broadinstitute · ekiernan · Sep 16, 2024 · Sep 12, 2024 · Sep 12, 2024 · Sep 12, 2024
diff --git a/pipelines/broad/dna_seq/somatic/single_sample/wgs/gdc_genome/README.md b/pipelines/broad/dna_seq/somatic/single_sample/wgs/gdc_genome/README.md
@@ -1,6 +1,6 @@
-## Announcing a new site for WARP documentation!
+## Announcement: GDC is Deprecated 9/12/2024
 
-GDC Whole Genome Somatic Single Sample documentation has moved! Read more about the [GDC Whole Genome Somatic Single Sample Pipeline](https://broadinstitute.github.io/warp/documentation/Pipelines/Genomic_Data_Commons_Whole_Genome_Somatic/) on the new [WARP documentation site](https://broadinstitute.github.io/warp/)!
+The GDC Whole Genome Somatic Single Sample workflow is deprecated and no longer supported. However, documentation is still available. Read  about the [GDC Whole Genome Somatic Single Sample Pipeline](https://broadinstitute.github.io/warp/documentation/Pipelines/Genomic_Data_Commons_Whole_Genome_Somatic/) on the [WARP documentation site](https://broadinstitute.github.io/warp/)!
 
 ## Introduction to the GDC Whole Genome Somatic Single Sample Pipeline
 The GDC Whole Genome Somatic Single Sample (abbreviated GDC here) pipeline is the alignment and preprocessing workflow for genomic data designed for the National Cancer Institute's [Genomic Data Commons](https://gdc.cancer.gov/about-gdc). 

diff --git a/pipelines/cemba/cemba_methylcseq/README.md b/pipelines/cemba/cemba_methylcseq/README.md
@@ -1,6 +1,6 @@
-## Announcing a new site for WARP documentation!
+## Announcement: CEMBA is Deprecated 9/12/2024
 
-CEMBA documentation has moved! Read more about the [CEMBA Pipeline](https://broadinstitute.github.io/warp/docs/Pipelines/CEMBA_MethylC_Seq_Pipeline/README) on the new [WARP documentation site](https://broadinstitute.github.io/warp/)!
+The CEMBA workflow is now deprecated and will no longer be supported. However, the CEMBA documentation is still available. See [CEMBA Pipeline Overview](https://broadinstitute.github.io/warp/docs/Pipelines/CEMBA_MethylC_Seq_Pipeline/README) on the [WARP documentation site](https://broadinstitute.github.io/warp/)!
 
 ### CEMBA summary
 

diff --git a/pipelines/skylab/scATAC/README.md b/pipelines/skylab/scATAC/README.md
@@ -1,7 +1,7 @@
 
-## Announcing a new site for WARP documentation!
+## Announcement: scATAC is Deprecated 9/12/2024
 
-scATAC documentation has moved! Read more about the [scATAC Pipeline](https://broadinstitute.github.io/warp/docs/Pipelines/Single_Cell_ATAC_Seq_Pipeline/README) on the new [WARP documentation site](https://broadinstitute.github.io/warp/)!
+The scATAC workflow is deprecated and is not longer supported. However, the scATAC documentation is still available. Read more about the [scATAC Pipeline](https://broadinstitute.github.io/warp/docs/Pipelines/Single_Cell_ATAC_Seq_Pipeline/README) on the [WARP documentation site](https://broadinstitute.github.io/warp/)!
 
 ### scATAC summary
 

diff --git a/pipelines/skylab/smartseq2_multisample/README.md b/pipelines/skylab/smartseq2_multisample/README.md
@@ -1,6 +1,6 @@
-## Announcing a new site for WARP documentation!
+## Announcement: Smart-seq2 Multi-Sample is Deprecated 9/12/2024
 
-Smart-seq2 Multi-Sample documentation has moved! Read more about the [Smart-seq2 Multi-Sample Pipeline](https://broadinstitute.github.io/warp/docs/Pipelines/Smart-seq2_Multi_Sample_Pipeline/README) on the new [WARP documentation site](https://broadinstitute.github.io/warp/)!
+The Smart-seq2 Multi-Sample workflow is deprecated and will no longer be supported. However, documentation is still available. Read about the [Smart-seq2 Multi-Sample Pipeline](https://broadinstitute.github.io/warp/docs/Pipelines/Smart-seq2_Multi_Sample_Pipeline/README) on the [WARP documentation site](https://broadinstitute.github.io/warp/)!
 
 
 ### Smart-seq2 Multi-Sample summary

diff --git a/pipelines/skylab/smartseq2_single_sample/README.md b/pipelines/skylab/smartseq2_single_sample/README.md
@@ -1,6 +1,6 @@
-## Announcing a new site for WARP documentation!
+## Announcement: Smart-seq2 Single Sample is Deprecated 9/12/2024
 
-Smart-seq2 Single Sample documentation has moved! Read more about the [Smart-seq2 Single Sample Pipeline](https://broadinstitute.github.io/warp/docs/Pipelines/Smart-seq2_Single_Sample_Pipeline/README) on the new [WARP documentation site](https://broadinstitute.github.io/warp/)!
+The Smart-seq2 Single Sample workflow is deprecated and will no longer be supported. However, documentation is still available Read about the [Smart-seq2 Single Sample Pipeline](https://broadinstitute.github.io/warp/docs/Pipelines/Smart-seq2_Single_Sample_Pipeline/README) on the [WARP documentation site](https://broadinstitute.github.io/warp/)!
 
 ### Smart-seq2 Single Sample summary
 

diff --git a/...MBA_MethylC_Seq_Pipeline/CEMBA.methods.md → ...MBA_MethylC_Seq_Pipeline/CEMBA.methods.md b/...MBA_MethylC_Seq_Pipeline/CEMBA.methods.md → ...MBA_MethylC_Seq_Pipeline/CEMBA.methods.md
diff --git a/...ines/CEMBA_MethylC_Seq_Pipeline/CEMBA.png → ...ines/CEMBA_MethylC_Seq_Pipeline/CEMBA.png b/...ines/CEMBA_MethylC_Seq_Pipeline/CEMBA.png → ...ines/CEMBA_MethylC_Seq_Pipeline/CEMBA.png
diff --git a/...ines/CEMBA_MethylC_Seq_Pipeline/README.md → ...ines/CEMBA_MethylC_Seq_Pipeline/README.md b/...ines/CEMBA_MethylC_Seq_Pipeline/README.md → ...ines/CEMBA_MethylC_Seq_Pipeline/README.md
@@ -2,9 +2,14 @@
 sidebar_position: 1
 slug: /Pipelines/CEMBA_MethylC_Seq_Pipeline/README
 ---
-
 # CEMBA Overview
 
+:::warning
+9/12/2024
+
+We are deprecating the CEMBA pipeline. Although the code will continue to be available, we are no longer supporting it. A possible alternative is the [Single-nucleus Methyl-seq and Chromatin Capture](../../Pipelines/snM3C/README.md) workflow.
+:::
+
 | Pipeline Version | Date Updated | Documentation Author | Questions or Feedback |
 | :----: | :---: | :----: | :--------------: |
 | [CEMBA_v1.1.6](https://github.com/broadinstitute/warp/releases) | December, 2023 | Elizabeth Kiernan| Please [file an issue in WARP](https://github.com/broadinstitute/warp/issues). |

diff --git a/...EMBA_MethylC_Seq_Pipeline/_category_.json → ...EMBA_MethylC_Seq_Pipeline/_category_.json b/...EMBA_MethylC_Seq_Pipeline/_category_.json → ...EMBA_MethylC_Seq_Pipeline/_category_.json
diff --git a/...A_MethylC_Seq_Pipeline/diagrampptx_1.pptx → ...A_MethylC_Seq_Pipeline/diagrampptx_1.pptx b/...A_MethylC_Seq_Pipeline/diagrampptx_1.pptx → ...A_MethylC_Seq_Pipeline/diagrampptx_1.pptx
diff --git a/...Data_Commons_Whole_Genome_Somatic/GDC.png → ...Data_Commons_Whole_Genome_Somatic/GDC.png b/...Data_Commons_Whole_Genome_Somatic/GDC.png → ...Data_Commons_Whole_Genome_Somatic/GDC.png
diff --git a/...ta_Commons_Whole_Genome_Somatic/README.md → ...ta_Commons_Whole_Genome_Somatic/README.md b/...ta_Commons_Whole_Genome_Somatic/README.md → ...ta_Commons_Whole_Genome_Somatic/README.md
@@ -4,6 +4,11 @@ slug: /Pipelines/Genomic_Data_Commons_Whole_Genome_Somatic/README
 ---
 
