Merge pull request #93 from uab-cgds-worthey/joss_manuscript

QuaC is published!!

README.md

@@ -1,17 +1,16 @@
 [![Snakemake](https://img.shields.io/badge/snakemake-6.0.5-brightgreen.svg?style=flat)](https://snakemake.readthedocs.io)
 [![ReadTheDocs](https://readthedocs.org/projects/quac/badge/?version=latest)](https://quac.readthedocs.io/en/stable/)
-[![DOI](https://zenodo.org/badge/593702083.svg)](https://zenodo.org/badge/latestdoi/593702083)
+[![DOI JOSS](https://joss.theoj.org/papers/10.21105/joss.05313/status.svg)](https://doi.org/10.21105/joss.05313)
+[![Zenodo](https://zenodo.org/badge/DOI/10.5281/zenodo.10002036.svg)](https://doi.org/10.5281/zenodo.10002036)
 
 # QuaC
 
 🦆🦆 Don't duck that QC thingy 🦆🦆
 
-
 > **_NOTE:_**  In a past life, QuaC used a different remote Git management provider, [UAB
 > Gitlab](https://gitlab.rc.uab.edu/center-for-computational-genomics-and-data-science/public/quac). It was migrated to
 > Github in Jan 2023, and the Gitlab version has been archived.
 
-
 ## What is QuaC?
 
 QuaC is a snakemake-based pipeline that runs several QC tools for WGS/WES samples and then summarizes their results
@@ -28,31 +27,31 @@ In summary, QuaC performs the following:
 - Optionally, above mentioned QuaC-Watch and QC aggregation steps can accept pre-run results from few QC tools (fastqc,
    fastq-screen, picard's markduplicates) when run with flag `--include_prior_qc`. 
 
-
 > **_NOTE:_**  QuaC is built to use with Human WGS/WES data. If you would like to use it with non-human data, please
 > modify the pipeline as needed -- especially the thresholds used in QuaC-Watch configs.
 
-
 ## Documentation
 
-Full documentation, including installation and how to run QuaC, is available at https://quac.readthedocs.io.
+Full documentation, including installation and how to run QuaC, is available at <https://quac.readthedocs.io>.
 
+## Citing QuaC
 
-## Repo owner
+If you use QuaC, please cite:
 
-* **Mana**valan Gajapathy
+Gajapathy et al., (2023). QuaC: A Pipeline Implementing Quality Control Best Practices for Genome Sequencing and Exome Sequencing Data. Journal of Open Source Software, 8(90), 5313, <https://doi.org/10.21105/joss.05313>
 
+## Repo owner
+
+- **Mana**valan Gajapathy
 
 ## License
 
 [GNU GPLv3](./LICENSE)
 
-
 ## Contributing
 
 See [here](./docs/CONTRIBUTING.md) for contributing guidelines.
 
-
 ## Changelog
 
-See [here](./docs/Changelog.md)
+See [here](./docs/Changelog.md)

docs/Changelog.md

@@ -14,6 +14,9 @@ YYYY-MM-DD  John Doe
 
 2023-10-09  Manavalan Gajapathy
 
+- Makes minor documentation updates - updating citation info, adding JOSS badge and updating zenodo badge to use generic
+  DOI
+
 * Merges `joss_manuscript` to the `master` branch to bring it up to date.
 
 2023-10-06  Manavalan Gajapathy

docs/faq.md

@@ -15,3 +15,8 @@ from it's last state.
 * If `--cli_cluster_config` was used, logs from the snakemake process are stored in the directory provided using `--log_dir`. Else, logs will be directed to stderr/stdout and not stored in a file.
 * If `--snakemake_cluster_config` was used, logs for the jobs triggered by snakemake workflow are stored in sub-directory `rule_logs/` under the directory provided using `--log_dir`. Else, logs will be directed to stderr/stdout.
 
+## How to cite QuaC?
+
+Please cite this article:
+
+Gajapathy et al., (2023). QuaC: A Pipeline Implementing Quality Control Best Practices for Genome Sequencing and Exome Sequencing Data. Journal of Open Source Software, 8(90), 5313, <https://doi.org/10.21105/joss.05313>

docs/index.md

@@ -75,3 +75,8 @@ Optionally QuaC can also utilize QC results produced by the tools listed below w
 
      * At CGDS, these optional tools were run by our small_variant_caller_pipeline.
 
+## Citing QuaC
+
+If you use QuaC, please cite:
+
+Gajapathy et al., (2023). QuaC: A Pipeline Implementing Quality Control Best Practices for Genome Sequencing and Exome Sequencing Data. Journal of Open Source Software, 8(90), 5313, <https://doi.org/10.21105/joss.05313>

paper/paper.md

@@ -24,9 +24,9 @@ authors:
     affiliation: "1, 2"
     corresponding: true
 affiliations:
- - name: Center for Computational Genomics and Data Science, The University of Alabama at Birmingham, Birmingham, AL, USA
+ - name: Center for Computational Genomics and Data Science, The University of Alabama at Birmingham, Birmingham, Alabama, United States of America
    index: 1
- - name: Department of Genetics, Heersink School of Medicine, The University of Alabama at Birmingham, Birmingham, AL, USA
+ - name: Department of Genetics, Heersink School of Medicine, The University of Alabama at Birmingham, Birmingham, Alabama, United States of America
    index: 2
 
 date: 15 January 2023