Km doc updates (#1290)

* update snm3c overview

* update snm3c overview

* update slide-seq overview

* update docs

* Update README.md

* Update README.md

website/docs/Pipelines/ATAC/README.md

@@ -8,7 +8,7 @@ slug: /Pipelines/ATAC/README
 
 | Pipeline Version | Date Updated | Documentation Author | Questions or Feedback |
 | :----: | :---: | :----: | :--------------: |
-| [1.2.3](https://github.com/broadinstitute/warp/releases) | May, 2024 | Kaylee Mathews | Please file GitHub issues in warp or contact [the WARP team](mailto:[email protected]) |
+| [2.0.0](https://github.com/broadinstitute/warp/releases) | May, 2024 | Kaylee Mathews | Please file GitHub issues in warp or contact [the WARP team](mailto:[email protected]) |
 
 
 ## Introduction to the ATAC workflow

website/docs/Pipelines/Multiome_Pipeline/README.md

@@ -7,7 +7,7 @@ slug: /Pipelines/Multiome_Pipeline/README
 
 | Pipeline Version | Date Updated | Documentation Author | Questions or Feedback |
 | :----: | :---: | :----: | :--------------: |
-| [Multiome v3.4.5](https://github.com/broadinstitute/warp/releases) | May, 2024 | Kaylee Mathews | Please file GitHub issues in warp or contact the [WARP Pipeline Development team](mailto:[email protected]) |
+| [Multiome v5.0.0](https://github.com/broadinstitute/warp/releases) | May, 2024 | Kaylee Mathews | Please file GitHub issues in warp or contact the [WARP Pipeline Development team](mailto:[email protected]) |
 
 ![Multiome_diagram](./multiome_diagram.png)
 

website/docs/Pipelines/Optimus_Pipeline/README.md

@@ -7,7 +7,7 @@ slug: /Pipelines/Optimus_Pipeline/README
 
 | Pipeline Version | Date Updated | Documentation Author | Questions or Feedback |
 | :----: | :---: | :----: | :--------------: |
-| [optimus_v6.6.2](https://github.com/broadinstitute/warp/releases?q=optimus&expanded=true) | May, 2024 | Elizabeth Kiernan | Please file GitHub issues in warp or contact [the WARP team](mailto:[email protected]) |
+| [optimus_v7.1.0](https://github.com/broadinstitute/warp/releases?q=optimus&expanded=true) | May, 2024 | Elizabeth Kiernan | Please file GitHub issues in warp or contact [the WARP team](mailto:[email protected]) |
 
 
 ![Optimus_diagram](Optimus_diagram.png)

website/docs/Pipelines/SlideSeq_Pipeline/README.md

@@ -7,13 +7,13 @@ slug: /Pipelines/SlideSeq_Pipeline/README
 
 | Pipeline Version | Date Updated | Documentation Author | Questions or Feedback |
 | :----: | :---: | :----: | :--------------: |
-| [SlideSeq v3.1.5](https://github.com/broadinstitute/warp/releases) | May, 2024 | Elizabeth Kiernan & Kaylee Mathews | Please file GitHub issues in warp or contact [documentation authors](mailto:[email protected]) |
+| [SlideSeq v3.1.6](https://github.com/broadinstitute/warp/releases) | May, 2024 | Elizabeth Kiernan & Kaylee Mathews | Please file GitHub issues in warp or contact [documentation authors](mailto:[email protected]) |
 
 ![SlideSeq_diagram](./slide-seq_diagram.png)
 
 ## Introduction to the Slide-seq workflow
 
-The [Slide-seq workflow](https://github.com/broadinstitute/warp/blob/master/pipelines/skylab/slideseq/SlideSeq.wdl) is an open-source, cloud-optimized pipeline developed in collaboration with the [BRAIN Initiative Cell Census Network](https://biccn.org/) (BICCN) and the BRAIN Initiative Cell Atlas Network (BICAN). It supports the processing of spatial transcriptomic data generated with the [Slide-seq](https://www.science.org/doi/10.1126/science.aaw1219) (commercialized as [Curio Seeker](https://curiobioscience.com/product/)) assay.
+The [Slide-seq workflow](https://github.com/broadinstitute/warp/blob/master/pipelines/skylab/slideseq/SlideSeq.wdl) is an open-source, cloud-optimized pipeline developed in collaboration with the [BRAIN Initiative Cell Census Network](https://biccn.org/) (BICCN) and the BRAIN Initiative Cell Atlas Network (BICAN). It supports the processing of spatial transcriptomic data generated with the [Slide-seq](https://www.science.org/doi/10.1126/science.aaw1219) (commercialized as [Curio Seeker](https://curiobioscience.com/seeker/)) assay.
 
 Overall, the workflow corrects bead barcodes, aligns reads to the genome, generates a count matrix, calculates summary metrics for genes, barcodes, and UMIs, returns read outputs in BAM format, and returns counts in numpy matrix and h5ad file formats.
 

website/docs/Pipelines/snM3C/README.md

@@ -13,9 +13,9 @@ slug: /Pipelines/snm3C/README
 
 The Single Nucleus Methly-Seq and Chromatin Capture (snm3C) workflow is an open-source, cloud-optimized computational workflow for processing single-nucleus methylome and chromatin contact (snm3C) sequencing data. The workflow is designed to demultiplex and align raw sequencing reads, call chromatin contacts, and generate summary metrics. 
 
-The workflow is developed in collaboration with Hanqing Liu, Wei Tian, Wubin Ding, Huaming Chen, Chongyuan Luo, Jingtian Zhou, and the entire laboratory of Joseph Ecker. 
+The workflow is developed in collaboration with Hanqing Liu, Wei Tian, Wubin Ding, Huaming Chen, Chongyuan Luo, Jingtian Zhou, and the entire laboratory of Joseph Ecker. Please see the [Acknowledgments](#acknowledgements) section below.
 
-For more information about the snm3C tools and analysis, please see the [YAP documentation](https://hq-1.gitbook.io/mc/) or the [cemba_data](https://github.com/lhqing/cemba_data) GitHub repository created by Hanqing Liu.
+For more information about the snm3C tools and analysis, please see the [YAP documentation](https://hq-1.gitbook.io/mc/) or the cemba_data GitHub repositories created by [Hanqing Liu](https://github.com/lhqing/cemba_data) and [Wubin Ding](https://github.com/DingWB/cemba_data).
 
 ## Quickstart table
 The following table provides a quick glance at the Multiome pipeline features: