Np deprecate cemba (#1386)

* pin all latest docker version * move cemba to deprecated folder * Updated pipeline_versions.txt with all pipeline version information * update cemba readme * update cemba readme * update cemba readme * changelogs --------- Co-authored-by: GitHub Action <[email protected]>
broadinstitute · Oct 18, 2024 · 5c8cc8a · 5c8cc8a
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diff --git a/...ecated/pipelines/cemba/build_cemba_references/BuildCembaReferences.changelog.md b/...ecated/pipelines/cemba/build_cemba_references/BuildCembaReferences.changelog.md
@@ -0,0 +1,12 @@
+# 1.0.1
+2024-10-16 (Date of Last Commit)
+
+* The CEMBA workflow is deprecated and is no longer 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/)!
+
+# 1.0.0
+2020-11-15 (Date of Last Commit)
+
+###Initial release of BuildCembareferences Pipeline
+Builds genomic reference files for [CEMBA pipeline](https://broadinstitute.github.io/warp/docs/Pipelines/CEMBA_MethylC_Seq_Pipeline/README)
+
+* Added version number to the BuildCembaReferences workflow
diff --git a/...erences/BuildCembaReferences.options.json → ...erences/BuildCembaReferences.options.json b/...erences/BuildCembaReferences.options.json → ...erences/BuildCembaReferences.options.json
diff --git a/...cemba_references/BuildCembaReferences.wdl → ...cemba_references/BuildCembaReferences.wdl b/...cemba_references/BuildCembaReferences.wdl → ...cemba_references/BuildCembaReferences.wdl
diff --git a/..._references/build_bisulfite_references.py → ..._references/build_bisulfite_references.py b/..._references/build_bisulfite_references.py → ..._references/build_bisulfite_references.py
diff --git a/...s/BuildCembaReferences.GRCh38.inputs.json → ...s/BuildCembaReferences.GRCh38.inputs.json b/...s/BuildCembaReferences.GRCh38.inputs.json → ...s/BuildCembaReferences.GRCh38.inputs.json
diff --git a/...s/BuildCembaReferences.GRCm38.inputs.json → ...s/BuildCembaReferences.GRCm38.inputs.json b/...s/BuildCembaReferences.GRCm38.inputs.json → ...s/BuildCembaReferences.GRCm38.inputs.json
diff --git a/...cemba/cemba_methylcseq/CEMBA.changelog.md → ...cemba/cemba_methylcseq/CEMBA.changelog.md b/...cemba/cemba_methylcseq/CEMBA.changelog.md → ...cemba/cemba_methylcseq/CEMBA.changelog.md
@@ -1,3 +1,8 @@
+# 1.1.8
+2024-10-16 (Date of Last Commit)
+
+* The CEMBA workflow is deprecated and is no longer 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/)!
+
 # 1.1.7
 2024-09-06 (Date of Last Commit)
 

diff --git a/...s/cemba/cemba_methylcseq/CEMBA.methods.md → ...s/cemba/cemba_methylcseq/CEMBA.methods.md b/...s/cemba/cemba_methylcseq/CEMBA.methods.md → ...s/cemba/cemba_methylcseq/CEMBA.methods.md
diff --git a/pipelines/cemba/cemba_methylcseq/CEMBA.png → ...ipelines/cemba/cemba_methylcseq/CEMBA.png b/pipelines/cemba/cemba_methylcseq/CEMBA.png → ...ipelines/cemba/cemba_methylcseq/CEMBA.png
diff --git a/pipelines/cemba/cemba_methylcseq/CEMBA.wdl → ...ipelines/cemba/cemba_methylcseq/CEMBA.wdl b/pipelines/cemba/cemba_methylcseq/CEMBA.wdl → ...ipelines/cemba/cemba_methylcseq/CEMBA.wdl
@@ -57,7 +57,7 @@ workflow CEMBA {
     }
 
     # version of this pipeline
-    String pipeline_version = "1.1.7"
+    String pipeline_version = "1.1.8"
 
   # trim off hardcoded sequence adapters
   call Trim as TrimAdapters {

diff --git a/pipelines/cemba/cemba_methylcseq/README.md → ...ipelines/cemba/cemba_methylcseq/README.md b/pipelines/cemba/cemba_methylcseq/README.md → ...ipelines/cemba/cemba_methylcseq/README.md
diff --git a/...thylcseq/example_inputs/CEMBA.inputs.json → ...thylcseq/example_inputs/CEMBA.inputs.json b/...thylcseq/example_inputs/CEMBA.inputs.json → ...thylcseq/example_inputs/CEMBA.inputs.json
diff --git a/...hylcseq/example_inputs/CEMBA.options.json → ...hylcseq/example_inputs/CEMBA.options.json b/...hylcseq/example_inputs/CEMBA.options.json → ...hylcseq/example_inputs/CEMBA.options.json
diff --git a/pipeline_versions.txt b/pipeline_versions.txt
@@ -38,5 +38,3 @@ Optimus	 7.7.0	2024-09-24
 atac	 2.3.1	2024-09-11 
 SmartSeq2SingleSample	 5.1.21	2024-09-11 
 SlideSeq	 3.4.2	2024-09-24 
-BuildCembaReferences	 1.0.0	2020-11-15 
-CEMBA	 1.1.7	2024-09-06 
diff --git a/pipelines/cemba/build_cemba_references/BuildCembaReferences.changelog.md b/pipelines/cemba/build_cemba_references/BuildCembaReferences.changelog.md
diff --git a/website/docs/Deprecated_Pipelines/CEMBA_MethylC_Seq_Pipeline/README.md b/website/docs/Deprecated_Pipelines/CEMBA_MethylC_Seq_Pipeline/README.md
@@ -5,9 +5,9 @@ slug: /Pipelines/CEMBA_MethylC_Seq_Pipeline/README
 # CEMBA Overview
 
 :::warning
-9/12/2024
+10/16/2024
 
-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.
+The CEMBA pipeline has been officially deprecated, with support ending on October 16, 2024. Users currently utilizing this pipeline are advised to transition to other options. A recommended alternative is the [Single-nucleus Methyl-seq and Chromatin Capture](../../Pipelines/snM3C/README.md) workflow, which offers similar capabilities for methylation and chromatin analysis.
 :::
 
 | Pipeline Version | Date Updated | Documentation Author | Questions or Feedback |