New version

CHANGELOG.md

@@ -3,17 +3,26 @@
 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 - [2022-10-11]
+
+Minor bugfix update.
+
+### Fixed
+
+- When a samplesheet is provided, do not process the individual command-line parameters
+
+
 ## v1.0.0 - [2022-10-07]
 
 Initial release of sanger-tol/ensemblgenedownload, created with the [nf-core](https://nf-co.re/) template.
 
-### `Added`
+### Added
 
 - Download from Ensembl
 - `samtools faidx` and `samtools dict` indices for the annotation fastas
 - tabix index for the GFF3 file
 
-### `Dependencies`
+### Dependencies
 
 All dependencies are automatically fetched by Singularity.
 

CITATION.cff

@@ -2,7 +2,7 @@
 # Visit https://bit.ly/cffinit to generate yours today!
 
 cff-version: 1.2.0
-title: sanger-tol/insdcdownload v1.0.0 - Hefty oliphaunt
+title: sanger-tol/insdcdownload v1.0.1 - Hefty mûmakil
 message: >-
   If you use this software, please cite it using the
   metadata from this file.
@@ -18,9 +18,9 @@ authors:
     affiliation: Wellcome Sanger Institute
 identifiers:
   - type: doi
-    value: 10.5281/zenodo.7155207
+    value: 10.5281/zenodo.7183206
 repository-code: "https://github.com/sanger-tol/ensemblgenedownload"
 license: MIT
 commit: TODO
-version: 1.0.0
-date-released: "2022-10-07"
+version: 1.0.1
+date-released: "2022-10-11"

README.md

@@ -4,7 +4,7 @@
 
 <!-- [![GitHub Actions Linting Status](https://github.com/sanger-tol/ensemblgenedownload/workflows/nf-core%20linting/badge.svg)](https://github.com/sanger-tol/ensemblgenedownload/actions?query=workflow%3A%22nf-core+linting%22) -->
 
-[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.7155207-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.7155207)
+[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.7183206-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.7183206)
 
 [![Nextflow](https://img.shields.io/badge/nextflow%20DSL2-%E2%89%A522.04.0-23aa62.svg)](https://www.nextflow.io/)
 [![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/)
@@ -81,7 +81,7 @@ For further information or help, don't hesitate to get in touch on the [Slack `#
 
 ## Citations
 
-If you use sanger-tol/ensemblgenedownload for your analysis, please cite it using the following doi: [10.5281/zenodo.7155207](https://doi.org/10.5281/zenodo.7155207)
+If you use sanger-tol/ensemblgenedownload for your analysis, please cite it using the following doi: [10.5281/zenodo.7183206](https://doi.org/10.5281/zenodo.7183206)
 
 An extensive list of references for the tools used by the pipeline can be found in the [`CITATIONS.md`](CITATIONS.md) file.
 

lib/WorkflowMain.groovy

@@ -10,7 +10,7 @@ class WorkflowMain {
     public static String citation(workflow) {
         return "If you use ${workflow.manifest.name} for your analysis please cite:\n\n" +
             "* The pipeline\n" +
-            "  https://doi.org/10.5281/zenodo.7155207\n\n" +
+            "  https://doi.org/10.5281/zenodo.7183206\n\n" +
             "* The nf-core framework\n" +
             "  https://doi.org/10.1038/s41587-020-0439-x\n\n" +
             "* Software dependencies\n" +

nextflow.config

@@ -174,7 +174,7 @@ manifest {
     description     = 'Pipeline that downloads gene annotations from Ensembl into the Tree of Life directory structure'
     mainScript      = 'main.nf'
     nextflowVersion = '!>=22.04.0'
-    version         = '1.0.0'
+    version         = '1.0.1'
 }
 
 // Load modules.config for DSL2 module specific options