From 2510aae8e7ef29d14951990a9cd824b114e615d2 Mon Sep 17 00:00:00 2001 From: npetrill Date: Thu, 1 Aug 2024 13:14:52 -0400 Subject: [PATCH 1/6] pin all latest docker version --- .../arrays/multi_sample/MultiSampleArrays.wdl | 2 +- .../cram_to_unmapped_bams/CramToUnmappedBams.wdl | 2 +- pipelines/skylab/atac/atac.wdl | 4 ++-- projects/tasks/AdapterTasks.wdl | 2 +- tasks/broad/IlluminaGenotypingArrayTasks.wdl | 2 +- tasks/broad/InternalArraysTasks.wdl | 6 +++--- tasks/broad/InternalTasks.wdl | 2 +- tasks/skylab/CheckInputs.wdl | 2 +- .../src/main/resources/dummy/dummyWorkflow.wdl | 2 +- verification/VerifyExternalReprocessing.wdl | 2 +- verification/VerifyGermlineSingleSample.wdl | 2 +- verification/VerifyIlluminaGenotypingArray.wdl | 4 ++-- verification/VerifyJointGenotyping.wdl | 2 +- verification/VerifyMetrics.wdl | 2 +- verification/VerifyTasks.wdl | 14 +++++++------- .../VerifyUltimaGenomicsJointGenotyping.wdl | 2 +- .../VerifyUltimaGenomicsWholeGenomeGermline.wdl | 2 +- 17 files changed, 27 insertions(+), 27 deletions(-) diff --git a/pipelines/broad/arrays/multi_sample/MultiSampleArrays.wdl b/pipelines/broad/arrays/multi_sample/MultiSampleArrays.wdl index 1633c8cd3..6e5757c10 100644 --- a/pipelines/broad/arrays/multi_sample/MultiSampleArrays.wdl +++ b/pipelines/broad/arrays/multi_sample/MultiSampleArrays.wdl @@ -83,7 +83,7 @@ task SplitFoFnToListFoFn { >>> runtime { - docker: "gcr.io/gcp-runtimes/ubuntu_16_0_4:latest" + docker: "gcr.io/gcp-runtimes/ubuntu_16_0_4@sha256:025124e2f1cf4d29149958f17270596bffe13fc6acca6252977c572dd5ba01bf" memory: "1 GiB" } diff --git a/pipelines/broad/reprocessing/cram_to_unmapped_bams/CramToUnmappedBams.wdl b/pipelines/broad/reprocessing/cram_to_unmapped_bams/CramToUnmappedBams.wdl index d54d9a4cf..bef7a7893 100644 --- a/pipelines/broad/reprocessing/cram_to_unmapped_bams/CramToUnmappedBams.wdl +++ b/pipelines/broad/reprocessing/cram_to_unmapped_bams/CramToUnmappedBams.wdl @@ -222,7 +222,7 @@ task SplitUpOutputMapFile { >>> runtime { - docker: "gcr.io/gcp-runtimes/ubuntu_16_0_4:latest" + docker: "gcr.io/gcp-runtimes/ubuntu_16_0_4@sha256:025124e2f1cf4d29149958f17270596bffe13fc6acca6252977c572dd5ba01bf" disks: "local-disk " + disk_size + " HDD" memory: "~{memory_in_MiB} MiB" } diff --git a/pipelines/skylab/atac/atac.wdl b/pipelines/skylab/atac/atac.wdl index 8526d0cbc..8b2fd36af 100644 --- a/pipelines/skylab/atac/atac.wdl +++ b/pipelines/skylab/atac/atac.wdl @@ -173,12 +173,12 @@ task GetNumSplits { Int nthreads Int mem_size String cpu_platform - String docker_image = "ubuntu:latest" + String docker_image = "ubuntu@sha256:2e863c44b718727c860746568e1d54afd13b2fa71b160f5cd9058fc436217b30" String vm_size } parameter_meta { - docker_image: "the ubuntu docker image (default: ubuntu:latest)" + docker_image: "the ubuntu docker image (default: ubuntu@sha256:2e863c44b718727c860746568e1d54afd13b2fa71b160f5cd9058fc436217b30)" nthreads: "Number of threads per node (default: 128)" mem_size: "the size of memory used during alignment" vm_size: "the virtual machine used for the task" diff --git a/projects/tasks/AdapterTasks.wdl b/projects/tasks/AdapterTasks.wdl index 8f57dd2e8..d8916e38b 100644 --- a/projects/tasks/AdapterTasks.wdl +++ b/projects/tasks/AdapterTasks.wdl @@ -452,7 +452,7 @@ task GetCloudFileCreationDate { input { String file_path - String docker = "gcr.io/google.com/cloudsdktool/cloud-sdk:latest" + String docker = "gcr.io/google.com/cloudsdktool/cloud-sdk:486.0.0" Int cpu = 1 Int memory_mb = 1000 Int disk_size_gb = 1 diff --git a/tasks/broad/IlluminaGenotypingArrayTasks.wdl b/tasks/broad/IlluminaGenotypingArrayTasks.wdl index 2598bed60..4ca4074fc 100644 --- a/tasks/broad/IlluminaGenotypingArrayTasks.wdl +++ b/tasks/broad/IlluminaGenotypingArrayTasks.wdl @@ -14,7 +14,7 @@ task Md5Sum { >>> runtime { - docker: "gcr.io/gcp-runtimes/ubuntu_16_0_4:latest" + docker: "gcr.io/gcp-runtimes/ubuntu_16_0_4@sha256:025124e2f1cf4d29149958f17270596bffe13fc6acca6252977c572dd5ba01bf" disks: "local-disk 10 HDD" memory: "3.5 GiB" preemptible: 3 diff --git a/tasks/broad/InternalArraysTasks.wdl b/tasks/broad/InternalArraysTasks.wdl index 76d56fb23..e9ec3afe1 100644 --- a/tasks/broad/InternalArraysTasks.wdl +++ b/tasks/broad/InternalArraysTasks.wdl @@ -335,7 +335,7 @@ task CreateChipWellBarcodeParamsFile { >>> runtime { - docker: "gcr.io/gcp-runtimes/ubuntu_16_0_4:latest" + docker: "gcr.io/gcp-runtimes/ubuntu_16_0_4@sha256:025124e2f1cf4d29149958f17270596bffe13fc6acca6252977c572dd5ba01bf" disks: "local-disk 10 HDD" memory: "2 GiB" preemptible: preemptible_tries @@ -445,7 +445,7 @@ task ResolveExtendedIlluminaManifestFile { >>> runtime { - docker: "gcr.io/gcp-runtimes/ubuntu_16_0_4:latest" + docker: "gcr.io/gcp-runtimes/ubuntu_16_0_4@sha256:025124e2f1cf4d29149958f17270596bffe13fc6acca6252977c572dd5ba01bf" disks: "local-disk 10 HDD" memory: "2 GiB" preemptible: preemptible_tries @@ -480,7 +480,7 @@ task ResolveMinorAlleleFrequencyFile { >>> runtime { - docker: "gcr.io/gcp-runtimes/ubuntu_16_0_4:latest" + docker: "gcr.io/gcp-runtimes/ubuntu_16_0_4@sha256:025124e2f1cf4d29149958f17270596bffe13fc6acca6252977c572dd5ba01bf" disks: "local-disk 10 HDD" memory: "2 GiB" preemptible: preemptible_tries diff --git a/tasks/broad/InternalTasks.wdl b/tasks/broad/InternalTasks.wdl index 75dc79adb..b3bef735a 100644 --- a/tasks/broad/InternalTasks.wdl +++ b/tasks/broad/InternalTasks.wdl @@ -17,7 +17,7 @@ task MakeSafeFilename { >>> runtime { - docker: "gcr.io/gcp-runtimes/ubuntu_16_0_4:latest" + docker: "gcr.io/gcp-runtimes/ubuntu_16_0_4@sha256:025124e2f1cf4d29149958f17270596bffe13fc6acca6252977c572dd5ba01bf" disks: "local-disk 10 HDD" memory: "1 GiB" preemptible: 3 diff --git a/tasks/skylab/CheckInputs.wdl b/tasks/skylab/CheckInputs.wdl index 57fbcaad1..526586fed 100644 --- a/tasks/skylab/CheckInputs.wdl +++ b/tasks/skylab/CheckInputs.wdl @@ -43,7 +43,7 @@ task checkInputArrays { } runtime { - docker: "bashell/alpine-bash:latest" + docker: "bashell/alpine-bash@sha256:965a718a07c700a5204c77e391961edee37477634ce2f9cf652a8e4c2db858ff" cpu: 1 memory: "1 GiB" disks: "local-disk ~{disk} HDD" diff --git a/tests/broad/scala_test/src/main/resources/dummy/dummyWorkflow.wdl b/tests/broad/scala_test/src/main/resources/dummy/dummyWorkflow.wdl index 38a973568..aed9ae2a9 100644 --- a/tests/broad/scala_test/src/main/resources/dummy/dummyWorkflow.wdl +++ b/tests/broad/scala_test/src/main/resources/dummy/dummyWorkflow.wdl @@ -33,6 +33,6 @@ task PrintMessageToStdout { } runtime { - docker: "gcr.io/gcp-runtimes/ubuntu_16_0_4:latest" + docker: "gcr.io/gcp-runtimes/ubuntu_16_0_4@sha256:025124e2f1cf4d29149958f17270596bffe13fc6acca6252977c572dd5ba01bf" } } \ No newline at end of file