From 5c8cc8afd5ae18337525d964b08e758da467ed19 Mon Sep 17 00:00:00 2001 From: Nikelle Petrillo <38223776+nikellepetrillo@users.noreply.github.com> Date: Fri, 18 Oct 2024 08:50:39 -0400 Subject: [PATCH] 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 --- .../BuildCembaReferences.changelog.md | 12 ++++++++++++ .../BuildCembaReferences.options.json | 0 .../build_cemba_references/BuildCembaReferences.wdl | 0 .../build_bisulfite_references.py | 0 .../BuildCembaReferences.GRCh38.inputs.json | 0 .../BuildCembaReferences.GRCm38.inputs.json | 0 .../cemba/cemba_methylcseq/CEMBA.changelog.md | 5 +++++ .../cemba/cemba_methylcseq/CEMBA.methods.md | 0 .../pipelines}/cemba/cemba_methylcseq/CEMBA.png | Bin .../pipelines}/cemba/cemba_methylcseq/CEMBA.wdl | 2 +- .../pipelines}/cemba/cemba_methylcseq/README.md | 0 .../example_inputs/CEMBA.inputs.json | 0 .../example_inputs/CEMBA.options.json | 0 pipeline_versions.txt | 2 -- .../BuildCembaReferences.changelog.md | 7 ------- .../CEMBA_MethylC_Seq_Pipeline/README.md | 4 ++-- 16 files changed, 20 insertions(+), 12 deletions(-) create mode 100644 deprecated/pipelines/cemba/build_cemba_references/BuildCembaReferences.changelog.md rename {pipelines => deprecated/pipelines}/cemba/build_cemba_references/BuildCembaReferences.options.json (100%) rename {pipelines => deprecated/pipelines}/cemba/build_cemba_references/BuildCembaReferences.wdl (100%) rename {pipelines => deprecated/pipelines}/cemba/build_cemba_references/build_bisulfite_references.py (100%) rename {pipelines => deprecated/pipelines}/cemba/build_cemba_references/input_files/BuildCembaReferences.GRCh38.inputs.json (100%) rename {pipelines => deprecated/pipelines}/cemba/build_cemba_references/input_files/BuildCembaReferences.GRCm38.inputs.json (100%) rename {pipelines => deprecated/pipelines}/cemba/cemba_methylcseq/CEMBA.changelog.md (69%) rename {pipelines => deprecated/pipelines}/cemba/cemba_methylcseq/CEMBA.methods.md (100%) rename {pipelines => deprecated/pipelines}/cemba/cemba_methylcseq/CEMBA.png (100%) rename {pipelines => deprecated/pipelines}/cemba/cemba_methylcseq/CEMBA.wdl (99%) rename {pipelines => deprecated/pipelines}/cemba/cemba_methylcseq/README.md (100%) rename {pipelines => deprecated/pipelines}/cemba/cemba_methylcseq/example_inputs/CEMBA.inputs.json (100%) rename {pipelines => deprecated/pipelines}/cemba/cemba_methylcseq/example_inputs/CEMBA.options.json (100%) delete mode 100644 pipelines/cemba/build_cemba_references/BuildCembaReferences.changelog.md diff --git a/deprecated/pipelines/cemba/build_cemba_references/BuildCembaReferences.changelog.md b/deprecated/pipelines/cemba/build_cemba_references/BuildCembaReferences.changelog.md new file mode 100644 index 0000000000..bfa1bee7dc --- /dev/null +++ b/deprecated/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/pipelines/cemba/build_cemba_references/BuildCembaReferences.options.json b/deprecated/pipelines/cemba/build_cemba_references/BuildCembaReferences.options.json similarity index 100% rename from pipelines/cemba/build_cemba_references/BuildCembaReferences.options.json rename to deprecated/pipelines/cemba/build_cemba_references/BuildCembaReferences.options.json diff --git a/pipelines/cemba/build_cemba_references/BuildCembaReferences.wdl b/deprecated/pipelines/cemba/build_cemba_references/BuildCembaReferences.wdl similarity index 100% rename from pipelines/cemba/build_cemba_references/BuildCembaReferences.wdl rename to deprecated/pipelines/cemba/build_cemba_references/BuildCembaReferences.wdl diff --git a/pipelines/cemba/build_cemba_references/build_bisulfite_references.py b/deprecated/pipelines/cemba/build_cemba_references/build_bisulfite_references.py similarity index 100% rename from pipelines/cemba/build_cemba_references/build_bisulfite_references.py rename to deprecated/pipelines/cemba/build_cemba_references/build_bisulfite_references.py