From 4abc514e63bc24f685c49275c0507aff1dca30cb Mon Sep 17 00:00:00 2001 From: Jonathan Manning Date: Thu, 15 Aug 2024 17:07:22 +0100 Subject: [PATCH 1/2] correct conditional for salmon indexing in proprocessing workflow --- workflows/rnaseq/main.nf | 6 +++++- 1 file changed, 5 insertions(+), 1 deletion(-) diff --git a/workflows/rnaseq/main.nf b/workflows/rnaseq/main.nf index 7bf5d36e0..facd42e5f 100755 --- a/workflows/rnaseq/main.nf +++ b/workflows/rnaseq/main.nf @@ -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, @@ -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, From 0e6d601a123c71e678cedc6df9a20396b006a50d Mon Sep 17 00:00:00 2001 From: Jonathan Manning Date: Thu, 15 Aug 2024 17:16:42 +0100 Subject: [PATCH 2/2] Update CHANGELOG.md --- CHANGELOG.md | 2 ++ 1 file changed, 2 insertions(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index ffc3b4db4..c7b25a6d9 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -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) @@ -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