACGT]+)'
@@ -32,10 +32,10 @@ params {
   // Track abundance by default
   track_abundance = true
   // Number of hashes from each sample
-  sketch_num_hashes = false
-  sketch_num_hashes_log2 = false
-  sketch_scaled = false
-  sketch_scaled_log2 = false
+  sketch_num_hashes = null
+  sketch_num_hashes_log2 = null
+  sketch_scaled = null
+  sketch_scaled_log2 = null
   skip_sig_merge = false
 
   // Comparing sketches
@@ -50,8 +50,8 @@ params {
   translate_peptide_ksize = 8
   translate_peptide_molecule = 'protein'
   translate_jaccard_threshold = 0.05
-  reference_proteome_fasta = false
-  bloomfilter_tablesize = '1e8'
+  reference_proteome_fasta = null
+  bloomfilter_tablesize = 1e8
   // Saving the translate results for each dataset makes it take extra long
   // Recommended for debugging purposes only
   save_translate_csv = false
@@ -65,45 +65,45 @@ params {
 
   // ska options
   split_kmer = false
-  subsample = false
+  subsample = null
 
   // 10x options
   save_fastas = "fastas"
-  tenx_min_umi_per_cell = '0'
-  write_barcode_meta_csv = false
-  bam = false
+  tenx_min_umi_per_cell = 0
+  write_barcode_meta_csv = null
+  bam = null
 
   // 10x optional input parameters set using the below pattern
   // https://github.com/nextflow-io/patterns/blob/master/docs/optional-input.adoc
-  barcodes_file = false
-  rename_10x_barcodes = false
+  barcodes_file = null
+  rename_10x_barcodes = null
 
   // Variables for testing
-  input_paths = false
-  fasta_paths = false
-  protein_fasta_paths = false
+  input_paths = null
+  fasta_paths = null
+  protein_fasta_paths = null
 
   // QC to skip
   skip_multiqc = false
 
   // Boilerplate options
   outdir = './results'
-  name = false
+  name = null
   publish_dir_mode = 'copy'
   multiqc_config = "$baseDir/assets/multiqc_config.yaml"
-  email = false
-  email_on_fail = false
+  email = null
+  email_on_fail = null
   max_multiqc_email_size = 25.MB
   plaintext_email = false
   monochrome_logs = false
   help = false
   tracedir = "${params.outdir}/pipeline_info"
   custom_config_version = 'master'
   custom_config_base = "https://raw.githubusercontent.com/nf-core/configs/${params.custom_config_version}"
-  hostnames = false
-  config_profile_description = false
-  config_profile_contact = false
-  config_profile_url = false
+  hostnames = null
+  config_profile_description = null
+  config_profile_contact = null
+  config_profile_url = null
 
   // Defaults only, expecting to be overwritten
   max_memory = 128.GB

nextflow_schema.json

@@ -178,15 +178,16 @@
                     "default": "protein"
                 },
                 "translate_jaccard_threshold": {
-                    "type": "string",
+                    "type": "number",
                     "fa_icon": "fas fa-code-branch",
                     "description": "Minimum fraction of overlapping translated k-mers from the read to match to the reference.",
-                    "default": 0.95
+                    "default": 0.05
                 },
                 "bloomfilter_tablesize": {
-                    "type": "integer",
+                    "type": "number",
                     "description": "Maximum table size for bloom filter creation",
-                    "fa_icon": "fas fa-code-branch"
+                    "fa_icon": "fas fa-code-branch",
+                    "default": 100000000
                 }
             }
         },
@@ -487,14 +488,14 @@
     ],
     "properties": {
         "save_translate_csv": {
-            "type": "string",
-            "description": "Path to save the coding scores as a csv",
-            "default": "False"
+            "type": "boolean",
+            "description": "Save the coding scores as a csv",
+            "help_text": "Saving the translate results for each dataset makes it take extra long, it is recommended for debugging purposes only."
         },
         "save_translate_json": {
-            "type": "string",
-            "description": "Path to save summarization of coding/\"     \"noncoding/other categorizations, the \"     \"min/max/mean/median/stddev of Jaccard scores, and other as a json",
-            "default": "False"
+            "type": "boolean",
+            "description": "Save summarization of coding/noncoding/other categorizations, the min/max/mean/median/stddev of Jaccard scores, and other as a json",
+            "help_text": "Saving the translate results for each dataset makes it take extra long, it is recommended for debugging purposes only."
         }
     }
 }