From c6119bb52704a61c9e8b98ce55a5ff7f2e853a6c Mon Sep 17 00:00:00 2001
From: Toni Hermoso Pulido <toni.hermoso@crg.eu>
Date: Wed, 23 Oct 2024 18:44:29 +0200
Subject: [PATCH] More stuff

---
 TODO.md              |  2 +-
 main.nf              |  9 ---------
 nextflow.config      | 39 ++++++++++++++++++++++++++++++++++++++-
 nextflow_schema.json |  2 +-
 4 files changed, 40 insertions(+), 12 deletions(-)

diff --git a/TODO.md b/TODO.md
index ce5eeba..3c43d4e 100644
--- a/TODO.md
+++ b/TODO.md
@@ -1,5 +1,5 @@
 - Remove all params from modules
-- Make nextflow_schema.json by default (optional)
+- Adding CITATIONS.cff
 - Convert params.config to params.yaml/json (optional)
 - Include colors into the terminal messages (optional)
 - Consider notifications
diff --git a/main.nf b/main.nf
index 921aef7..99ad281 100644
--- a/main.nf
+++ b/main.nf
@@ -23,17 +23,8 @@ ExOrthist pipeline for Bioinformatics Core @ CRG
 
 nextflow.enable.dsl=2
 
-version = '2.0.0'
-
-/*
- * Input parameters:
-*/
-
-// params.resume          = false
-
 
 log_main = """
-
 ╔╦╗┬ ┬┌─┐  ╔═╗─┐ ┬╔═╗┬─┐┌┬┐┬ ┬┬┌─┐┌┬┐
  ║ ├─┤├┤   ║╣ ┌┴┬┘║ ║├┬┘ │ ├─┤│└─┐ │
  ╩ ┴ ┴└─┘  ╚═╝┴ └─╚═╝┴└─ ┴ ┴ ┴┴└─┘ ┴
diff --git a/nextflow.config b/nextflow.config
index c874119..506377d 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -5,7 +5,14 @@ env {
 }
 
 manifest {
-    mainScript = 'main.nf'
+  name            = 'biocorecrg/ExOrthist'
+  mainScript      = 'main.nf'
+  author          = """Luca Cozzuto, Federica Mantica, Toni Hermoso Pulido"""
+  homePage        = 'https://github.com/biocorecrg/ExOrthist'
+  description     = """ExOrthist is a Nextflow-based pipeline to obtain groups of exon orthologous at all evolutionary timescales."""
+  nextflowVersion = '!>=24.04.2'
+  version         = '2.0.0'
+  doi             = 'https://doi.org/10.1186/s13059-021-02441-9'
 }
 
 plugins {
@@ -16,6 +23,36 @@ validation {
     help {
         enabled = true
         command = "nextflow run main.nf -with-docker"
+        fullParameter = "help_full"
+        showHiddenParameter = "show_hidden"
+        beforeText = """
+╔╦╗┬ ┬┌─┐  ╔═╗─┐ ┬╔═╗┬─┐┌┬┐┬ ┬┬┌─┐┌┬┐
+ ║ ├─┤├┤   ║╣ ┌┴┬┘║ ║├┬┘ │ ├─┤│└─┐ │
+ ╩ ┴ ┴└─┘  ╚═╝┴ └─╚═╝┴└─ ┴ ┴ ┴┴└─┘ ┴
+
+==============================================================================
+INFORMATION ABOUT OPTIONS:
+The long, medium, short distance cut-offs are in the format: "int_num;ex_seq;ex_len;prot_sim".
+Only exon matches respecting all cut-offs are considered homologous.
+- int_num (0,1,2): Number of surrounding intron positions required to be conserved.
+- ex_seq (from 0 to 1): Minimum sequence similarity % between a
+     pair of homologous exons and their corresponding upstream and
+     downstream exons.
+- ex_len (from 0 to 1): Maximum size difference between two homologous exons
+     (as a fraction of either exon).
+- prot_sim (from 0 to 1): Minimum sequence similarity over the entire pairwise alignment
+     for a pair of protein isoforms to be considered for comparison.
+
+See online README at https://github.com/biocorecrg/ExOrthist for further information about the options.
+"""
+        afterText = """${manifest.doi ? "* The pipeline\n" : ""}${manifest.doi.tokenize(",").collect { "  https://doi.org/${it.trim().replace('https://doi.org/','')}"}.join("\n")}${manifest.doi ? "\n" : ""}
+* Software dependencies
+    https://github.com/${manifest.name}/blob/master/CITATIONS.md
+"""
+      summary {
+        beforeText = validation.help.beforeText
+        afterText = validation.help.afterText
+      }
     }
 }
 
diff --git a/nextflow_schema.json b/nextflow_schema.json
index 3dcd0be..f991ad4 100644
--- a/nextflow_schema.json
+++ b/nextflow_schema.json
@@ -2,7 +2,7 @@
   "$schema": "https://json-schema.org/draft/2020-12/schema",
   "$id": "https://raw.githubusercontent.com/biocorecrg/exorthist/master/nextflow_schema.json",
   "title": "ExOrthist pipeline parameters",
-  "description": "Schema for the parameters of your ExOrthist pipeline",
+  "description": "ExOrthist is a Nextflow-based pipeline to obtain groups of exon orthologous at all evolutionary timescales",
   "type": "object",
   "$defs": {
     "generic_options": {