Merge pull request #187 from Plant-Food-Research-Open/fix/185

[GH-185] Fixed malformed STAR ALIGN command

Author: GallVp

.nf-core.yml

@@ -35,4 +35,4 @@ template:
   outdir: .
   skip_features:
     - igenomes
-  version: 1.0.0
+  version: 1.0.1

CHANGELOG.md

@@ -3,6 +3,17 @@
 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).
 
+## v1.0.1 - [03-Feb-2026]
+
+### `Fixed`
+
+1. Fixed malformed STAR ALIGN command which caused the pipeline to fail when RNASeq data was provided [#185](https://github.com/Plant-Food-Research-Open/genepal/issues/185)
+
+### `Dependencies`
+
+1. Nextflow!>=25.04.0
+2. nf-schema@2.5.1
+
 ## v1.0.0 - [05-Nov-2025]
 
 ### `Added`

CITATION.cff

@@ -31,7 +31,7 @@ authors:
   - family-names: "Thomson"
     given-names: "Susan"
 title: "genepal: A Nextflow pipeline for genome and pan-genome annotation"
-version: 1.0.0
+version: 1.0.1
 date-released: 2024-11-21
 url: "https://github.com/Plant-Food-Research-Open/genepal"
 doi: 10.5281/zenodo.14195006

assets/multiqc_config.yml

@@ -1,7 +1,7 @@
 report_comment: >
   This report has been generated by the <a href="https://github.com/plant-food-research-open/genepal" target="_blank">plant-food-research-open/genepal</a>
   analysis pipeline. For information about how to interpret these results, please see the
-  <a href="https://github.com/plant-food-research-open/genepal/blob/1.0.0/docs/usage.md" target="_blank">documentation</a>.
+  <a href="https://github.com/plant-food-research-open/genepal/blob/1.0.1/docs/usage.md" target="_blank">documentation</a>.
 
 report_section_order:
   "plant-food-research-open-genepal-methods-description":

conf/modules.config

@@ -148,7 +148,7 @@ process { // SUBWORKFLOW: ALIGN_RNASEQ
             "--outSAMstrandField intronMotif",
             "--outSAMtype BAM SortedByCoordinate",
             "--readFilesCommand gunzip -c",
-            "outBAMsortingBinsN 200",
+            "--outBAMsortingBinsN 200",
             "--alignIntronMax ${params.star_max_intron_length}",
             params.star_align_extra_args ? params.star_align_extra_args.split("\\s(?=--)") : ''
         ].flatten().unique(false).join(' ').trim()

nextflow.config

@@ -289,7 +289,7 @@ manifest {
     mainScript      = 'main.nf'
     defaultBranch   = 'main'
     nextflowVersion = '!>=25.04.0'
-    version         = '1.0.0'
+    version         = '1.0.1'
     doi             = 'https://doi.org/10.5281/zenodo.14195006'
 
     author          = """Usman Rashid, Jason Shiller"""

ro-crate-metadata.json

@@ -82,7 +82,7 @@
                         "tsebra": "1.1.2.5"
                     },
                     "Workflow": {
-                        "plant-food-research-open/genepal": "v1.0.0"
+                        "plant-food-research-open/genepal": "v1.0.1"
                     }
                 },
                 "stable paths": [
@@ -123,7 +123,7 @@
                         "seqkit": "v2.9.0"
                     },
                     "Workflow": {
-                        "plant-food-research-open/genepal": "v1.0.0"
+                        "plant-food-research-open/genepal": "v1.0.1"
                     }
                 },
                 "stable paths": [

tests/invalid/main.nf.test.snap

@@ -67,7 +67,7 @@
                         "tsebra": "1.1.2.5"
                     },
                     "Workflow": {
-                        "plant-food-research-open/genepal": "v1.0.0"
+                        "plant-food-research-open/genepal": "v1.0.1"
                     }
                 },
                 "stable paths": [

tests/minimal/main.nf.test.snap

@@ -5,7 +5,7 @@
                 "successful tasks": 0,
                 "versions": {
                     "Workflow": {
-                        "plant-food-research-open/genepal": "v1.0.0"
+                        "plant-food-research-open/genepal": "v1.0.1"
                     }
                 },
                 "stable paths": [