From ab680b751a34a1e51f013466e6417eed5dc1834f Mon Sep 17 00:00:00 2001 From: Jonathan Manning Date: Fri, 16 Feb 2024 10:16:41 +0000 Subject: [PATCH 1/2] Pass transcriptome fasta through to samtools stats --- workflows/rnaseq/main.nf | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/workflows/rnaseq/main.nf b/workflows/rnaseq/main.nf index c62ca66bd..1b88ed2e5 100755 --- a/workflows/rnaseq/main.nf +++ b/workflows/rnaseq/main.nf @@ -334,7 +334,7 @@ workflow NFCORE_RNASEQ { // Co-ordinate sort, index and run stats on transcriptome BAM BAM_SORT_STATS_SAMTOOLS ( ch_transcriptome_bam, - ch_fasta.map { [ [:], it ] } + ch_transcript_fasta.map { [ [:], it ] } ) ch_transcriptome_sorted_bam = BAM_SORT_STATS_SAMTOOLS.out.bam ch_transcriptome_sorted_bai = BAM_SORT_STATS_SAMTOOLS.out.bai From 34f57c0f32727924f333ffe7ab02d4ac8a12225d Mon Sep 17 00:00:00 2001 From: Jonathan Manning Date: Fri, 16 Feb 2024 10:21:05 +0000 Subject: [PATCH 2/2] update changelog --- CHANGELOG.md | 1 + 1 file changed, 1 insertion(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index c93a8f724..a1a6fe5b8 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -14,6 +14,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - [PR #1206](https://github.com/nf-core/rnaseq/pull/1206) - Remove `lib/` directory and `modules.config` - [PR #1212](https://github.com/nf-core/rnaseq/pull/1212) - Update all modules and subworkflows to latest versions - [PR #1210](https://github.com/nf-core/rnaseq/pull/1210) - Use pseudoalignment subworkflow components from nf-core/modules +- [PR #1213](https://github.com/nf-core/rnaseq/pull/1213) - Pass transcriptome fasta through to samtools stats ### Parameters