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biocorecrg · Oct 24, 2024 · 8c52857 · 8c52857
1 parent 67e8367
commit 8c52857
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Showing 4 changed files with 34 additions and 97 deletions.
diff --git a/main.nf b/main.nf
@@ -1,15 +1,10 @@
 #!/usr/bin/env nextflow
 
-
 /*
  * Copyright (c) 2019-2024, Centre for Genomic Regulation (CRG)
  *
- * This Source Code Form is subject to the terms of the Mozilla Public
- * License, v. 2.0. If a copy of the MPL was not distributed with this
- * file, You can obtain one at http://mozilla.org/MPL/2.0/.
  */
 
-
 /*
 ===========================================================
 ExOrthist pipeline for Bioinformatics Core @ CRG
@@ -23,60 +18,6 @@ ExOrthist pipeline for Bioinformatics Core @ CRG
 
 nextflow.enable.dsl=2
 
-
-log_main = """
-╔╦╗┬ ┬┌─┐  ╔═╗─┐ ┬╔═╗┬─┐┌┬┐┬ ┬┬┌─┐┌┬┐
- ║ ├─┤├┤   ║╣ ┌┴┬┘║ ║├┬┘ │ ├─┤│└─┐ │
- ╩ ┴ ┴└─┘  ╚═╝┴ └─╚═╝┴└─ ┴ ┴ ┴┴└─┘ ┴
-
-==============================================================================
-annotations (GTF files)             : ${params.annotations}
-genomes (fasta files)               : ${params.genomes}
-cluster file (txt files)            : ${params.cluster}
-pairwise evo distances              : ${params.evodists}
-long distance parameters            : ${params.long_dist}
-medium distance parameters          : ${params.medium_dist}
-short distance parameters           : ${params.short_dist}
-pre-computed alignments             : ${params.prevaln}
-alignment number                    : ${params.alignmentnum}
-orthogroup number                   : ${params.orthogroupnum}
-extraexons (e.g. from VastDB)       : ${params.extraexons}
-bona fide orthologous exon pairs    : ${params.bonafide_pairs}
-orthopairs                          : ${params.orthopairs}
-output (output folder)              : ${params.output}
-email for notification              : ${params.email}
-hook_url                            : ${params.hook_url}
-
-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.
-"""
-
-log_plot = """
-Executing with the following parameters:
-
-output main                         : ${params.output}
-output plot                         : ${params.output_plot}
-geneID                              : ${params.geneID}
-isoformID                           : ${params.isoformID}
-relevant exons                      : ${params.relevant_exs}
-reclustered gene orthology file     : ${params.sub_orthologs}
-email for notification              : ${params.email}
-hook_url                            : ${params.hook_url}
-"""
-
-include { paramsHelp; validateParameters } from 'plugin/nf-schema'
-
 // if( !workflow.resume ) {
 //     println "Removing the output folder"
 // 	  new File("${params.output}").delete()
@@ -87,19 +28,23 @@ WORKFLOWS='./workflows/'
 
 include { ALIGN } from "${LOCAL_SUBWORKFLOWS}/align.nf"
 include { CLUSTER } from "${LOCAL_SUBWORKFLOWS}/cluster.nf"
+
+include { PIPELINE_COMPLETION; PIPELINE_INITIALISATION } from "${LOCAL_SUBWORKFLOWS}/util.nf"
+
 include { PREPARE } from "${LOCAL_SUBWORKFLOWS}/prepare.nf"
 include { SCORE } from "${LOCAL_SUBWORKFLOWS}/score.nf"
 
 include { PLOT } from "${WORKFLOWS}/plot.nf"
 
-include { final_message; notify_slack } from "./lib/functions.nf"
-
 workflow {
 
-    validateParameters()
+    PIPELINE_INITIALISATION(
+        params,
+        args
+    )
 
     if (params.wf == "plot" ) {
-        log.info(log_plot)
+
         PLOT(
             params.output,
             params.geneID,
@@ -110,7 +55,6 @@ workflow {
         )
 
     } else {
-        log.info(log_main)
 
         PREPARE(
             params.evodists,
@@ -154,15 +98,10 @@ workflow {
         )
     }
 
-}
+    PIPELINE_COMPLETION(
+        params.wf,
+        params.email,
+        params.hook_url
+    )
 
-workflow.onComplete {
-    def text = final_message("ExOrthist", params.wf)
-    println text
-    if (params.email) {
-        sendMail(to: params.email, subject: "[ExOrthist] Execution finished", body: msg)
-    }
-    if (params.hook_url) {
-        notify_slack(text, params.hook_url)
-    }
 }
diff --git a/nextflow.config b/nextflow.config
@@ -30,24 +30,11 @@ validation {
  ║ ├─┤├┤   ║╣ ┌┴┬┘║ ║├┬┘ │ ├─┤│└─┐ │
  ╩ ┴ ┴└─┘  ╚═╝┴ └─╚═╝┴└─ ┴ ┴ ┴┴└─┘ ┴
 
-==============================================================================
-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.
+See online README at https://github.com/biocorecrg/ExOrthist for further information.
 """
         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/${manifest.name}/blob/master/CITATIONS.md
+  https://github.com/${manifest.name}/blob/master/CITATIONS.md
 """
       summary {
         beforeText = validation.help.beforeText

diff --git a/nextflow_schema.json b/nextflow_schema.json
@@ -15,6 +15,13 @@
           "type": "string",
           "description": "Workflow to be run, by default the main one. Alternative is plot",
           "default": "main"
+        },
+        "validate_params": {
+          "type": "boolean",
+          "description": "Boolean whether to validate parameters against the schema at runtime",
+          "default": true,
+          "fa_icon": "fas fa-check-square",
+          "hidden": true
         }
       }
     },
@@ -85,11 +92,6 @@
           "description": "Short distance parameters",
           "default": "2,0.50,0.60,0.25"
         },
-        "prevaln": {
-          "type": "string",
-          "description": "Pre-computed alignments",
-          "format": "directory-path"
-        },
         "alignmentnum": {
           "type": "integer",
           "description": "Alignment number",
@@ -120,6 +122,11 @@
           "type": "string",
           "description": "Orthopairs",
           "format": "file-path"
+        },
+        "prevaln": {
+          "type": "string",
+          "description": "Pre-computed alignments",
+          "format": "directory-path"
         }
       }
     },

diff --git a/params.config.test b/params.config.test
@@ -1,6 +1,8 @@
 params {
     // Generic options
     wf               = "main"
+    // Schema validation default options
+    validate_params  = true
     // Notification options
     hook_url         = null
     email            = null
@@ -10,14 +12,16 @@ params {
     annotations      = "$projectDir/test/GTF/*_annot-subsetted.gtf.gz"
     alignmentnum     = 1000
     orthogroupnum    = 500
-    extraexons       = null
-    bonafide_pairs   = null
-    orthopairs       = null
     evodists         = "$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"
+    // Additional data
+    extraexons       = null
+    bonafide_pairs   = null
+    orthopairs       = null
     prevaln          = null
+    // Output folder
     output           = "$projectDir/output_test"
     // Plot pipeline specific options
     geneID           = "ENSG00000159055"