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Fix invalid named parameter syntax #1376

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Merged
pinin4fjords merged 5 commits into from
Sep 20, 2024
Merged

Fix invalid named parameter syntax #1376

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7b6915c
Update main.nf
pditommaso Sep 6, 2024
41bbfdf
Merge branch 'dev' into pditommaso-patch-1
ewels Sep 6, 2024
5d20e28
Update CHANGELOG.md
pinin4fjords Sep 10, 2024
41b44b0
Merge branch 'dev' into pditommaso-patch-1
maxulysse Sep 20, 2024
82c833d
Apply suggestions from code review
maxulysse Sep 20, 2024
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5 changes: 3 additions & 2 deletions CHANGELOG.md
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Expand Up @@ -7,8 +7,9 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0

### Enhancements & fixes

- [PR #1388](https://github.com/nf-core/rnaseq/pull/1351) - Adding Kraken2/Bracken on unaligned reads as an additional quality control step to detect sample contamination
- [PR #1186](https://github.com/nf-core/rnaseq/pull/1186) - Bump pipeline version to 3.16.0dev
- [PR #1376](https://github.com/nf-core/rnaseq/pull/1376) - Fix invalid named parameter syntax
- [PR #1386](https://github.com/nf-core/rnaseq/pull/1386) - Bump pipeline version to 3.16.0dev
- [PR #1388](https://github.com/nf-core/rnaseq/pull/1388) - Adding Kraken2/Bracken on unaligned reads as an additional quality control step to detect sample contamination

### Parameters

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2 changes: 1 addition & 1 deletion workflows/rnaseq/main.nf
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Expand Up @@ -597,7 +597,7 @@ workflow RNASEQ {
ch_strand_comparison = BAM_RSEQC.out.inferexperiment_txt
.map {
meta, strand_log ->
def rseqc_inferred_strand = getInferexperimentStrandedness(strand_log, stranded_threshold = params.stranded_threshold, unstranded_threshold = params.unstranded_threshold)
def rseqc_inferred_strand = getInferexperimentStrandedness(strand_log, params.stranded_threshold, params.unstranded_threshold)
rseqc_strandedness = rseqc_inferred_strand.inferred_strandedness

def status = 'fail'
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