From 254ad0466eafd702ed79c10096946ccdb5a1d1ab Mon Sep 17 00:00:00 2001 From: Jonathan Manning Date: Wed, 18 Dec 2024 11:45:13 +0000 Subject: [PATCH 1/2] Fix prepare_genome subworkflow for sortmerna --- subworkflows/local/prepare_genome/main.nf | 8 +++++--- 1 file changed, 5 insertions(+), 3 deletions(-) diff --git a/subworkflows/local/prepare_genome/main.nf b/subworkflows/local/prepare_genome/main.nf index 92f8cc04a..c1b8b4c66 100644 --- a/subworkflows/local/prepare_genome/main.nf +++ b/subworkflows/local/prepare_genome/main.nf @@ -233,16 +233,18 @@ workflow PREPARE_GENOME { if ('sortmerna' in prepare_tool_indices) { ribo_db = file(sortmerna_fasta_list) + // SortMeRNA needs the rRNAs even if we're providing the index + ch_rrna_fastas = Channel.from(ribo_db.readLines()) + .map { row -> file(row, checkIfExists: true) } + if (sortmerna_index) { if (sortmerna_index.endsWith('.tar.gz')) { ch_sortmerna_index = UNTAR_SORTMERNA_INDEX ( [ [:], sortmerna_index ] ).untar.map { it[1] } ch_versions = ch_versions.mix(UNTAR_SORTMERNA_INDEX.out.versions) } else { - ch_sortmerna_index = Channel.value(file(sortmerna_index)) + ch_sortmerna_index = Channel.value([[:], file(sortmerna_index)]) } } else { - ch_rrna_fastas = Channel.from(ribo_db.readLines()) - .map { row -> file(row, checkIfExists: true) } SORTMERNA_INDEX ( Channel.of([ [],[] ]), From ae6990ac300197bf9f499017b6aa63694c22d23b Mon Sep 17 00:00:00 2001 From: Jonathan Manning Date: Wed, 18 Dec 2024 15:13:31 +0000 Subject: [PATCH 2/2] Update CHANGELOG.md --- CHANGELOG.md | 1 + 1 file changed, 1 insertion(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index a1059f292..5f82b2dd1 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -21,6 +21,7 @@ Special thanks to the following for their contributions to the release: - [PR #1466](https://github.com/nf-core/rnaseq/pull/1466) - Factor out UMI handling - [PR #1469](https://github.com/nf-core/rnaseq/pull/1469) - Minor docs fix - [PR #1459](https://github.com/nf-core/rnaseq/pull/1466) - Remove reference to unused "skip_sample_count" value in email templates +- [PR #1471](https://github.com/nf-core/rnaseq/pull/1471) - Fix prepare_genome subworkflow for sortmerna ### Software dependencies