Merge branch 'dev' into ci_relative_paths

Author: adamrtalbot

.github/workflows/cloud_tests_full.yml

@@ -1,18 +1,20 @@
 name: full-sized tests on cloud providers
 run-name: Submitting workflow to all cloud providers using full sized data
 on:
+  release:
+    types: [published]
   workflow_dispatch:
     inputs:
-        platform:
-          description: 'Platform to run test'
-          required: true
-          default: 'all'
-          type: choice
-          options:
-            - all
-            - aws
-            - azure
-            - gcp
+      platform:
+        description: "Platform to run test"
+        required: true
+        default: "all"
+        type: choice
+        options:
+          - all
+          - aws
+          - azure
+          - gcp
 jobs:
   run-full-tests-on-aws:
     if: ${{ github.event.inputs.platform == 'all' || github.event.inputs.platform == 'aws' }}

.github/workflows/cloud_tests_small.yml

@@ -3,16 +3,16 @@ run-name: Submitting workflow to all cloud providers using small sized data
 on:
   workflow_dispatch:
     inputs:
-        platform:
-          description: 'Platform to run test'
-          required: true
-          default: 'all'
-          type: choice
-          options:
-            - all
-            - aws
-            - azure
-            - gcp
+      platform:
+        description: "Platform to run test"
+        required: true
+        default: "all"
+        type: choice
+        options:
+          - all
+          - aws
+          - azure
+          - gcp
 jobs:
   run-small-tests-on-aws:
     if: ${{ github.event.inputs.platform == 'all' || github.event.inputs.platform == 'aws' }}

CHANGELOG.md

@@ -3,7 +3,7 @@
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/)
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
-## [[3.11.0](https://github.com/nf-core/rnaseq/releases/tag/3.11.0)] - 2023-03-29
+## [[3.11.0](https://github.com/nf-core/rnaseq/releases/tag/3.11.0)] - 2023-03-30
 
 ### Credits
 
@@ -37,6 +37,7 @@ Thank you to everyone else that has contributed by reporting bugs, enhancements
 - [[#961](https://github.com/nf-core/rnaseq/issues/961)] - Add warnings to STDOUT for all skipped and failed strandedness check samples
 - [[#975](https://github.com/nf-core/rnaseq/issues/975)] - `SALMON_INDEX` runs when using `--aligner star_rsem` even if samples have explicit strandedness
 - Remove HISAT2 from automated AWS full-sized tests
+- [[#988](https://github.com/nf-core/rnaseq/issues/988)] - `DESEQ2_QC_STAR_SALMON` fails when sample names have many components
 - Fix issue with incorrect cacheing of test datasets during CI/CD
 
 ### Parameters

bin/deseq2_qc.r

@@ -77,10 +77,10 @@ decompose       <- n_components!=1 && all(sapply(name_components, length)==n_com
 coldata         <- data.frame(samples.vec, sample=samples.vec, row.names=1)
 if (decompose) {
     groupings        <- as.data.frame(lapply(1:n_components, function(i) sapply(name_components, "[[", i)))
-    names(groupings) <- paste0("Group", 1:n_components)
     n_distinct       <- sapply(groupings, function(grp) length(unique(grp)))
     groupings        <- groupings[n_distinct!=1 & n_distinct!=length(samples.vec)]
     if (ncol(groupings)!=0) {
+        names(groupings) <- paste0("Group", 1:ncol(groupings))
         coldata <- cbind(coldata, groupings)
     } else {
         decompose <- FALSE