Merge pull request #34 from PacificBiosciences/feature/cell_deconv

updates for cell deconv

Author: holtjma

.github/workflows/README.md

@@ -12,71 +12,9 @@ on:
         type: string
 
 jobs:
-  update-release:
-    runs-on: ubuntu-latest
+  call-external:
+    uses: holtjma/shared_github_workflows/.github/workflows/update-release.yml@286c4ec0efbe7aac72a7149cfbd2a00f57457881
     permissions:
       contents: write
-    steps:
-      - name: Checkout code
-        uses: actions/checkout@v4
-
-      - name: Extract version from tag
-        id: extract_version
-        run: |
-          # Handle both automatic tag pushes and manual workflow dispatch
-          if [ "${{ github.event_name }}" = "workflow_dispatch" ]; then
-            # Manual trigger - use input parameter
-            TAG="${{ github.event.inputs.tag }}"
-            VERSION=${TAG#v}
-          else
-            # Automatic trigger - extract from git tag
-            TAG=${GITHUB_REF#refs/tags/}
-            VERSION=${TAG#v}
-          fi
-          echo "version=$VERSION" >> $GITHUB_OUTPUT
-          echo "tag=$TAG" >> $GITHUB_OUTPUT
-
-      - name: Extract changelog section
-        id: changelog
-        run: |
-          # Find the changelog section for this version
-          if grep -q "^# v${{ steps.extract_version.outputs.version }}$" CHANGELOG.md; then
-            # Extract from the version header to the next version header or end of file
-            awk '
-              /^# v${{ steps.extract_version.outputs.version }}$/ { 
-                in_section = 1; 
-                next 
-              }
-              /^# v[0-9]+\.[0-9]+\.[0-9]+$/ && in_section { 
-                exit 
-              }
-              in_section { 
-                print 
-              }
-            ' CHANGELOG.md > release_body.txt
-
-            echo "" >> release_body.txt
-            echo "---" >> release_body.txt
-            echo "" >> release_body.txt
-            echo "This release was automatically updated from tag ${{ steps.extract_version.outputs.tag }}." >> release_body.txt
-          else
-            echo "No changelog found for version ${{ steps.extract_version.outputs.version }}" > release_body.txt
-          fi
-
-      - name: Get Release ID
-        id: get_release
-        run: |
-          # Get the release ID for this tag
-          RELEASE_ID=$(gh api repos/${{ github.repository }}/releases/tags/${{ steps.extract_version.outputs.tag }} --jq '.id')
-          echo "release_id=$RELEASE_ID" >> $GITHUB_OUTPUT
-        env:
-          GH_TOKEN: ${{ secrets.GITHUB_TOKEN }}
-
-      - name: Update Release
-        run: |
-          # Update the existing release with new changelog content
-          gh api repos/${{ github.repository }}/releases/${{ steps.get_release.outputs.release_id }} \
-            --method PATCH \
-            --field body=@release_body.txt
-        env:
-          GH_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+    secrets:
+      token: ${{ secrets.GITHUB_TOKEN }}

.github/workflows/simple-release.yml

@@ -1,3 +1,8 @@
+# v0.16.0
+## Changes
+- Added new `methbat deconvolve` sub-command for cell type deconvolution from bulk methylation data. See [deconvolution guide](./docs/deconvolution_guide.md) for details on usage.
+- Added two example atlas files derived from public atlases: [data/cell_atlas](./data/cell_atlas/)
+
 # v0.15.0
 ## Changes
 - **Breaking**: Added five new columns to the output of `profile`:

CHANGELOG.md

@@ -6,6 +6,7 @@ Key features include:
 * Creation of cohort / background profiles from a collection of methylation profiles
 * Analysis of cohort profiles comparing sub-groups (e.g., case v. control, male v. female)
 * Segmentation of the CpGs in a dataset into Methylated, Unmethylated, or ASM regions
+* Cell type deconvolution from bulk methylation data using reference atlases
 
 Authors: [Matt Holt](https://github.com/holtjma), [Chris Saunders](https://github.com/ctsa)
 

README.md

@@ -0,0 +1,10 @@
+# Cell atlases
+This folder contains publicly available cell atlases converted to the MethBat format.
+While limited testing has been done on each atlas listed here, we recommend additional verification of performance prior to broad implementation.
+If you would like to generate your own atlas, refer to our documentation for the [expected MethBat atlas format](../../docs/deconvolution_guide.md#atlas-format).
+
+List of atlas files included:
+
+* [Nanomix atlases](./nanomix) - Atlases released as part of [nanomix](https://github.com/Jonbroad15/nanomix/tree/main/atlases), which were released under the MIT license. The nanomix GitHub does not specify the reference build for these atlases, but it is presumed hg38 from internal testing.
+
+If a public atlas you would like to use is missing, please file a GitHub ticket to investigate inclusion in this list.