moving to params.yaml

TODO.md

@@ -1,4 +1,3 @@
-- Convert params.config to params.yaml/json (optional)
 - Review params.output from modules (optional)
 - Add stub to modules (optional)
 - Include colors into the terminal messages (optional)

nextflow.config

@@ -43,8 +43,40 @@ See online README at https://github.com/biocorecrg/ExOrthist for further informa
     }
 }
 
-includeConfig "$projectDir/params.config"
-
+// Default params
+params {
+    // Generic options
+    wf               = "main"
+    // Schema validation default options
+    validate_params  = true
+    // Notification options
+    hook_url         = null
+    email            = null
+    // Main pipeline options
+    cluster          = "$projectDir/test/hg38_mm10_bosTau9.tab"
+    genomes          = "$projectDir/test/GENOMES/*_gDNA-subsetted.fasta.gz"
+    annotations      = "$projectDir/test/GTF/*_annot-subsetted.gtf.gz"
+    alignmentnum     = 1000
+    orthogroupnum    = 500
+    evodists         = "$projectDir/test/evodists.txt"
+    long_dist        = "2,0.10,0.40,0.15"
+    medium_dist      = "2,0.30,0.60,0.20"
+    short_dist       = "2,0.50,0.60,0.25"
+    // Additional data
+    extraexons       = null
+    bonafide_pairs   = null
+    orthopairs       = null
+    prevaln          = null
+    // Output folder
+    output           = "$projectDir/output_test"
+    // Plot pipeline specific options
+    geneID           = "ENSG00000159055"
+    output_plot      = "$projectDir/output_plot"
+    relevant_exs     = "chr21:32274830-32274896"
+    ordered_species  = "hg38,mm10,bosTau9"
+    isoformID        = "ENSP00000290130"
+    sub_orthologs    = null
+}
 
 process {
     containerOptions = { workflow.containerEngine == "docker" ? '-e USER=$USER -e HOME=$HOME -u $(id -u):$(id -g)': null}

params.yaml

@@ -0,0 +1,31 @@
+# Generic options
+wf: "main"
+# Schema validation default options
+validate_params: true
+# Notification options
+hook_url: null
+email: null
+# Main pipeline options
+cluster: "./test/hg38_mm10_bosTau9.tab"
+genomes: "./test/GENOMES/*_gDNA-subsetted.fasta.gz"
+annotations: "./test/GTF/*_annot-subsetted.gtf.gz"
+alignmentnum: 1000
+orthogroupnum: 500
+evodists: "./test/evodists.new.txt"
+long_dist: "2,0.10,0.40,0.15"
+medium_dist: "2,0.30,0.60,0.20"
+short_dist: "2,0.50,0.60,0.25"
+# Additional data
+extraexons: null
+bonafide_pairs: null
+orthopairs: null
+prevaln: null
+# Output folder
+output: "./output_test"
+# Plot pipeline specific options
+geneID: "ENSG00000159055"
+output_plot: "./output_plot"
+relevant_exs: "chr21:32274830-32274896"
+ordered_species: "hg38,mm10,bosTau9"
+isoformID: "ENSP00000290130"
+sub_orthologs: null