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Update warning about additional_fasta and gene BED #1038

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Jun 1, 2023
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Update warning about additional_fasta and gene BED #1038

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65ed2b9
Update warning when using --additional_fasta to show clarify gene_bed
adamrtalbot Jun 1, 2023
58f005e
changelog
adamrtalbot Jun 1, 2023
73eae67
Update WorkflowRnaseq.groovy
drpatelh Jun 1, 2023
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1 change: 1 addition & 0 deletions CHANGELOG.md
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Expand Up @@ -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

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4 changes: 2 additions & 2 deletions lib/WorkflowRnaseq.groovy
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Expand Up @@ -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" +
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