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kelly-sovacool merged 4 commits into from
Apr 27, 2026
Merged

[pre-commit.ci] pre-commit autoupdate #58

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20c8807
[pre-commit.ci] pre-commit autoupdate
pre-commit-ci[bot] Apr 20, 2026
aca1b40
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Apr 20, 2026
0aea10e
Merge branch 'main' into pre-commit-ci-update-config
kelly-sovacool Apr 27, 2026
ed6648b
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Apr 27, 2026
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2 changes: 1 addition & 1 deletion .pre-commit-config.yaml
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Expand Up @@ -39,7 +39,7 @@ repos:
- prettier@3.4.0
# Python formatting
- repo: https://github.com/astral-sh/ruff-pre-commit
rev: v0.15.10
rev: v0.15.11
hooks:
- id: ruff-check
args: [--fix]
Expand Down
98 changes: 52 additions & 46 deletions profile/README.md
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@@ -1,46 +1,49 @@
[<img src="https://raw.githubusercontent.com/CCBR/.github/main/img/ccbrbanner.png">](https://bioinformatics.ccr.cancer.gov/ccbr/)

## Table of Contents
- [NEW Releases](#new-releases)
- [TOP contributors](#top-contributors)
- [About Us](#about-us)
- [Our model](#our-model)
- [Pipelines](#pipelines)
- [Tools](#tools)
- [`ccbrpipeliner` module release history on BIOWULF](#`ccbrpipeliner`-module-release-history-on-biowulf)
- [Latest Releases of pipelines/tools:](#latest-releases-of-pipelines/tools:)
- [Days since last activity](#days-since-last-activity)
- [Citation](#citation)

## NEW Releases

| Repo Name | Release Name | Release Date | Open Issues |
|:-----------------------------------------------|:----------------------------------------------------------------|:---------------|--------------:|
| [actions](https://github.com/CCBR/actions) | [v0.6.2](https://github.com/CCBR/actions/releases/tag/v0.6.2) | 2026-04-23 | 11 |
| [SINCLAIR](https://github.com/CCBR/SINCLAIR) | [v0.3.6](https://github.com/CCBR/SINCLAIR/releases/tag/v0.3.6) | 2026-04-22 | 30 |
| [CHAMPAGNE](https://github.com/CCBR/CHAMPAGNE) | [v0.6.0](https://github.com/CCBR/CHAMPAGNE/releases/tag/v0.6.0) | 2026-04-17 | 30 |
| [RENEE](https://github.com/CCBR/RENEE) | [v2.7.5](https://github.com/CCBR/RENEE/releases/tag/v2.7.5) | 2026-04-06 | 23 |
| [Tools](https://github.com/CCBR/Tools) | [v0.5.2](https://github.com/CCBR/Tools/releases/tag/v0.5.2) | 2026-03-24 | 8 |
| [CARLISLE](https://github.com/CCBR/CARLISLE) | [v2.7.5](https://github.com/CCBR/CARLISLE/releases/tag/v2.7.5) | 2026-03-09 | 21 |
| [HowTos](https://github.com/CCBR/HowTos) | [v1.1.0](https://github.com/CCBR/HowTos/releases/tag/v1.1.0) | 2026-02-23 | 15 |
| [parkit](https://github.com/CCBR/parkit) | [v3.0.1](https://github.com/CCBR/parkit/releases/tag/v3.0.1) | 2026-02-19 | 3 |
| [LOGAN](https://github.com/CCBR/LOGAN) | [v0.3.3](https://github.com/CCBR/LOGAN/releases/tag/v0.3.3) | 2026-02-12 | 21 |
| [MOSuite](https://github.com/CCBR/MOSuite) | [v0.3.0](https://github.com/CCBR/MOSuite/releases/tag/v0.3.0) | 2026-02-06 | 30 |
| [XAVIER](https://github.com/CCBR/XAVIER) | [v3.2.2](https://github.com/CCBR/XAVIER/releases/tag/v3.2.2) | 2026-01-29 | 11 |

## TOP contributors

| User | Total Commits | Commits in Last Month | Commits in Last 6 Months |
|:----------------------------------------------------|----------------:|------------------------:|---------------------------:|
| [kelly-sovacool](https://github.com/kelly-sovacool) | 5791 | 101 | 705 |
| [kopardev](https://github.com/kopardev) | 2790 | 3 | 112 |
| [finneyr](https://github.com/finneyr) | 323 | 0 | 0 |
| [kvaldez](https://github.com/kvaldez) | 222 | 0 | 0 |
| [escauley](https://github.com/escauley) | 192 | 0 | 54 |
| [samarth8392](https://github.com/samarth8392) | 161 | 0 | 19 |
| [wong-nw](https://github.com/wong-nw) | 112 | 1 | 1 |
| [pajailwala](https://github.com/pajailwala) | 47 | 24 | 24 |
| [maggiecam](https://github.com/maggiecam) | 46 | 0 | 0 |
| [phoman14](https://github.com/phoman14) | 19 | 11 | 11 |

