From 4805060ef685aa965355de4997e145157b156a6f Mon Sep 17 00:00:00 2001
From: atrigila <18577080+atrigila@users.noreply.github.com>
Date: Sun, 13 Oct 2024 20:30:59 +0000
Subject: [PATCH] remove duplicates from new template

---
 nextflow.config | 43 -------------------------------------------
 1 file changed, 43 deletions(-)

diff --git a/nextflow.config b/nextflow.config
index d03d2919..c45ce2f9 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -106,7 +106,6 @@ params {
 
     // Schema validation default options
     validate_params            = true
-    validate_params            = true
 }
 
 // Load base.config by default for all pipelines
@@ -126,7 +125,6 @@ profiles {
         shifter.enabled         = false
         charliecloud.enabled    = false
         conda.channels          = ['conda-forge', 'bioconda']
-        conda.channels          = ['conda-forge', 'bioconda']
         apptainer.enabled       = false
     }
     mamba {
@@ -248,11 +246,6 @@ docker.registry       = 'quay.io'
 podman.registry       = 'quay.io'
 singularity.registry  = 'quay.io'
 charliecloud.registry = 'quay.io'
-apptainer.registry    = 'quay.io'
-docker.registry       = 'quay.io'
-podman.registry       = 'quay.io'
-singularity.registry  = 'quay.io'
-charliecloud.registry = 'quay.io'
 
 // Load igenomes.config if required
 includeConfig !params.igenomes_ignore ? 'conf/igenomes.config' : 'conf/igenomes_ignored.config'
@@ -354,41 +347,5 @@ validation {
     }
 }
 
-// Nextflow plugins
-plugins {
-    id 'nf-schema@2.1.1' // Validation of pipeline parameters and creation of an input channel from a sample sheet
-}
-
-validation {
-    defaultIgnoreParams = ["genomes"]
-    help {
-        enabled = true
-        command = "nextflow run $manifest.name -profile <docker/singularity/.../institute> --input samplesheet.csv --outdir <OUTDIR>"
-        fullParameter = "help_full"
-        showHiddenParameter = "show_hidden"
-        beforeText = """
--\033[2m----------------------------------------------------\033[0m-
-                                        \033[0;32m,--.\033[0;30m/\033[0;32m,-.\033[0m
-\033[0;34m        ___     __   __   __   ___     \033[0;32m/,-._.--~\'\033[0m
-\033[0;34m  |\\ | |__  __ /  ` /  \\ |__) |__         \033[0;33m}  {\033[0m
-\033[0;34m  | \\| |       \\__, \\__/ |  \\ |___     \033[0;32m\\`-._,-`-,\033[0m
-                                        \033[0;32m`._,._,\'\033[0m
-\033[0;35m  ${manifest.name} ${manifest.version}\033[0m
--\033[2m----------------------------------------------------\033[0m-
-"""
-        afterText = """${manifest.doi ? "* The pipeline\n" : ""}${manifest.doi.tokenize(",").collect { "  https://doi.org/${it.trim().replace('https://doi.org/','')}"}.join("\n")}${manifest.doi ? "\n" : ""}
-* The nf-core framework
-    https://doi.org/10.1038/s41587-020-0439-x
-
-* Software dependencies
-    https://github.com/${manifest.name}/blob/master/CITATIONS.md
-"""
-    }
-    summary {
-        beforeText = validation.help.beforeText
-        afterText = validation.help.afterText
-    }
-}
-
 // Load modules.config for DSL2 module specific options
 includeConfig 'conf/modules.config'