From 457bdd992a86116dc6b3e5278e381b59024919e7 Mon Sep 17 00:00:00 2001 From: Jonathan Manning Date: Fri, 13 Sep 2024 11:29:53 +0100 Subject: [PATCH 1/2] Fix R module name-mangling issues --- modules.json | 4 ++-- .../summarizedexperiment/summarizedexperiment/environment.yml | 2 -- .../summarizedexperiment/templates/summarizedexperiment.r | 2 +- modules/nf-core/tximeta/tximport/environment.yml | 2 -- modules/nf-core/tximeta/tximport/templates/tximport.r | 2 +- 5 files changed, 4 insertions(+), 8 deletions(-) diff --git a/modules.json b/modules.json index 6e266bc86..fc53bd567 100644 --- a/modules.json +++ b/modules.json @@ -227,7 +227,7 @@ }, "summarizedexperiment/summarizedexperiment": { "branch": "master", - "git_sha": "4e5f4687318f24ba944a13609d3ea6ebd890737d", + "git_sha": "625fbbc0531fb1717349c7f1b1c677a3b8619767", "installed_by": ["modules", "quantify_pseudo_alignment"] }, "trimgalore": { @@ -237,7 +237,7 @@ }, "tximeta/tximport": { "branch": "master", - "git_sha": "d612c281cf2fae62cdd79c70a22fc6349108570c", + "git_sha": "625fbbc0531fb1717349c7f1b1c677a3b8619767", "installed_by": ["modules", "quantify_pseudo_alignment"] }, "ucsc/bedclip": { diff --git a/modules/nf-core/summarizedexperiment/summarizedexperiment/environment.yml b/modules/nf-core/summarizedexperiment/summarizedexperiment/environment.yml index 252ace791..dc4e6c936 100644 --- a/modules/nf-core/summarizedexperiment/summarizedexperiment/environment.yml +++ b/modules/nf-core/summarizedexperiment/summarizedexperiment/environment.yml @@ -1,9 +1,7 @@ --- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json -name: "summarizedexperiment_summarizedexperiment" channels: - conda-forge - bioconda - - defaults dependencies: - "bioconda::bioconductor-summarizedexperiment=1.32.0" diff --git a/modules/nf-core/summarizedexperiment/summarizedexperiment/templates/summarizedexperiment.r b/modules/nf-core/summarizedexperiment/summarizedexperiment/templates/summarizedexperiment.r index 6c705350a..60ea3179f 100644 --- a/modules/nf-core/summarizedexperiment/summarizedexperiment/templates/summarizedexperiment.r +++ b/modules/nf-core/summarizedexperiment/summarizedexperiment/templates/summarizedexperiment.r @@ -13,7 +13,7 @@ library(SummarizedExperiment) #' #' @return output Data frame -read_delim_flexible <- function(file, header = TRUE, row.names = NULL, check.names = TRUE, stringsAsFactors = FALSE){ +read_delim_flexible <- function(file, header = TRUE, row.names = NULL, check.names = FALSE, stringsAsFactors = FALSE){ ext <- tolower(tail(strsplit(basename(file), split = "\\\\.")[[1]], 1)) diff --git a/modules/nf-core/tximeta/tximport/environment.yml b/modules/nf-core/tximeta/tximport/environment.yml index 24b202222..4b6df0cfe 100644 --- a/modules/nf-core/tximeta/tximport/environment.yml +++ b/modules/nf-core/tximeta/tximport/environment.yml @@ -1,9 +1,7 @@ --- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json -name: "tximeta_tximport" channels: - conda-forge - bioconda - - defaults dependencies: - "bioconda::bioconductor-tximeta=1.20.1" diff --git a/modules/nf-core/tximeta/tximport/templates/tximport.r b/modules/nf-core/tximeta/tximport/templates/tximport.r index e8235c8b0..5986c05d9 100755 --- a/modules/nf-core/tximeta/tximport/templates/tximport.r +++ b/modules/nf-core/tximeta/tximport/templates/tximport.r @@ -26,7 +26,7 @@ library(tximport) #' @return A data frame combining the first two columns of the rowData with the assay data from the specified slot. build_table <- function(se.obj, slot) { - cbind(rowData(se.obj)[,1:2], assays(se.obj)[[slot]]) + data.frame(cbind(rowData(se.obj)[,1:2], assays(se.obj)[[slot]]), check.names = FALSE) } #' Write a table to a file from a SummarizedExperiment object with given parameters From 765e67df300d2399d45efcf95271a87d4d598e41 Mon Sep 17 00:00:00 2001 From: Jonathan Manning Date: Fri, 13 Sep 2024 11:35:44 +0100 Subject: [PATCH 2/2] Bump changelog --- CHANGELOG.md | 1 + 1 file changed, 1 insertion(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index e1976f761..76a96cf3a 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -6,6 +6,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ## v3.16.0dev - [date] - [PR #1374](https://github.com/nf-core/rnaseq/pull/1374) - Bump pipeline version to 3.16.0dev +- [PR #1380](https://github.com/nf-core/rnaseq/pull/1380) - Fix issues with R modules changing sample names ### Credits