diff --git a/verification/VerifyExternalReprocessing.wdl b/verification/VerifyExternalReprocessing.wdl index 7e6a697d5..a6b6005b5 100644 --- a/verification/VerifyExternalReprocessing.wdl +++ b/verification/VerifyExternalReprocessing.wdl @@ -32,7 +32,7 @@ task AssertTrue { } runtime { - docker: "gcr.io/gcp-runtimes/ubuntu_16_0_4:latest" + docker: "gcr.io/gcp-runtimes/ubuntu_16_0_4@sha256:025124e2f1cf4d29149958f17270596bffe13fc6acca6252977c572dd5ba01bf" disks: "local-disk 10 HDD" memory: "3.5 GiB" preemptible: 3 diff --git a/verification/VerifyGermlineSingleSample.wdl b/verification/VerifyGermlineSingleSample.wdl index 314f3f51a..9bea981c3 100755 --- a/verification/VerifyGermlineSingleSample.wdl +++ b/verification/VerifyGermlineSingleSample.wdl @@ -90,7 +90,7 @@ task CompareGvcfs { } runtime { - docker: "gcr.io/gcp-runtimes/ubuntu_16_0_4:latest" + docker: "gcr.io/gcp-runtimes/ubuntu_16_0_4@sha256:025124e2f1cf4d29149958f17270596bffe13fc6acca6252977c572dd5ba01bf" disks: "local-disk 300 HDD" memory: "${memory_mb} MiB" preemptible: 3 diff --git a/verification/VerifyIlluminaGenotypingArray.wdl b/verification/VerifyIlluminaGenotypingArray.wdl index a5422ee5c..6b3bc77ef 100644 --- a/verification/VerifyIlluminaGenotypingArray.wdl +++ b/verification/VerifyIlluminaGenotypingArray.wdl @@ -155,7 +155,7 @@ task CompareFiles { } runtime { - docker: "gcr.io/gcp-runtimes/ubuntu_16_0_4:latest" + docker: "gcr.io/gcp-runtimes/ubuntu_16_0_4@sha256:025124e2f1cf4d29149958f17270596bffe13fc6acca6252977c572dd5ba01bf" disks: "local-disk 10 HDD" memory: "2 GiB" preemptible: 3 @@ -175,7 +175,7 @@ task CompareMetricFilesAsText { } runtime { - docker: "gcr.io/gcp-runtimes/ubuntu_16_0_4:latest" + docker: "gcr.io/gcp-runtimes/ubuntu_16_0_4@sha256:025124e2f1cf4d29149958f17270596bffe13fc6acca6252977c572dd5ba01bf" disks: "local-disk 10 HDD" memory: "2 GiB" preemptible: 3 diff --git a/verification/VerifyJointGenotyping.wdl b/verification/VerifyJointGenotyping.wdl index 8f5c54458..64311f55e 100644 --- a/verification/VerifyJointGenotyping.wdl +++ b/verification/VerifyJointGenotyping.wdl @@ -93,7 +93,7 @@ task CompareFingerprints { } runtime { - docker: "gcr.io/gcp-runtimes/ubuntu_16_0_4:latest" + docker: "gcr.io/gcp-runtimes/ubuntu_16_0_4@sha256:025124e2f1cf4d29149958f17270596bffe13fc6acca6252977c572dd5ba01bf" disks: "local-disk 10 HDD" memory: "2 GiB" preemptible: 3 diff --git a/verification/VerifyMetrics.wdl b/verification/VerifyMetrics.wdl index 53a638259..3baa40099 100644 --- a/verification/VerifyMetrics.wdl +++ b/verification/VerifyMetrics.wdl @@ -58,7 +58,7 @@ task CompareTwoNumbers { } runtime { - docker: "gcr.io/gcp-runtimes/ubuntu_16_0_4:latest" + docker: "gcr.io/gcp-runtimes/ubuntu_16_0_4@sha256:025124e2f1cf4d29149958f17270596bffe13fc6acca6252977c572dd5ba01bf" disks: "local-disk 10 HDD" memory: "3.5 GiB" preemptible: 3 diff --git a/verification/VerifyTasks.wdl b/verification/VerifyTasks.wdl index 547fac62e..e6be84138 100644 --- a/verification/VerifyTasks.wdl +++ b/verification/VerifyTasks.wdl @@ -19,7 +19,7 @@ task CompareVcfs { } runtime { - docker: "gcr.io/gcp-runtimes/ubuntu_16_0_4:latest" + docker: "gcr.io/gcp-runtimes/ubuntu_16_0_4@sha256:025124e2f1cf4d29149958f17270596bffe13fc6acca6252977c572dd5ba01bf" disks: "local-disk 70 HDD" memory: "32 GiB" preemptible: 3 @@ -49,7 +49,7 @@ task