diff --git a/README.md b/README.md index 71b85b2..1b7dac3 100644 --- a/README.md +++ b/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 Github in Jan 2023, and the Gitlab version has been archived.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 . +## 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, +## Repo owner + +- **Mana**valan Gajapathy ## License [GNU GPLv3](./LICENSE) - ## Contributing See [here](./docs/CONTRIBUTING.md) for contributing guidelines. - ## Changelog -See [here](./docs/Changelog.md) \ No newline at end of file +See [here](./docs/Changelog.md) diff --git a/docs/Changelog.md b/docs/Changelog.md index 1f8cde6..edf8fd3 100644 --- a/docs/Changelog.md +++ b/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 diff --git a/docs/faq.md b/docs/faq.md index a645a66..c9978dc 100644 --- a/docs/faq.md +++ b/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, diff --git a/docs/index.md b/docs/index.md index 71388c3..389f4af 100644 --- a/docs/index.md +++ b/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, diff --git a/paper/paper.md b/paper/paper.md index 2834237..ff2679a 100644 --- a/paper/paper.md +++ b/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