Merge pull request #1038 from adamrtalbot/update_warning_about_additional_fasta

Update warning about additional_fasta and gene BED

Author: drpatelh

CHANGELOG.md

@@ -11,6 +11,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - [[#1018](https://github.com/nf-core/rnaseq/issues/1018)] - Ability to skip both alignment and pseudo-alignment to only run pre-processing QC steps.
 - [PR #1016](https://github.com/nf-core/rnaseq/pull/1016) - Updated pipeline template to [nf-core/tools 2.8](https://github.com/nf-core/tools/releases/tag/2.8)
 - [PR #1025](https://github.com/nf-core/fetchngs/pull/1025) - Add `public_aws_ecr.config` to source mulled containers when using `public.ecr.aws` Docker Biocontainer registry
+- [PR #1038](https://github.com/nf-core/rnaseq/pull/1038) - Updated error log for count values when supplying `--additional_fasta`
 
 ### Parameters
 

lib/WorkflowRnaseq.groovy

@@ -402,8 +402,8 @@ class WorkflowRnaseq {
             "  When using '--additional_fasta <FASTA_FILE>' the aligner index will not\n" +
             "  be re-built with the transgenes incorporated by default since you have \n" +
             "  already provided an index via '--${index}_index <INDEX>'.\n\n" +
-            "  Set '--additional_fasta <FASTA_FILE> --${index}_index false --save_reference' to\n" +
-            "  re-build the index with transgenes included and the index will be saved in\n" +
+            "  Set '--additional_fasta <FASTA_FILE> --${index}_index false --gene_bed false --save_reference'\n" +
+            "  to re-build the index with transgenes included and the index and gene BED file will be saved in\n" +
             "  'results/genome/index/${index}/' for re-use with '--${index}_index'.\n\n" +
             "  Ignore this warning if you know that the index already contains transgenes.\n\n" +
             "  Please see:\n" +