diff --git a/pipelines/cemba/build_cemba_references/input_files/BuildCembaReferences.GRCh38.inputs.json b/deprecated/pipelines/cemba/build_cemba_references/input_files/BuildCembaReferences.GRCh38.inputs.json similarity index 100% rename from pipelines/cemba/build_cemba_references/input_files/BuildCembaReferences.GRCh38.inputs.json rename to deprecated/pipelines/cemba/build_cemba_references/input_files/BuildCembaReferences.GRCh38.inputs.json diff --git a/pipelines/cemba/build_cemba_references/input_files/BuildCembaReferences.GRCm38.inputs.json b/deprecated/pipelines/cemba/build_cemba_references/input_files/BuildCembaReferences.GRCm38.inputs.json similarity index 100% rename from pipelines/cemba/build_cemba_references/input_files/BuildCembaReferences.GRCm38.inputs.json rename to deprecated/pipelines/cemba/build_cemba_references/input_files/BuildCembaReferences.GRCm38.inputs.json diff --git a/pipelines/cemba/cemba_methylcseq/CEMBA.changelog.md b/deprecated/pipelines/cemba/cemba_methylcseq/CEMBA.changelog.md similarity index 69% rename from pipelines/cemba/cemba_methylcseq/CEMBA.changelog.md rename to deprecated/pipelines/cemba/cemba_methylcseq/CEMBA.changelog.md index 0a7178369f..9dc8a0f319 100644 --- a/pipelines/cemba/cemba_methylcseq/CEMBA.changelog.md +++ b/deprecated/pipelines/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/pipelines/cemba/cemba_methylcseq/CEMBA.methods.md b/deprecated/pipelines/cemba/cemba_methylcseq/CEMBA.methods.md similarity index 100% rename from pipelines/cemba/cemba_methylcseq/CEMBA.methods.md rename to deprecated/pipelines/cemba/cemba_methylcseq/CEMBA.methods.md diff --git a/pipelines/cemba/cemba_methylcseq/CEMBA.png b/deprecated/pipelines/cemba/cemba_methylcseq/CEMBA.png similarity index 100% rename from pipelines/cemba/cemba_methylcseq/CEMBA.png rename to deprecated/pipelines/cemba/cemba_methylcseq/CEMBA.png diff --git a/pipelines/cemba/cemba_methylcseq/CEMBA.wdl b/deprecated/pipelines/cemba/cemba_methylcseq/CEMBA.wdl similarity index 99% rename from pipelines/cemba/cemba_methylcseq/CEMBA.wdl rename to deprecated/pipelines/cemba/cemba_methylcseq/CEMBA.wdl index 1779c89194..3c23723a02 100644 --- a/pipelines/cemba/cemba_methylcseq/CEMBA.wdl +++ b/deprecated/pipelines/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 b/deprecated/pipelines/cemba/cemba_methylcseq/README.md similarity index 100% rename from pipelines/cemba/cemba_methylcseq/README.md rename to deprecated/pipelines/cemba/cemba_methylcseq/README.md diff --git a/pipelines/cemba/cemba_methylcseq/example_inputs/CEMBA.inputs.json b/deprecated/pipelines/cemba/cemba_methylcseq/example_inputs/CEMBA.inputs.json similarity index 100% rename from pipelines/cemba/cemba_methylcseq/example_inputs/CEMBA.inputs.json rename to deprecated/pipelines/cemba/cemba_methylcseq/example_inputs/CEMBA.inputs.json diff --git a/pipelines/cemba/cemba_methylcseq/example_inputs/CEMBA.options.json b/deprecated/pipelines/cemba/cemba_methylcseq/example_inputs/CEMBA.options.json similarity index 100% rename from pipelines/cemba/cemba_methylcseq/example_inputs/CEMBA.options.json rename to deprecated/pipelines/cemba/cemba_methylcseq/example_inputs/CEMBA.options.json diff --git a/pipeline_versions.txt b/pipeline_versions.txt index 58e9900074..6911635220 100644 --- 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 deleted file mode 100644 index 7120bb57d4..0000000000 --- a/pipelines/cemba/build_cemba_references/BuildCembaReferences.changelog.md +++ /dev/null @@ -1,7 +0,0 @@ -# 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/website/docs/Deprecated_Pipelines/CEMBA_MethylC_Seq_Pipeline/README.md b/website/docs/Deprecated_Pipelines/CEMBA_MethylC_Seq_Pipeline/README.md index af41088ee8..0938488887 100644 --- 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 |