Merge branch 'dev' into flexible_tx2gene

Author: drpatelh

CHANGELOG.md

@@ -17,6 +17,15 @@ Special thanks to the following for their contributions to the release:
 - [Phil Ewels](https://github.com/ewels)
 - [Vlad Savelyev](https://github.com/vladsavelyev)
 
+### Enhancements & fixes
+
+- [PR #1135](https://github.com/nf-core/rnaseq/pull/1135) - Update [action-tower-launch](https://github.com/marketplace/actions/action-tower-launch) to v2 which supports more variable handling
+- [PR #1141](https://github.com/nf-core/rnaseq/pull/1141) - Important! Template update for nf-core/tools v2.11
+- [PR #1143](https://github.com/nf-core/rnaseq/pull/1143) - Move fasta check back to Groovy ([#1142](https://github.com/nf-core/rnaseq/issues/1142))
+- [PR #1144](https://github.com/nf-core/rnaseq/pull/1144) - Interface to kmer size for pseudoaligners
+- [PR #1149](https://github.com/nf-core/rnaseq/pull/1149) - Fix and patch version commands for Fastp, FastQC and UMI-tools modules ([#1103](https://github.com/nf-core/rnaseq/issues/1103))
+- [PR #1150](https://github.com/nf-core/rnaseq/pull/1150) - Be more flexible on attribute values in GTFs ([#1132](https://github.com/nf-core/rnaseq/issues/1132))
+
 ### Parameters
 
 | Old parameter | New parameter                |
@@ -27,14 +36,6 @@ Special thanks to the following for their contributions to the release:
 > **NB:** Parameter has been **added** if just the new parameter information is present.
 > **NB:** Parameter has been **removed** if new parameter information isn't present.
 
-### Enhancements & fixes
-
-- [PR #1135](https://github.com/nf-core/rnaseq/pull/1135) - Update [action-tower-launch](https://github.com/marketplace/actions/action-tower-launch) to v2 which supports more variable handling
-- [PR #1141](https://github.com/nf-core/rnaseq/pull/1141) - Important! Template update for nf-core/tools v2.11
-- [PR #1149](https://github.com/nf-core/rnaseq/pull/1149) - Fix and patch version commands for Fastp, FastQC and UMI-tools modules ([#1103](https://github.com/nf-core/rnaseq/issues/1103))
-- [PR #1144](https://github.com/nf-core/rnaseq/pull/1144) - Interface to kmer size for pseudoaligners
-- [PR #1150](https://github.com/nf-core/rnaseq/pull/1150) - Be more flexible on attribute values in GTFs ([#1132](https://github.com/nf-core/rnaseq/issues/1132))
-
 ## [[3.13.2](https://github.com/nf-core/rnaseq/releases/tag/3.13.2)] - 2023-11-21
 
 ### Credits

lib/WorkflowRnaseq.groovy

@@ -14,6 +14,10 @@ class WorkflowRnaseq {
     public static void initialise(params, log) {
         genomeExistsError(params, log)
 
+        if (!params.fasta) {
+            Nextflow.error("Genome fasta file not specified with e.g. '--fasta genome.fa' or via a detectable config file.")
+        }
+
         if (!params.gtf && !params.gff) {
             Nextflow.error("No GTF or GFF3 annotation specified! The pipeline requires at least one of these files.")
         }

nextflow_schema.json

@@ -211,8 +211,7 @@
                     "hidden": true,
                     "help_text": "Do not load `igenomes.config` when running the pipeline. You may choose this option if you observe clashes between custom parameters and those supplied in `igenomes.config`."
                 }
-            },
-            "required": ["fasta"]
+            }
         },
         "read_trimming_options": {
             "title": "Read trimming options",