Remove unused --bustools_correct and --skip_bustools

nf-core · Apr 20, 2023 · 5e15b65 · 5e15b65
1 parent 4f66ce8
commit 5e15b65
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diff --git a/nextflow.config b/nextflow.config
@@ -11,7 +11,6 @@ params {
 
     // generic options
     aligner           = 'alevin'
-    bustools_correct  = true
     outdir            = null
     input             = null
     save_reference    = false
@@ -30,7 +29,6 @@ params {
     // kallist bustools parameters
     kallisto_gene_map = null
     kallisto_index    = null
-    skip_bustools     = false
     kb_workflow       = "standard"
 
     // STARsolo parameters

diff --git a/nextflow_schema.json b/nextflow_schema.json
@@ -206,16 +206,6 @@
                     "description": "Specify a Kallisto gene mapping file here. If you don't, this will be automatically created in the Kallisto workflow when specifying a valid `--gtf` file.",
                     "fa_icon": "fas fa-fish"
                 },
-                "bustools_correct": {
-                    "type": "boolean",
-                    "description": "If set to false, skip the correct steps after mapping with Kallisto.",
-                    "fa_icon": "fas fa-bus-alt"
-                },
-                "skip_bustools": {
-                    "type": "boolean",
-                    "description": "Skip BUStools entirely in workflow",
-                    "fa_icon": "fas fa-forward"
-                },
                 "kallisto_index": {
                     "type": "string",
                     "description": "Specify a path to the precomputed Kallisto index.",