bugfix/update-fasta-help

CHANGELOG.md

@@ -3,6 +3,9 @@
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/)
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
+## Unreleased
+- ([#491](https://github.com/nf-core/smrnaseq/issues/491)) - Update help text for --fasta parameter.
+
 ## v2.4.0 - 2024-10-14 - Navy Iron Boxer
 
 - [[#349]](https://github.com/nf-core/smrnaseq/pull/349) - Fix [MIRTOP_QUANT conda issue](https://github.com/nf-core/smrnaseq/issues/347) - change conda-base to conda-forge channel.

nextflow_schema.json

@@ -133,7 +133,7 @@
                     "mimetype": "text/plain",
                     "pattern": "^\\S+\\.fn?a(sta)?(\\.gz)?$",
                     "description": "Path to FASTA genome file.",
-                    "help_text": "This parameter is *mandatory* if `--genome` is not specified. If you don't have a BWA index available this will be generated for you automatically. Combine with `--save_reference` to save BWA index for future runs.",
+                    "help_text": "FASTA file used for genome quantification and identification of novel miRNAs.  If you don't have a Bowtie1 index available, this will be generated for you automatically. Combine with `--save_reference` to save Bowtie1 index for future runs.",
                     "fa_icon": "far fa-file-code"
                 },
                 "mirna_gtf": {
@@ -254,8 +254,7 @@
                 },
                 "save_merged": {
                     "type": "boolean",
-                    "description": "Save merged reads.",
-                    "default": false
+                    "description": "Save merged reads."
                 },
                 "phred_offset": {
                     "type": "integer",

subworkflows/local/utils_nfcore_smrnaseq_pipeline/main.nf

@@ -169,10 +169,6 @@ workflow PIPELINE_COMPLETION {
 def validateInputParameters() {
     genomeExistsError()
 
-    if (!params.mirgenedb && !params.mirtrace_species) {
-            error("Reference species for miRTrace is not defined via the `--mirtrace_species` parameter.")
-    }
-
     if (!params.mirgenedb) {
         // Validate mature miRNA fasta file
         if (!params.mature) {