From 1c9757bb65d0b54a0e425e3f8f65c716e78054a4 Mon Sep 17 00:00:00 2001 From: Manavalan Gajapathy Date: Wed, 18 Oct 2023 12:43:08 -0500 Subject: [PATCH 1/8] expands affiliation abbreviations --- paper/paper.md | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) 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 From 8538621ec8b1e62ae8e45d4bb28e4899922a4e5c Mon Sep 17 00:00:00 2001 From: Manavalan Gajapathy Date: Fri, 27 Oct 2023 14:00:45 -0500 Subject: [PATCH 2/8] lint formatting --- README.md | 14 +++----------- 1 file changed, 3 insertions(+), 11 deletions(-) diff --git a/README.md b/README.md index 71b85b2..0e306ce 100644 --- a/README.md +++ b/README.md @@ -6,12 +6,10 @@ 🦆🦆 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 Github in Jan 2023, and the Gitlab version has been archived.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 +26,25 @@ 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 . ## Repo owner -* **Mana**valan Gajapathy - +- **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) From 3225a2155cce76a004f8c34c993bd79c99e3f20a Mon Sep 17 00:00:00 2001 From: Manavalan Gajapathy Date: Fri, 27 Oct 2023 14:01:16 -0500 Subject: [PATCH 3/8] updates zenodo to all-versions doi --- README.md | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/README.md b/README.md index 0e306ce..a51b72d 100644 --- a/README.md +++ b/README.md @@ -1,6 +1,7 @@ [![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](https://zenodo.org/badge/DOI/10.5281/zenodo.10002036.svg)](https://doi.org/10.5281/zenodo.10002036) + # QuaC From f1a1402eba0be42d56ed2fa66517b783713dbc02 Mon Sep 17 00:00:00 2001 From: Manavalan Gajapathy Date: Fri, 27 Oct 2023 14:02:12 -0500 Subject: [PATCH 4/8] Adds JOSS badge --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index a51b72d..9a624d6 100644 --- a/README.md +++ b/README.md @@ -1,7 +1,7 @@ [![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/DOI/10.5281/zenodo.10002036.svg)](https://doi.org/10.5281/zenodo.10002036) - +[![DOI](https://joss.theoj.org/papers/10.21105/joss.05313/status.svg)](https://doi.org/10.21105/joss.05313) # QuaC From 3faaa6ab88736a7e52b6cb01a3f763c4f3e815e7 Mon Sep 17 00:00:00 2001 From: Manavalan Gajapathy Date: Fri, 27 Oct 2023 14:03:15 -0500 Subject: [PATCH 5/8] changes label and order --- README.md | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/README.md b/README.md index 9a624d6..36667a5 100644 --- a/README.md +++ b/README.md @@ -1,7 +1,7 @@ [![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/DOI/10.5281/zenodo.10002036.svg)](https://doi.org/10.5281/zenodo.10002036) -[![DOI](https://joss.theoj.org/papers/10.21105/joss.05313/status.svg)](https://doi.org/10.21105/joss.05313) +[![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 From 339246023cfb32a32238a2380ebd308ac96a124c Mon Sep 17 00:00:00 2001 From: Manavalan Gajapathy Date: Fri, 27 Oct 2023 14:09:56 -0500 Subject: [PATCH 6/8] adds how to cite --- README.md | 6 ++++++ docs/faq.md | 5 +++++ docs/index.md | 5 +++++ 3 files changed, 16 insertions(+) diff --git a/README.md b/README.md index 36667a5..b3e9ddf 100644 --- a/README.md +++ b/README.md @@ -34,6 +34,12 @@ In summary, QuaC performs the following: Full documentation, including installation and how to run QuaC, is available at . +## 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 + ## Repo owner - **Mana**valan Gajapathy diff --git a/docs/faq.md b/docs/faq.md index a645a66..88982e5 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, https://doi.org/10.21105/joss.05313 diff --git a/docs/index.md b/docs/index.md index 71388c3..f36790d 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, https://doi.org/10.21105/joss.05313 From abe9117028dc7fcaa9476b30af241f96a353707c Mon Sep 17 00:00:00 2001 From: Manavalan Gajapathy Date: Fri, 27 Oct 2023 14:17:14 -0500 Subject: [PATCH 7/8] updates changelog --- docs/Changelog.md | 3 +++ 1 file changed, 3 insertions(+) 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 From 6985f6e535d231b13707992a06345cd5d6d7d3c5 Mon Sep 17 00:00:00 2001 From: Manavalan Gajapathy Date: Fri, 27 Oct 2023 15:46:51 -0500 Subject: [PATCH 8/8] updates url to make it clickable --- README.md | 2 +- docs/faq.md | 2 +- docs/index.md | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) diff --git a/README.md b/README.md index b3e9ddf..1b7dac3 100644 --- a/README.md +++ b/README.md @@ -38,7 +38,7 @@ Full documentation, including installation and how to run QuaC, is available at 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 +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 diff --git a/docs/faq.md b/docs/faq.md index 88982e5..c9978dc 100644 --- a/docs/faq.md +++ b/docs/faq.md @@ -19,4 +19,4 @@ from it's last state. 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 +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 f36790d..389f4af 100644 --- a/docs/index.md +++ b/docs/index.md @@ -79,4 +79,4 @@ Optionally QuaC can also utilize QC results produced by the tools listed below w 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 +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,