- [NEW Releases](#new-releases)
- [TOP contributors](#top-contributors)
- [About Us](#about-us)
- [Our model](#our-model)
- [Pipelines](#pipelines)
- [Tools](#tools)
- [`ccbrpipeliner` module release history on BIOWULF](#`ccbrpipeliner`-module-release-history-on-biowulf)
- [Latest Releases of pipelines/tools:](#latest-releases-of-pipelines/tools:)
- [Days since last activity](#days-since-last-activity)
- [Citation](#citation)

## NEW Releases

| Repo Name | Release Name | Release Date | Open Issues |
| :--------------------------------------------- | :-------------------------------------------------------------- | :----------- | ----------: |
| [actions](https://github.com/CCBR/actions) | [v0.6.2](https://github.com/CCBR/actions/releases/tag/v0.6.2) | 2026-04-23 | 11 |
| [SINCLAIR](https://github.com/CCBR/SINCLAIR) | [v0.3.6](https://github.com/CCBR/SINCLAIR/releases/tag/v0.3.6) | 2026-04-22 | 30 |
| [CHAMPAGNE](https://github.com/CCBR/CHAMPAGNE) | [v0.6.0](https://github.com/CCBR/CHAMPAGNE/releases/tag/v0.6.0) | 2026-04-17 | 30 |
| [RENEE](https://github.com/CCBR/RENEE) | [v2.7.5](https://github.com/CCBR/RENEE/releases/tag/v2.7.5) | 2026-04-06 | 23 |
| [Tools](https://github.com/CCBR/Tools) | [v0.5.2](https://github.com/CCBR/Tools/releases/tag/v0.5.2) | 2026-03-24 | 8 |
| [CARLISLE](https://github.com/CCBR/CARLISLE) | [v2.7.5](https://github.com/CCBR/CARLISLE/releases/tag/v2.7.5) | 2026-03-09 | 21 |
| [HowTos](https://github.com/CCBR/HowTos) | [v1.1.0](https://github.com/CCBR/HowTos/releases/tag/v1.1.0) | 2026-02-23 | 15 |
| [parkit](https://github.com/CCBR/parkit) | [v3.0.1](https://github.com/CCBR/parkit/releases/tag/v3.0.1) | 2026-02-19 | 3 |
| [LOGAN](https://github.com/CCBR/LOGAN) | [v0.3.3](https://github.com/CCBR/LOGAN/releases/tag/v0.3.3) | 2026-02-12 | 21 |
| [MOSuite](https://github.com/CCBR/MOSuite) | [v0.3.0](https://github.com/CCBR/MOSuite/releases/tag/v0.3.0) | 2026-02-06 | 30 |
| [XAVIER](https://github.com/CCBR/XAVIER) | [v3.2.2](https://github.com/CCBR/XAVIER/releases/tag/v3.2.2) | 2026-01-29 | 11 |

## TOP contributors

| User | Total Commits | Commits in Last Month | Commits in Last 6 Months |
| :-------------------------------------------------- | ------------: | --------------------: | -----------------------: |
| [kelly-sovacool](https://github.com/kelly-sovacool) | 5791 | 101 | 705 |
| [kopardev](https://github.com/kopardev) | 2790 | 3 | 112 |
| [finneyr](https://github.com/finneyr) | 323 | 0 | 0 |
| [kvaldez](https://github.com/kvaldez) | 222 | 0 | 0 |
| [escauley](https://github.com/escauley) | 192 | 0 | 54 |
| [samarth8392](https://github.com/samarth8392) | 161 | 0 | 19 |
| [wong-nw](https://github.com/wong-nw) | 112 | 1 | 1 |
| [pajailwala](https://github.com/pajailwala) | 47 | 24 | 24 |
| [maggiecam](https://github.com/maggiecam) | 46 | 0 | 0 |
| [phoman14](https://github.com/phoman14) | 19 | 11 | 11 |

## About Us

- 👋 Hi, we're the [**@CCBR**](https://bioinformatics.ccr.cancer.gov/ccbr/), a group of bioinformatics analysts and engineers
Expand All @@ -53,6 +56,7 @@
<p align="center">
<a href="##table-of-contents">Back to Top</a>
</p>

## Our model

[<img src="https://raw.githubusercontent.com/CCBR/.github/main/img/CCBR_circle_diagram.png" width=600>](https://bioinformatics.ccr.cancer.gov/ccbr/)
Expand All @@ -68,6 +72,7 @@ The CCBR comprises of the core team and the embedded team. These teams serve dif
- The embedded team members are bioinformaticians who are integrated within specific research groups or labs. Their role is to provide more focused, day-to-day bioinformatics support tailored to the specific needs of the research group they are embedded in. This allows for a deeper collaboration and a more nuanced understanding of the ongoing research projects within that group.