 # Genomic Data Commons (GDC) Whole Genome Somatic Single Sample Overview
+:::warning
+9/12/2014
+
+We are deprecating the Genomic Data Commons Whole Genome Somatic Single Sample Pipeline. Although the code will continue to be available, we are no longer supporting it.
+:::
 
 | Pipeline Version | Date Updated | Documentation Author | Questions or Feedback |
 | :----: | :---: | :----: | :--------------: |

diff --git a/...mons_Whole_Genome_Somatic/_category_.json → ...mons_Whole_Genome_Somatic/_category_.json b/...mons_Whole_Genome_Somatic/_category_.json → ...mons_Whole_Genome_Somatic/_category_.json
diff --git a/...s/Single_Cell_ATAC_Seq_Pipeline/README.md → ...s/Single_Cell_ATAC_Seq_Pipeline/README.md b/...s/Single_Cell_ATAC_Seq_Pipeline/README.md → ...s/Single_Cell_ATAC_Seq_Pipeline/README.md
@@ -4,7 +4,11 @@ slug: /Pipelines/Single_Cell_ATAC_Seq_Pipeline/README
 ---
 
 # scATAC Overview
+:::warning
+9/12/2024
 
+We are deprecating the Single-cell ATAC Seq Pipeline. Although the code will continue to be available, we are no longer supporting it. This workflow has been replaced with the [ATAC workflow](../../Pipelines/ATAC/README.md).
+:::
 | Pipeline Version | Date Updated | Documentation Author | Questions or Feedback |
 | :----: | :---: | :----: | :--------------: |
 | [scATAC 1.3.2](https://github.com/broadinstitute/warp/releases) | May 2024 | Elizabeth Kiernan | Please [file an issue in WARP](https://github.com/broadinstitute/warp/issues). |

diff --git a/...le_Cell_ATAC_Seq_Pipeline/_category_.json → ...le_Cell_ATAC_Seq_Pipeline/_category_.json b/...le_Cell_ATAC_Seq_Pipeline/_category_.json → ...le_Cell_ATAC_Seq_Pipeline/_category_.json
diff --git a/...Cell_ATAC_Seq_Pipeline/scATAC_diagram.png → ...Cell_ATAC_Seq_Pipeline/scATAC_diagram.png b/...Cell_ATAC_Seq_Pipeline/scATAC_diagram.png → ...Cell_ATAC_Seq_Pipeline/scATAC_diagram.png
diff --git a/...Cell_ATAC_Seq_Pipeline/scATAC_diagram.svg → ...Cell_ATAC_Seq_Pipeline/scATAC_diagram.svg b/...Cell_ATAC_Seq_Pipeline/scATAC_diagram.svg → ...Cell_ATAC_Seq_Pipeline/scATAC_diagram.svg
diff --git a/..._Cell_ATAC_Seq_Pipeline/scatac.methods.md → ..._Cell_ATAC_Seq_Pipeline/scatac.methods.md b/..._Cell_ATAC_Seq_Pipeline/scatac.methods.md → ..._Cell_ATAC_Seq_Pipeline/scatac.methods.md
diff --git a/...seq2_Multi_Sample_Pipeline/Loom_schema.md → ...seq2_Multi_Sample_Pipeline/Loom_schema.md b/...seq2_Multi_Sample_Pipeline/Loom_schema.md → ...seq2_Multi_Sample_Pipeline/Loom_schema.md
diff --git a/...mart-seq2_Multi_Sample_Pipeline/README.md → ...mart-seq2_Multi_Sample_Pipeline/README.md b/...mart-seq2_Multi_Sample_Pipeline/README.md → ...mart-seq2_Multi_Sample_Pipeline/README.md
@@ -4,6 +4,11 @@ slug: /Pipelines/Smart-seq2_Multi_Sample_Pipeline/README
 ---
 
