From fce18745e7bee40fba5246d8482d3f3bd51ae3a1 Mon Sep 17 00:00:00 2001 From: "pre-commit-ci[bot]" <66853113+pre-commit-ci[bot]@users.noreply.github.com> Date: Mon, 18 May 2026 20:03:36 +0000 Subject: [PATCH 1/2] [pre-commit.ci] pre-commit autoupdate MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit updates: - [github.com/astral-sh/ruff-pre-commit: v0.15.12 → v0.15.13](https://github.com/astral-sh/ruff-pre-commit/compare/v0.15.12...v0.15.13) --- .pre-commit-config.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index b23ef42..1e3ab61 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -39,7 +39,7 @@ repos: - prettier@3.4.0 # Python formatting - repo: https://github.com/astral-sh/ruff-pre-commit - rev: v0.15.12 + rev: v0.15.13 hooks: - id: ruff-check args: [--fix] From 42c7260d6c9d19807762d39c37d5c055dcb252da Mon Sep 17 00:00:00 2001 From: "pre-commit-ci[bot]" <66853113+pre-commit-ci[bot]@users.noreply.github.com> Date: Mon, 18 May 2026 20:06:03 +0000 Subject: [PATCH 2/2] [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci --- profile/README.md | 94 +++++++++++++++------------- profile/activity_data/CCBR/README.md | 85 +++++++++++++------------ 2 files changed, 92 insertions(+), 87 deletions(-) diff --git a/profile/README.md b/profile/README.md index e18fc4e..73de195 100644 --- a/profile/README.md +++ b/profile/README.md @@ -1,44 +1,47 @@ [](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 | -|:-----------------------------------------------|:----------------------------------------------------------------|:---------------|--------------:| -| [SINCLAIR](https://github.com/CCBR/SINCLAIR) | [v0.4.0](https://github.com/CCBR/SINCLAIR/releases/tag/v0.4.0) | 2026-05-13 | 30 | -| [MOSuite](https://github.com/CCBR/MOSuite) | [v0.3.1](https://github.com/CCBR/MOSuite/releases/tag/v0.3.1) | 2026-05-07 | 30 | -| [CARLISLE](https://github.com/CCBR/CARLISLE) | [v2.7.6](https://github.com/CCBR/CARLISLE/releases/tag/v2.7.6) | 2026-05-06 | 20 | -| [actions](https://github.com/CCBR/actions) | [v0.6.2](https://github.com/CCBR/actions/releases/tag/v0.6.2) | 2026-04-23 | 12 | -| [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 | 22 | -| [Tools](https://github.com/CCBR/Tools) | [v0.5.2](https://github.com/CCBR/Tools/releases/tag/v0.5.2) | 2026-03-24 | 8 | -| [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 | - -## TOP contributors - -| User | Total Commits | Commits in Last Month | Commits in Last 6 Months | -|:----------------------------------------------------|----------------:|------------------------:|---------------------------:| -| [kelly-sovacool](https://github.com/kelly-sovacool) | 6096 | 150 | 871 | -| [kopardev](https://github.com/kopardev) | 2791 | 4 | 113 | -| [finneyr](https://github.com/finneyr) | 323 | 0 | 0 | -| [kvaldez](https://github.com/kvaldez) | 222 | 0 | 0 | -| [wong-nw](https://github.com/wong-nw) | 196 | 4 | 49 | -| [escauley](https://github.com/escauley) | 192 | 0 | 32 | -| [samarth8392](https://github.com/samarth8392) | 163 | 2 | 19 | -| [pajailwala](https://github.com/pajailwala) | 47 | 3 | 24 | -| [maggiecam](https://github.com/maggiecam) | 46 | 0 | 0 | -| [phoman14](https://github.com/phoman14) | 19 | 2 | 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 | +| :--------------------------------------------- | :-------------------------------------------------------------- | :----------- | ----------: | +| [SINCLAIR](https://github.com/CCBR/SINCLAIR) | [v0.4.0](https://github.com/CCBR/SINCLAIR/releases/tag/v0.4.0) | 2026-05-13 | 30 | +| [MOSuite](https://github.com/CCBR/MOSuite) | [v0.3.1](https://github.com/CCBR/MOSuite/releases/tag/v0.3.1) | 2026-05-07 | 30 | +| [CARLISLE](https://github.com/CCBR/CARLISLE) | [v2.7.6](https://github.com/CCBR/CARLISLE/releases/tag/v2.7.6) | 2026-05-06 | 20 | +| [actions](https://github.com/CCBR/actions) | [v0.6.2](https://github.com/CCBR/actions/releases/tag/v0.6.2) | 2026-04-23 | 12 | +| [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 | 22 | +| [Tools](https://github.com/CCBR/Tools) | [v0.5.2](https://github.com/CCBR/Tools/releases/tag/v0.5.2) | 2026-03-24 | 8 | +| [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 | + +## TOP contributors + +| User | Total Commits | Commits in Last Month | Commits in Last 6 Months | +| :-------------------------------------------------- | ------------: | --------------------: | -----------------------: | +| [kelly-sovacool](https://github.com/kelly-sovacool) | 6096 | 150 | 871 | +| [kopardev](https://github.com/kopardev) | 2791 | 4 | 113 | +| [finneyr](https://github.com/finneyr) | 323 | 0 | 0 | +| [kvaldez](https://github.com/kvaldez) | 222 | 0 | 0 | +| [wong-nw](https://github.com/wong-nw) | 196 | 4 | 49 | +| [escauley](https://github.com/escauley) | 192 | 0 | 32 | +| [samarth8392](https://github.com/samarth8392) | 163 | 2 | 19 | +| [pajailwala](https://github.com/pajailwala) | 47 | 3 | 24 | +| [maggiecam](https://github.com/maggiecam) | 46 | 0 | 0 | +| [phoman14](https://github.com/phoman14) | 19 | 2 | 11 | + ## About Us - 👋 Hi, we're the [**@CCBR**](https://bioinformatics.ccr.cancer.gov/ccbr/), a group of bioinformatics analysts and engineers @@ -51,6 +54,7 @@