CompareVcfsAllowingQualityDifferences { } runtime { - docker: "gcr.io/gcp-runtimes/ubuntu_16_0_4:latest" + docker: "gcr.io/gcp-runtimes/ubuntu_16_0_4@sha256:025124e2f1cf4d29149958f17270596bffe13fc6acca6252977c572dd5ba01bf" disks: "local-disk 50 HDD" memory: "3 GiB" preemptible: 3 @@ -182,7 +182,7 @@ task CompareTextFiles { } runtime { - docker: "gcr.io/gcp-runtimes/ubuntu_16_0_4:latest" + docker: "gcr.io/gcp-runtimes/ubuntu_16_0_4@sha256:025124e2f1cf4d29149958f17270596bffe13fc6acca6252977c572dd5ba01bf" disks: "local-disk 100 HDD" memory: "50 GiB" preemptible: 3 @@ -210,7 +210,7 @@ task CompareCrams { cmp -i "$test_offset:$truth_offset" ~{test_cram} ~{truth_cram} } runtime { - docker: "gcr.io/gcp-runtimes/ubuntu_16_0_4:latest" + docker: "gcr.io/gcp-runtimes/ubuntu_16_0_4@sha256:025124e2f1cf4d29149958f17270596bffe13fc6acca6252977c572dd5ba01bf" disks: "local-disk " + disk_size_gb + " HDD" memory: "2 GiB" preemptible: 3 @@ -230,7 +230,7 @@ task CompareCrais { cmp <(zcat ~{test_crai} | cut -f1,2,3,5,6) <(zcat ~{truth_crai} | cut -f1,2,3,5,6) } runtime { - docker: "gcr.io/gcp-runtimes/ubuntu_16_0_4:latest" + docker: "gcr.io/gcp-runtimes/ubuntu_16_0_4@sha256:025124e2f1cf4d29149958f17270596bffe13fc6acca6252977c572dd5ba01bf" disks: "local-disk 10 HDD" memory: "2 GiB" preemptible: 3 @@ -320,7 +320,7 @@ task CompareCompressedTextFiles { } runtime { - docker: "gcr.io/gcp-runtimes/ubuntu_16_0_4:latest" + docker: "gcr.io/gcp-runtimes/ubuntu_16_0_4@sha256:025124e2f1cf4d29149958f17270596bffe13fc6acca6252977c572dd5ba01bf" disks: "local-disk " + disk_size + " HDD" memory: "20 GiB" preemptible: 3 @@ -589,7 +589,7 @@ task CompareSnapTextFiles { >>> runtime { - docker: "gcr.io/gcp-runtimes/ubuntu_16_0_4:latest" + docker: "gcr.io/gcp-runtimes/ubuntu_16_0_4@sha256:025124e2f1cf4d29149958f17270596bffe13fc6acca6252977c572dd5ba01bf" disks: "local-disk 50 HDD" memory: "25 GiB" preemptible: 3 diff --git a/verification/VerifyUltimaGenomicsJointGenotyping.wdl b/verification/VerifyUltimaGenomicsJointGenotyping.wdl index 4d2c19a5c..aa0c6ded0 100644 --- a/verification/VerifyUltimaGenomicsJointGenotyping.wdl +++ b/verification/VerifyUltimaGenomicsJointGenotyping.wdl @@ -79,7 +79,7 @@ task CompareFingerprints { } runtime { - docker: "gcr.io/gcp-runtimes/ubuntu_16_0_4:latest" + docker: "gcr.io/gcp-runtimes/ubuntu_16_0_4@sha256:025124e2f1cf4d29149958f17270596bffe13fc6acca6252977c572dd5ba01bf" disks: "local-disk 10 HDD" memory: "2 GiB" preemptible: 3 diff --git a/verification/VerifyUltimaGenomicsWholeGenomeGermline.wdl b/verification/VerifyUltimaGenomicsWholeGenomeGermline.wdl index c206f0492..bf7cfdfb8 100755 --- a/verification/VerifyUltimaGenomicsWholeGenomeGermline.wdl +++ b/verification/VerifyUltimaGenomicsWholeGenomeGermline.wdl @@ -135,7 +135,7 @@ task CompareGvcfs { } runtime { - docker: "gcr.io/gcp-runtimes/ubuntu_16_0_4:latest" + docker: "gcr.io/gcp-runtimes/ubuntu_16_0_4@sha256:025124e2f1cf4d29149958f17270596bffe13fc6acca6252977c572dd5ba01bf" disks: "local-disk 70 HDD" memory: "2 GiB" preemptible: 3 From 8112500c2a73b4dbb926db7fa88235ce780b650a Mon Sep 17 00:00:00 2001 From: npetrill Date: Wed, 16 Oct 2024 14:05:39 -0400 Subject: [PATCH 2/6] move cemba to deprecated folder --- .../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 | 0 .../pipelines}/cemba/cemba_methylcseq/README.md | 0 .../example_inputs/CEMBA.inputs.json | 0 .../example_inputs/CEMBA.options.json | 0 .../BuildCembaReferences.changelog.md | 7 ------- 14 files changed, 17 insertions(+), 7 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 (100%) 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 000000000..bfa1bee7d --- /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 0a7178369..17613a67b 100644 --- a/pipelines/cemba/cemba_methylcseq/CEMBA.changelog.md +++ b/deprecated/pipelines/cemba/cemba_methylcseq/CEMBA.changelog.md @@ -1,3 +1,8 @@ +# 1.1.08 +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 100% rename from pipelines/cemba/cemba_methylcseq/CEMBA.wdl rename to deprecated/pipelines/cemba/cemba_methylcseq/CEMBA.wdl 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/pipelines/cemba/build_cemba_references/BuildCembaReferences.changelog.md b/pipelines/cemba/build_cemba_references/BuildCembaReferences.changelog.md deleted file mode 100644 index 7120bb57d..000000000 --- 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 From 3ed524faee388f2f4375b66b1a5cb963daf2a02b Mon Sep 17 00:00:00 2001 From: GitHub Action Date: Wed, 16 Oct 2024 18:07:02 +0000 Subject: [PATCH 3/6] Updated pipeline_versions.txt with all pipeline version information --- pipeline_versions.txt | 2 -- 1 file changed, 2 deletions(-) diff --git a/pipeline_versions.txt b/pipeline_versions.txt index 58e990007..691163522 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 From e1a8d91f8610f5e2e4b52712d910d7ff41ddc597 Mon Sep 17 00:00:00 2001 From: npetrill Date: Wed, 16 Oct 2024 14:24:16 -0400 Subject: [PATCH 4/6] update cemba readme --- .../Deprecated_Pipelines/CEMBA_MethylC_Seq_Pipeline/README.md | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) 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 af41088ee..093848888 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 | From de4e3a10fe06da2bbb0fd4e555bacb3329a2877f Mon Sep 17 00:00:00 2001 From: npetrill Date: Wed, 16 Oct 2024 14:24:41 -0400 Subject: [PATCH 5/6] update cemba readme --- .../Deprecated_Pipelines/CEMBA_MethylC_Seq_Pipeline/README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) 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 093848888..d6c316481 100644 --- a/website/docs/Deprecated_Pipelines/CEMBA_MethylC_Seq_Pipeline/README.md +++ b/website/docs/Deprecated_Pipelines/CEMBA_MethylC_Seq_Pipeline/README.md @@ -13,7 +13,7 @@ The CEMBA pipeline has been officially deprecated, with support ending on Octobe | 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). | - +tab ![CEMBA](./CEMBA.png) ## Introduction to the CEMBA Workflow From 0b9447ed678d30755ca2c49d577bb1f607702cea Mon Sep 17 00:00:00 2001 From: npetrill Date: Wed, 16 Oct 2024 14:26:10 -0400 Subject: [PATCH 6/6] update cemba readme --- .../Deprecated_Pipelines/CEMBA_MethylC_Seq_Pipeline/README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) 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 d6c316481..093848888 100644 --- a/website/docs/Deprecated_Pipelines/CEMBA_MethylC_Seq_Pipeline/README.md +++ b/website/docs/Deprecated_Pipelines/CEMBA_MethylC_Seq_Pipeline/README.md @@ -13,7 +13,7 @@ The CEMBA pipeline has been officially deprecated, with support ending on Octobe | 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). | -tab + ![CEMBA](./CEMBA.png) ## Introduction to the CEMBA Workflow