Fix --gtf_extra_attributes to support multiple comma-separated values

CHANGELOG.md

@@ -9,6 +9,7 @@ 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:
 
+- [Ahwan Pandey](https://github.com/ahwanpandey)
 - [Elad Herzog](https://github.com/EladH1)
 - [Emily Miyoshi](https://github.com/emilymiyoshi)
 - [Pontus Höjer](https://github.com/pontushojer)
@@ -29,6 +30,7 @@ Special thanks to the following for their contributions to the release:
 - [PR #1628](https://github.com/nf-core/rnaseq/pull/1628) - Template update for nf-core/tools v3.5.1
 - [PR #1630](https://github.com/nf-core/rnaseq/pull/1630) - Fix arm64 profile to use pre-built ARM containers and update documentation
 - [PR #1631](https://github.com/nf-core/rnaseq/pull/1631) - Fix bbsplit index staging by using symlinks instead of full copy
+- [PR #1635](https://github.com/nf-core/rnaseq/pull/1635) - Fix `--gtf_extra_attributes` to support multiple comma-separated values and correct deprecated parameter name in docs ([#1626](https://github.com/nf-core/rnaseq/issues/1626))
 
 ## [[3.21.0](https://github.com/nf-core/rnaseq/releases/tag/3.21.0)] - 2025-09-18
 

docs/usage.md

@@ -358,7 +358,7 @@ Remember to note the genome and annotation versions as well as the versions of t
 
 If you are using [GENCODE](https://www.gencodegenes.org/) reference genome files please specify the `--gencode` parameter because the format of these files is slightly different to ENSEMBL genome files:
 
-- The `--gtf_group_features_type` parameter will automatically be set to `gene_type` as opposed to `gene_biotype`, respectively.
+- The `--featurecounts_group_type` parameter will automatically be set to `gene_type` as opposed to `gene_biotype`, respectively.
 - If you are running Salmon, the `--gencode` flag will also be passed to the index building step to overcome parsing issues resulting from the transcript IDs in GENCODE fasta files being separated by vertical pipes (`|`) instead of spaces (see [this issue](https://github.com/COMBINE-lab/salmon/issues/15)).
 
 As well as the standard annotations, GENCODE also provides "basic" annotations, which include only representative transcripts, but we do not recommend using these.

modules.json

@@ -37,7 +37,7 @@
                     },
                     "custom/tx2gene": {
                         "branch": "master",
-                        "git_sha": "05954dab2ff481bcb999f24455da29a5828af08d",
+                        "git_sha": "e0bdf8637721e27792a38c6b622f0a2345f3cbc9",
                         "installed_by": ["modules", "quantify_pseudo_alignment"]
                     },
                     "dupradar": {