From 382f7f4b36036c917bdc5937fa14be81326408b6 Mon Sep 17 00:00:00 2001
From: DLBPointon <damonlbp@hotmail.co.uk>
Date: Fri, 15 Nov 2024 12:16:51 +0000
Subject: [PATCH] Update to add default to flag

---
 nextflow.config      | 2 +-
 workflows/treeval.nf | 4 ++--
 2 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/nextflow.config b/nextflow.config
index e4763ca0..b9439082 100755
--- a/nextflow.config
+++ b/nextflow.config
@@ -14,7 +14,7 @@ params {
     input                      = null
     outdir                     = "./results"
     juicer                     = false
-    steps                      = ""
+    steps                      = "NONE"
     tracedir                   = "${params.outdir}/pipeline_info"
     publish_dir_mode           = 'copy'
     email                      = null
diff --git a/workflows/treeval.nf b/workflows/treeval.nf
index 64d55a2a..8dc903bc 100755
--- a/workflows/treeval.nf
+++ b/workflows/treeval.nf
@@ -63,9 +63,9 @@ workflow TREEVAL {
     //
     ch_versions     = Channel.empty()
 
-    exclude_workflow_steps  = params.steps ? params.steps.split(",") : ""
+    exclude_workflow_steps  = params.steps ? params.steps.split(",") : "NONE"
 
-    full_list       = ["insilico_digest", "gene_alignments", "repeat_density", "gap_finder", "selfcomp", "synteny", "read_coverage", "telo_finder", "busco", "kmer", "hic_mapping", ""]
+    full_list       = ["insilico_digest", "gene_alignments", "repeat_density", "gap_finder", "selfcomp", "synteny", "read_coverage", "telo_finder", "busco", "kmer", "hic_mapping", "NONE"]
 
     if (!full_list.containsAll(exclude_workflow_steps)) {
         exit 1, "There is an extra argument given on Command Line: \n Check contents of --exclude: $exclude_workflow_steps\nMaster list is: $full_list"