> For details, please visit [CCBR's official website](https://bioinformatics.ccr.cancer.gov/ccbr/).

<hr>
<p align="center">
<a href="##table-of-contents">Back to Top</a>
Expand Down Expand Up @@ -123,6 +128,7 @@ CCBR offers end-to-end analysis pipelines for NGS data analysis.
<sup> **11** SPENCER=_SPatial seqeENCing Resource_.</sup>

For any other datatype or pipeline, please [email :mailbox:](mailto:ccbr_pipeliner@mail.nih.gov) us directly to get the conversation started!

<hr>
<p align="center">
<a href="##table-of-contents">Back to Top</a>
Expand All @@ -139,6 +145,7 @@ In additions to end-to-end analysis pipelines, the CCBR dev team also builds too
<p align="center">
<a href="##table-of-contents">Back to Top</a>
</p>

## `ccbrpipeliner` module release history on BIOWULF

`module load ccbrpipeliner` loads default release of ccbrpipeliner. Each release comprises of a unique combination of the version numbers of the different pipelines offered as part of the ccbrpipeliner suite.
Expand All @@ -161,6 +168,7 @@ In additions to end-to-end analysis pipelines, the CCBR dev team also builds too
> <sup>#</sup> = GUI available

> `module load ccbrpipeliner` is also available on HELIX. It only loads the **tools** and not the **pipelines** as HELIX does not have a job scheduler

<hr>
<p align="center">
<a href="##table-of-contents">Back to Top</a>
Expand Down Expand Up @@ -207,12 +215,9 @@ In additions to end-to-end analysis pipelines, the CCBR dev team also builds too
<a href="##table-of-contents">Back to Top</a>
</p>

## Days since last activity



- [CCBR](activity_data/CCBR/README.md)
## Days since last activity

- [CCBR](activity_data/CCBR/README.md)

<hr>
<p align="center">
Expand All @@ -222,6 +227,7 @@ In additions to end-to-end analysis pipelines, the CCBR dev team also builds too
## Citation

Most of our end-to-end pipelines which have been used in published research work have been made available to the entire bioinformatics community via a Zenodo DOI. Please feel free to visit our [Zenodo community page](https://zenodo.org/communities/ccbr). And if you use our pipelines, don't forget to cite us!

