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Correct conditional for salmon indexing in preprocessing workflow #1353

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Aug 16, 2024
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Correct conditional for salmon indexing in preprocessing workflow #1353

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4abc514
correct conditional for salmon indexing in proprocessing workflow
pinin4fjords Aug 15, 2024
0e6d601
Update CHANGELOG.md
pinin4fjords Aug 15, 2024
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2 changes: 2 additions & 0 deletions CHANGELOG.md
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Expand Up @@ -10,6 +10,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
Special thanks to the following for their contributions to the release:

- [Adam Talbot](https://github.com/adamrtalbot)
- [David Carlson](https://github.com/davidecarlson)
- [Edmund Miller](https://github.com/edmundmiller)
- [Jonathan Manning](https://github.com/pinin4fjords)
- [Laramie Lindsey](https://github.com/laramiellindsey)
Expand Down Expand Up @@ -107,6 +108,7 @@ Thank you to everyone else that has contributed by reporting bugs, enhancements
- [PR #1342](https://github.com/nf-core/rnaseq/pull/1342) - Factor out preprocessing
- [PR #1345](https://github.com/nf-core/rnaseq/pull/1345) - Fix preprocessing call
- [PR #1350](https://github.com/nf-core/rnaseq/pull/1350) - Reduce resource usage for sort process in bedtools/genomecov
- [PR #1353](https://github.com/nf-core/rnaseq/pull/1353) - Correct conditional for salmon indexing in preprocessing workflow

### Parameters

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6 changes: 5 additions & 1 deletion workflows/rnaseq/main.nf
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Expand Up @@ -126,6 +126,10 @@ workflow RNASEQ {
// Run RNA-seq FASTQ preprocessing subworkflow
//

// The subworkflow only has to do Salmon indexing if it discovers 'auto'
// samples, and if we haven't already made one elsewhere
salmon_index_available = params.salmon_index || (!params.skip_pseudo_alignment && params.pseudo_aligner == 'salmon')

FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS (
ch_fastq,
ch_fasta,
Expand All @@ -139,7 +143,7 @@ workflow RNASEQ {
params.skip_fastqc || params.skip_qc,
params.skip_trimming,
params.skip_umi_extract,
!params.salmon_index && params.pseudo_aligner == 'salmon' && !params.skip_pseudo_alignment,
!salmon_index_available,
!params.sortmerna_index && params.remove_ribo_rna,
params.trimmer,
params.min_trimmed_reads,
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