Merge branch 'master' into develop

CHANGELOG.md

@@ -9,6 +9,8 @@ All changed fall under either one of these types: `Added`, `Changed`, `Deprecate
 
 ## [Unreleased]
 
+## [1.2.0] - 2023-09-18
+
 ### Changed
 
 - DESeq2 now uses more samples to estimate count dispersions
@@ -827,7 +829,8 @@ Many minor bug- and quality of life fixes.
 
 First release of seq2science!
 
-[Unreleased]: https://github.com/vanheeringen-lab/seq2science/compare/v1.1.0...develop
+[Unreleased]: https://github.com/vanheeringen-lab/seq2science/compare/v1.2.0...develop
+[1.2.0]: https://github.com/vanheeringen-lab/seq2science/compare/v1.1.0...v1.2.0
 [1.1.0]: https://github.com/vanheeringen-lab/seq2science/compare/v1.0.4...v1.1.0
 [1.0.4]: https://github.com/vanheeringen-lab/seq2science/compare/v1.0.3...v1.0.4
 [1.0.3]: https://github.com/vanheeringen-lab/seq2science/compare/v1.0.2...v1.0.3

README.md

@@ -5,6 +5,7 @@
 [![star this repo](https://img.shields.io/github/stars/vanheeringen-lab/seq2science?style=flat&color=brightgreen)](https://github.com/vanheeringen-lab/seq2science/stargazers)
 [![Test Status](http://ocimum.science.ru.nl/jenkins/buildStatus/icon?job=seq2science%2Fmaster&subject=tests)](http://ocimum.science.ru.nl/jenkins/job/seq2science/job/master/lastBuild/display/redirect/)
 [![docs](https://github.com/vanheeringen-lab/seq2science/workflows/docs/badge.svg)](https://vanheeringen-lab.github.io/seq2science)
+[![DOI](https://img.shields.io/badge/DOI-10.7717%2Fpeerj.16380-%2302A7FC)](https://doi.org/10.7717/peerj.16380)
 [![DOI](https://zenodo.org/badge/196379320.svg)](https://zenodo.org/badge/latestdoi/196379320)
 
 Seq2science is the attempt of the *van heeringen lab* to generate a collection of generic pipelines/workflows which can be used by complete beginners to bioinformatics and experienced bioinformaticians alike. Please take a look at our [docs](https://vanheeringen-lab.github.io/seq2science/) for help with installation, how to run it, and best practices.
@@ -25,3 +26,6 @@ Information for new users, such as how to install and configure can be found in
 
 ## Feedback
 Anything not working as expected? Please reach out to us via our [issues](https://github.com/vanheeringen-lab/seq2science/issues) page and we'll try to help you as soon as possible!
+
+## Cite us
+van der Sande M, Frölich S, Schäfers T, Smits JGA, Snabel RR, Rinzema S, van Heeringen SJ. 2023. Seq2science: an end-to-end workflow for functional genomics analysis. PeerJ 11:e16380 https://doi.org/10.7717/peerj.16380

seq2science/__init__.py

@@ -1,4 +1,4 @@
 from . import util
 
 __all__ = ["util"]
-__version__ = "1.1.0"
+__version__ = "1.2.0"

seq2science/cli.py

@@ -505,13 +505,13 @@ def _explain(args, base_dir, workflows_dir, config_path):
     if args.hyperref:
         rules_used = {
             "start": f"Preprocessing of reads was done automatically by "
-            f"<a href=https://doi.org/10.5281/zenodo.3921913>seq2science v{seq2science.__version__}</a> "
+            f"<a href=https://doi.org/10.7717/peerj.16380>seq2science v{seq2science.__version__}</a> "
             f"using the {args.workflow} workflow."
         }
     else:
         rules_used = {
             "start": f"Preprocessing of reads was done automatically by "
-            f"seq2science v{seq2science.__version__} (https://doi.org/10.5281/zenodo.3921913) "
+            f"seq2science v{seq2science.__version__} (https://doi.org/10.7717/peerj.16380) "
             f"using the {args.workflow} workflow."
         }
 

tests/dag_tests.sh

@@ -564,7 +564,7 @@ if [ $1 = "explain" ]; then
     fi;
 
     # exit if only the default line is returned
-    if [[ $val == *"(https://doi.org/10.5281/zenodo.3921913)." ]]; then
+    if [[ $val == *"(https://doi.org/10.7717/peerj.16380)." ]]; then
       printf "\nExplain message appears truncated! Exiting.\n"
       exit 1;
     fi;