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+ ## Our model [](https://bioinformatics.ccr.cancer.gov/ccbr/) @@ -66,6 +70,7 @@ 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/). +

Back to Top @@ -121,6 +126,7 @@ CCBR offers end-to-end analysis pipelines for NGS data analysis. **11** SPENCER=_SPatial seqeENCing Resource_. For any other datatype or pipeline, please [email :mailbox:](mailto:ccbr_pipeliner@mail.nih.gov) us directly to get the conversation started! +

Back to Top @@ -137,6 +143,7 @@ In additions to end-to-end analysis pipelines, the CCBR dev team also builds too

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+ ## `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. @@ -159,6 +166,7 @@ In additions to end-to-end analysis pipelines, the CCBR dev team also builds too > # = 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 +

Back to Top @@ -205,12 +213,9 @@ In additions to end-to-end analysis pipelines, the CCBR dev team also builds too Back to Top

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

@@ -220,6 +225,7 @@ 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! +

Back to Top diff --git a/profile/activity_data/CCBR/README.md b/profile/activity_data/CCBR/README.md index 092a79b..67c40a5 100644 --- a/profile/activity_data/CCBR/README.md +++ b/profile/activity_data/CCBR/README.md @@ -1,43 +1,42 @@ - -| github_handle | member/collaborator | days_inactive | -|-----------------|----------------------|---------------| -| [bfugaru2025](https://github.com/bfugaru2025) | member | No Activity Found | -| [bianjh-cloud](https://github.com/bianjh-cloud) | member | 7 | -| [burnskd](https://github.com/burnskd) | member | No Activity Found | -| [epehrsson](https://github.com/epehrsson) | member | 13 | -| [escauley](https://github.com/escauley) | member | 2 | -| [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 | 4 | -| [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 | -| [onealka](https://github.com/onealka) | member | No Activity Found | -| [pajailwala](https://github.com/pajailwala) | member | 27 | -| [phoman14](https://github.com/phoman14) | member | 27 | -| [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 | 9 | -| [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 | -| [yongmzhao](https://github.com/yongmzhao) | member | No Activity Found | -| [abombin](https://github.com/abombin) | collaborator | No Activity Found | -| [AlecSilver](https://github.com/AlecSilver) | collaborator | 2 | -| [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 | 2 | -| [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 | +| ----------------------------------------------------------- | ------------------- | ----------------- | +| [bfugaru2025](https://github.com/bfugaru2025) | member | No Activity Found | +| [bianjh-cloud](https://github.com/bianjh-cloud) | member | 7 | +| [burnskd](https://github.com/burnskd) | member | No Activity Found | +| [epehrsson](https://github.com/epehrsson) | member | 13 | +| [escauley](https://github.com/escauley) | member | 2 | +| [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 | 4 | +| [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 | +| [onealka](https://github.com/onealka) | member | No Activity Found | +| [pajailwala](https://github.com/pajailwala) | member | 27 | +| [phoman14](https://github.com/phoman14) | member | 27 | +| [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 | 9 | +| [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 | +| [yongmzhao](https://github.com/yongmzhao) | member | No Activity Found | +| [abombin](https://github.com/abombin) | collaborator | No Activity Found | +| [AlecSilver](https://github.com/AlecSilver) | collaborator | 2 | +| [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 | 2 | +| [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 |