From 450c62b02a7b5397de89b70615d2c44506d36c9c Mon Sep 17 00:00:00 2001
From: Toni Hermoso Pulido <toni.hermoso@crg.eu>
Date: Wed, 23 Oct 2024 13:21:36 +0200
Subject: [PATCH] Minor updates

---
 main.nf              | 11 +++++------
 nextflow.config      |  9 ++++++++-
 nextflow_schema.json |  2 +-
 params.config.test   | 12 ++++++------
 4 files changed, 20 insertions(+), 14 deletions(-)

diff --git a/main.nf b/main.nf
index 2f57584..3b6635e 100644
--- a/main.nf
+++ b/main.nf
@@ -29,7 +29,6 @@ version = '2.0.0'
  * Input parameters:
 */
 
-params.help            = false
 params.resume          = false
 
 
@@ -83,12 +82,8 @@ reclustered gene orthology file     : ${params.sub_orthologs}
 
 """
 
+include { paramsHelp; paramsSummaryMap; validateParameters } from 'plugin/nf-schema'
 
-if (params.help) {
-    log.info """ExOrthist v2.0.0"""
-    log.info """ExOrthist is a Nextflow-based pipeline to obtain groups of exon orthologous at all evolutionary timescales.\n"""
-    exit 1
-}
 if (params.resume) exit 1, "Are you making the classical --resume typo? Be careful!!!! ;)"
 
 // if( !workflow.resume ) {
@@ -106,8 +101,12 @@ include { SCORE } from "${LOCAL_SUBWORKFLOWS}/score.nf"
 
 include { PLOT } from "${WORKFLOWS}/plot.nf"
 
+// println paramsSummaryMap(workflow)
+
 workflow {
 
+    // validateParameters()
+
     if (params.wf == "plot" ) {
         log.info(log_plot)
         geneclusters_path = "${params.output}/gene_cluster_file.gz"
diff --git a/nextflow.config b/nextflow.config
index 089a225..c874119 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -9,7 +9,14 @@ manifest {
 }
 
 plugins {
-  id 'nf-schema@2.0.0'
+  id 'nf-schema@2.1.2'
+}
+
+validation {
+    help {
+        enabled = true
+        command = "nextflow run main.nf -with-docker"
+    }
 }
 
 includeConfig "$projectDir/params.config"
diff --git a/nextflow_schema.json b/nextflow_schema.json
index 49bd2d0..dab100b 100644
--- a/nextflow_schema.json
+++ b/nextflow_schema.json
@@ -174,7 +174,7 @@
           "type": "string",
           "description": "Email for notification",
           "format": "email",
-          "default": "yourmail@yourdomain"
+          "default": "yourmail@yourdomain.xyz"
         }
       }
     }
diff --git a/params.config.test b/params.config.test
index c87bc74..a061ba0 100644
--- a/params.config.test
+++ b/params.config.test
@@ -5,20 +5,20 @@ params {
     annotations    = "$projectDir/test/GTF/*_annot-subsetted.gtf.gz"
     alignmentnum   = 1000
     orthogroupnum  = 500
-    extraexons     = ""
-    bonafide_pairs = ""
-    orthopairs     = ""
+    extraexons     = null
+    bonafide_pairs = null
+    orthopairs     = null
     evodists       = "$projectDir/test/evodists.txt"
     long_dist      = "2,0.10,0.40,0.15"
     medium_dist    = "2,0.30,0.60,0.20"
     short_dist     = "2,0.50,0.60,0.25"
-    prevaln        = ""
+    prevaln        = null
     output         = "$projectDir/output_test"
-    email          = "yourmail@yourdomain"
+    email          = "yourmail@yourdomain.xyz"
     geneID         = "ENSG00000159055"
     output_plot    = "$projectDir/output_plot"
     relevant_exs   = "chr21:32274830-32274896"
     ordered_species= "hg38,mm10,bosTau9"
     isoformID      = "ENSP00000290130"
-    sub_orthologs  = ""
+    sub_orthologs  = null
 }