Update to add default to flag

sanger-tol · Nov 15, 2024 · 5fb3c96 · 5fb3c96
1 parent 382f7f4
commit 5fb3c96
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Showing 2 changed files with 4 additions and 4 deletions.
diff --git a/workflows/treeval_rapid.nf b/workflows/treeval_rapid.nf
@@ -53,9 +53,9 @@ workflow TREEVAL_RAPID {
     main:
     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"

diff --git a/workflows/treeval_rapid_tol.nf b/workflows/treeval_rapid_tol.nf
@@ -53,9 +53,9 @@ workflow TREEVAL_RAPID_TOL {
     main:
     ch_versions     = Channel.empty()
 
-    exclude_workflow_steps  = params.exclude ? params.exclude.split(",") : ""
+    exclude_workflow_steps  = params.exclude ? params.exclude.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"