From ce2308da4f1c2e51f5a81f5ab703704eec409070 Mon Sep 17 00:00:00 2001 From: "CCBR-bot[bot]" <258092125+CCBR-bot[bot]@users.noreply.github.com> Date: Sun, 3 May 2026 05:43:22 +0000 Subject: [PATCH] ci: update readme with createreadme github action. --- profile/README.md | 105 +++++++++++++-------------- profile/activity_data/CCBR/README.md | 85 +++++++++++----------- 2 files changed, 92 insertions(+), 98 deletions(-) diff --git a/profile/README.md b/profile/README.md index c7731c2..0d7b1e0 100644 --- a/profile/README.md +++ b/profile/README.md @@ -1,49 +1,45 @@ [](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 | 22 | +| [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 | 23 | +| [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 | + +## TOP contributors + +| User | Total Commits | Commits in Last Month | Commits in Last 6 Months | +|:----------------------------------------------------|----------------:|------------------------:|---------------------------:| +| [kelly-sovacool](https://github.com/kelly-sovacool) | 5869 | 89 | 736 | +| [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 | 51 | +| [samarth8392](https://github.com/samarth8392) | 161 | 0 | 19 | +| [wong-nw](https://github.com/wong-nw) | 159 | 0 | 23 | +| [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 @@ -56,7 +52,6 @@

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- ## Our model [](https://bioinformatics.ccr.cancer.gov/ccbr/) @@ -72,7 +67,6 @@ 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 @@ -128,7 +122,6 @@ 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 @@ -145,7 +138,6 @@ 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. @@ -168,7 +160,6 @@ 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 @@ -180,9 +171,9 @@ In additions to end-to-end analysis pipelines, the CCBR dev team also builds too | [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 | +| [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 | -| [CARLISLE](https://github.com/CCBR/CARLISLE) | [v2.7.5](https://github.com/CCBR/CARLISLE/releases/tag/v2.7.5) | 2026-03-09 | 21 | +| [CARLISLE](https://github.com/CCBR/CARLISLE) | [v2.7.5](https://github.com/CCBR/CARLISLE/releases/tag/v2.7.5) | 2026-03-09 | 23 | | [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 | @@ -194,11 +185,11 @@ In additions to end-to-end analysis pipelines, the CCBR dev team also builds too | [TRANQUIL](https://github.com/CCBR/TRANQUIL) | [v0.3.0](https://github.com/CCBR/TRANQUIL/releases/tag/v0.3.0) | 2025-06-16 | 3 | | [CRISPIN](https://github.com/CCBR/CRISPIN) | [v1.2.1](https://github.com/CCBR/CRISPIN/releases/tag/v1.2.1) | 2025-05-28 | 16 | | [CHARLIE](https://github.com/CCBR/CHARLIE) | [v0.12.0](https://github.com/CCBR/CHARLIE/releases/tag/v0.12.0) | 2025-05-20 | 14 | -| [Dockers2](https://github.com/CCBR/Dockers2) | [v0.1.2](https://github.com/CCBR/Dockers2/releases/tag/v0.1.2) | 2024-12-02 | 8 | +| [Dockers2](https://github.com/CCBR/Dockers2) | [v0.1.2](https://github.com/CCBR/Dockers2/releases/tag/v0.1.2) | 2024-12-02 | 6 | | [METRO](https://github.com/CCBR/METRO) | [v2.1](https://github.com/CCBR/METRO/releases/tag/v2.1) | 2024-03-28 | 2 | | [CCBR-1144](https://github.com/CCBR/CCBR-1144) | [v1.0.0](https://github.com/CCBR/CCBR-1144/releases/tag/v1.0.0) | 2024-03-04 | 0 | | [ccbr1271_ERVpipeline](https://github.com/CCBR/ccbr1271_ERVpipeline) | [v1.0.3](https://github.com/CCBR/ccbr1271_ERVpipeline/releases/tag/v1.0.3) | 2024-02-21 | 1 | -| [nf-modules](https://github.com/CCBR/nf-modules) | [v0.1.0](https://github.com/CCBR/nf-modules/releases/tag/v0.1.0) | 2023-11-29 | 13 | +| [nf-modules](https://github.com/CCBR/nf-modules) | [v0.1.0](https://github.com/CCBR/nf-modules/releases/tag/v0.1.0) | 2023-11-29 | 16 | | [CRISPRAnnotation](https://github.com/CCBR/CRISPRAnnotation) | [v1.0](https://github.com/CCBR/CRISPRAnnotation/releases/tag/v1.0) | 2023-10-19 | 0 | | [SharanLab](https://github.com/CCBR/SharanLab) | [v1.0.0](https://github.com/CCBR/SharanLab/releases/tag/v1.0.0) | 2023-07-18 | 0 | | [Pipeliner](https://github.com/CCBR/Pipeliner) | [v4.0.7](https://github.com/CCBR/Pipeliner/releases/tag/v4.0.7) | 2023-05-09 | 24 | @@ -215,9 +206,12 @@ In additions to end-to-end analysis pipelines, the CCBR dev team also builds too Back to Top

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

@@ -227,7 +221,6 @@ 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 2ea917e..00d1c14 100644 --- a/profile/activity_data/CCBR/README.md +++ b/profile/activity_data/CCBR/README.md @@ -1,42 +1,43 @@ -| 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 | 2 | +| [burnskd](https://github.com/burnskd) | member | No Activity Found | +| [epehrsson](https://github.com/epehrsson) | member | 3 | +| [escauley](https://github.com/escauley) | member | 11 | +| [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 | 13 | +| [phoman14](https://github.com/phoman14) | member | 13 | +| [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 | 12 | +| [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 | 13 | +| [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 |