Merge pull request #122 from Plant-Food-Research-Open/rc/2.1.0

Release candidate for 2.1.0

.github/workflows/ci.yml

@@ -29,6 +29,7 @@ jobs:
           - minimal
           - invalid
           - stub
+          - noltr
         include:
           - OPTION_STUB: ""
           - OPTION_STUB: "-stub"

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).
 
-## v2.1.0+dev - [31-July-2024]
+## v2.1.0 - [31-July-2024]
 
 ### `Added`
 

CITATION.cff

@@ -25,7 +25,7 @@ authors:
   - family-names: "Deng"
     given-names: "Cecilia"
 title: "AssemblyQC: A Nextflow pipeline for reproducible reporting of assembly quality"
-version: 2.1.0+dev
+version: 2.1.0
 date-released: 2024-07-30
 url: "https://github.com/Plant-Food-Research-Open/assemblyqc"
 doi: 10.1093/bioinformatics/btae477

nextflow.config

@@ -283,7 +283,7 @@ manifest {
     description     = """A Nextflow pipeline which evaluates assembly quality with multiple QC tools and presents the results in a unified html report."""
     mainScript      = 'main.nf'
     nextflowVersion = '!>=23.04.0'
-    version         = '2.1.0+dev'
+    version         = '2.1.0'
     doi             = 'https://doi.org/10.1093/bioinformatics/btae477'
 }
 

tests/README.md

@@ -0,0 +1,27 @@
+# **plant-food-research-open/assemblyqc** Tests
+
+## Minimal Testing
+
+If [Nextflow](https://www.nextflow.io/docs/latest/install.html#install-nextflow) and [Docker](https://docs.docker.com/install) are installed on the system, the pipeline can be minimally tested with the following command:
+
+```bash
+nextflow run plant-food-research-open/assemblyqc -r main -profile docker,test --outdir results
+```
+
+Or using [singularity](https://docs.sylabs.io/guides/3.0/user-guide/installation.html):
+
+```bash
+nextflow run plant-food-research-open/assemblyqc -r main -profile singularity,test --outdir results
+```
+
+## Local Testing
+
+The test sets included in this directory can be executed by first downloading the pipeline from GitHub and then executing the following command:
+
+```bash
+./main.nf -profile docker -params-file tests/minimal/params.json --outdir results
+```
+
+## Continuous Integration (CI)
+
+The GitHub [CI action](../.github/workflows/ci.yml) included with the pipeline continuously tests the pipeline with the various test sets listed in this directory.