 # Smart-seq2 Multi-Sample Overview
+:::warning
+9/12/2014
+
+We are deprecating the Smart-seq2 Multi-Sample Pipeline. Although the code will continue to be available, we are no longer supporting it. For an alternative, see the [Smart-seq2 Single Nucleus Multi Sample workflow](../../Pipelines/Smart-seq2_Single_Nucleus_Multi_Sample_Pipeline/README.md).
+:::
 
 | Pipeline Version | Date Updated | Documentation Author | Questions or Feedback |
 | :----: | :---: | :----: | :--------------: |

diff --git a/...eq2_Multi_Sample_Pipeline/_category_.json → ...eq2_Multi_Sample_Pipeline/_category_.json b/...eq2_Multi_Sample_Pipeline/_category_.json → ...eq2_Multi_Sample_Pipeline/_category_.json
diff --git a/...lti_Sample_Pipeline/smart-seq2.methods.md → ...lti_Sample_Pipeline/smart-seq2.methods.md b/...lti_Sample_Pipeline/smart-seq2.methods.md → ...lti_Sample_Pipeline/smart-seq2.methods.md
diff --git a/...eq2_Single_Sample_Pipeline/Loom_schema.md → ...eq2_Single_Sample_Pipeline/Loom_schema.md b/...eq2_Single_Sample_Pipeline/Loom_schema.md → ...eq2_Single_Sample_Pipeline/Loom_schema.md
diff --git a/...art-seq2_Single_Sample_Pipeline/README.md → ...art-seq2_Single_Sample_Pipeline/README.md b/...art-seq2_Single_Sample_Pipeline/README.md → ...art-seq2_Single_Sample_Pipeline/README.md
@@ -5,6 +5,12 @@ slug: /Pipelines/Smart-seq2_Single_Sample_Pipeline/README
 
 # Smart-seq2 Single Sample Overview
 
+:::warning
+9/12/2014
+
+We are deprecating the Smart-seq2 Single Sample Pipeline. Although the code will continue to be available, we are no longer supporting it. For an alternative, see the [Smart-seq2 Single Nucleus Multi Sample workflow](../../Pipelines/Smart-seq2_Single_Nucleus_Multi_Sample_Pipeline/README.md).
+:::
+
 | Pipeline Version | Date Updated | Documentation Author | Questions or Feedback |
 | :----: | :---: | :----: | :--------------: |
 | [smartseq2_v5.1.20](https://github.com/broadinstitute/warp/releases) | February, 2024 | Elizabeth Kiernan | Please [file an issue in WARP](https://github.com/broadinstitute/warp/issues). |

diff --git a/...q2_Single_Sample_Pipeline/_category_.json → ...q2_Single_Sample_Pipeline/_category_.json b/...q2_Single_Sample_Pipeline/_category_.json → ...q2_Single_Sample_Pipeline/_category_.json
diff --git a/...Single_Sample_Pipeline/smartseq_image.png → ...Single_Sample_Pipeline/smartseq_image.png b/...Single_Sample_Pipeline/smartseq_image.png → ...Single_Sample_Pipeline/smartseq_image.png
diff --git a/...ingle_Sample_Pipeline/smartseq_image.pptx → ...ingle_Sample_Pipeline/smartseq_image.pptx b/...ingle_Sample_Pipeline/smartseq_image.pptx → ...ingle_Sample_Pipeline/smartseq_image.pptx
diff --git a/website/docs/Deprecated_Pipelines/_category_.json b/website/docs/Deprecated_Pipelines/_category_.json
@@ -0,0 +1,4 @@
+{
+  "label": "Deprecated Pipelines",
+  "position": 100
+}