<hr>
<p align="center">
<a href="##table-of-contents">Back to Top</a>
Expand Down
85 changes: 42 additions & 43 deletions profile/activity_data/CCBR/README.md
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| github_handle | member/collaborator | days_inactive |
|-----------------|----------------------|---------------|
| [aemmons90](https://github.com/aemmons90) | member | No Activity Found |
| [bfugaru2025](https://github.com/bfugaru2025) | member | No Activity Found |
| [bianjh-cloud](https://github.com/bianjh-cloud) | member | 24 |
| [burnskd](https://github.com/burnskd) | member | No Activity Found |
| [epehrsson](https://github.com/epehrsson) | member | No Activity Found |
| [escauley](https://github.com/escauley) | member | 4 |
| [finneyr](https://github.com/finneyr) | member | No Activity Found |
| [HidetakaOhnuki-NCI](https://github.com/HidetakaOhnuki-NCI) | member | No Activity Found |
| [huaitian1129](https://github.com/huaitian1129) | member | No Activity Found |
| [JWrows2014](https://github.com/JWrows2014) | member | No Activity Found |
| [kcgfarb](https://github.com/kcgfarb) | member | No Activity Found |
| [kelly-sovacool](https://github.com/kelly-sovacool) | member | 2 |
| [kopardev](https://github.com/kopardev) | member | 3 |
| [kvaldez](https://github.com/kvaldez) | member | No Activity Found |
| [lobanovav](https://github.com/lobanovav) | member | No Activity Found |
| [maggiecam](https://github.com/maggiecam) | member | No Activity Found |
| [McIntoshC](https://github.com/McIntoshC) | member | No Activity Found |
| [onealka](https://github.com/onealka) | member | No Activity Found |
| [pajailwala](https://github.com/pajailwala) | member | 6 |
| [phoman14](https://github.com/phoman14) | member | 6 |
| [raraslw-nih](https://github.com/raraslw-nih) | member | No Activity Found |
| [RobSchultz4](https://github.com/RobSchultz4) | member | No Activity Found |
| [samarth8392](https://github.com/samarth8392) | member | 5 |
| [shaoli86](https://github.com/shaoli86) | member | No Activity Found |
| [TJoshMeyer](https://github.com/TJoshMeyer) | member | No Activity Found |
| [VidhurDS](https://github.com/VidhurDS) | member | No Activity Found |
| [vinegang](https://github.com/vinegang) | member | No Activity Found |
| [wilfriedguiblet](https://github.com/wilfriedguiblet) | member | No Activity Found |
| [wong-nw](https://github.com/wong-nw) | member | 2 |
| [wuy24](https://github.com/wuy24) | member | No Activity Found |
| [abombin](https://github.com/abombin) | collaborator | No Activity Found |
| [dnousome](https://github.com/dnousome) | collaborator | No Activity Found |
| [e-hutchins](https://github.com/e-hutchins) | collaborator | No Activity Found |
| [fangliu117](https://github.com/fangliu117) | collaborator | 6 |
| [nanobio-jcjones](https://github.com/nanobio-jcjones) | collaborator | No Activity Found |
| [skchronicles](https://github.com/skchronicles) | collaborator | No Activity Found |
| [slsevilla](https://github.com/slsevilla) | collaborator | No Activity Found |
| [stephchid](https://github.com/stephchid) | collaborator | No Activity Found |
| [syding327](https://github.com/syding327) | collaborator | No Activity Found |
| [tsnetterfield](https://github.com/tsnetterfield) | collaborator | No Activity Found |
| github_handle | member/collaborator | days_inactive |
| ----------------------------------------------------------- | ------------------- | ----------------- |
| [aemmons90](https://github.com/aemmons90) | member | No Activity Found |
| [bfugaru2025](https://github.com/bfugaru2025) | member | No Activity Found |
| [bianjh-cloud](https://github.com/bianjh-cloud) | member | 24 |
| [burnskd](https://github.com/burnskd) | member | No Activity Found |
| [epehrsson](https://github.com/epehrsson) | member | No Activity Found |
| [escauley](https://github.com/escauley) | member | 4 |
| [finneyr](https://github.com/finneyr) | member | No Activity Found |
| [HidetakaOhnuki-NCI](https://github.com/HidetakaOhnuki-NCI) | member | No Activity Found |
| [huaitian1129](https://github.com/huaitian1129) | member | No Activity Found |
| [JWrows2014](https://github.com/JWrows2014) | member | No Activity Found |
| [kcgfarb](https://github.com/kcgfarb) | member | No Activity Found |
| [kelly-sovacool](https://github.com/kelly-sovacool) | member | 2 |
| [kopardev](https://github.com/kopardev) | member | 3 |
| [kvaldez](https://github.com/kvaldez) | member | No Activity Found |
| [lobanovav](https://github.com/lobanovav) | member | No Activity Found |
| [maggiecam](https://github.com/maggiecam) | member | No Activity Found |
| [McIntoshC](https://github.com/McIntoshC) | member | No Activity Found |
| [onealka](https://github.com/onealka) | member | No Activity Found |
| [pajailwala](https://github.com/pajailwala) | member | 6 |
| [phoman14](https://github.com/phoman14) | member | 6 |
| [raraslw-nih](https://github.com/raraslw-nih) | member | No Activity Found |
| [RobSchultz4](https://github.com/RobSchultz4) | member | No Activity Found |
| [samarth8392](https://github.com/samarth8392) | member | 5 |
| [shaoli86](https://github.com/shaoli86) | member | No Activity Found |
| [TJoshMeyer](https://github.com/TJoshMeyer) | member | No Activity Found |
| [VidhurDS](https://github.com/VidhurDS) | member | No Activity Found |
| [vinegang](https://github.com/vinegang) | member | No Activity Found |
| [wilfriedguiblet](https://github.com/wilfriedguiblet) | member | No Activity Found |
| [wong-nw](https://github.com/wong-nw) | member | 2 |
| [wuy24](https://github.com/wuy24) | member | No Activity Found |
| [abombin](https://github.com/abombin) | collaborator | No Activity Found |
| [dnousome](https://github.com/dnousome) | collaborator | No Activity Found |
| [e-hutchins](https://github.com/e-hutchins) | collaborator | No Activity Found |
| [fangliu117](https://github.com/fangliu117) | collaborator | 6 |
| [nanobio-jcjones](https://github.com/nanobio-jcjones) | collaborator | No Activity Found |
| [skchronicles](https://github.com/skchronicles) | collaborator | No Activity Found |
| [slsevilla](https://github.com/slsevilla) | collaborator | No Activity Found |
| [stephchid](https://github.com/stephchid) | collaborator | No Activity Found |
| [syding327](https://github.com/syding327) | collaborator | No Activity Found |
| [tsnetterfield](https://github.com/tsnetterfield) | collaborator | No Activity Found |
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