Merge pull request kircherlab#120 from kircherlab/master

chore: update development to 0.1.0
visze · Sep 19, 2024 · e8d4007 · e8d4007
2 parents 62b043c + a4f9f5c
commit e8d4007
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diff --git a/.github/workflows/release-please.yml b/.github/workflows/release-please.yml
@@ -3,14 +3,14 @@ on:
     branches:
       - master
 
+permissions:
+  contents: write
+  pull-requests: write
+
 name: release-please
 
 jobs:
   release-please:
     runs-on: ubuntu-latest
     steps:
-      - uses: GoogleCloudPlatform/release-please-action@v3
-        id: release
-        with:
-          release-type: go # just keep a changelog, no version anywhere outside of git tags
-          package-name: MPRASnakeflow
+      - uses: googleapis/release-please-action@v4
diff --git a/.release-please-manifest.json b/.release-please-manifest.json
@@ -0,0 +1,3 @@
+{
+  ".": "0.1.0"
+}
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -0,0 +1,14 @@
+# Changelog
+
+## [0.1.0](https://github.com/kircherlab/MPRAsnakeflow/compare/MPRAsnakeflow-v0.0.1...MPRAsnakeflow-v0.1.0) (2024-09-18)
+
+First release of MPRAsnakeflow! 
+
+### Feature highlights
+
+* Multiple assignment mapping strategies (BBMap, exact, bwa)
+* Optimized assignment for variants with BBMap
+* QC report for assignment and experiment workflow
+* Barcode count output
+* Snakemake 8 support
+* Extended documentation: https://mprasnakeflow.readthedocs.io
diff --git a/Dockerfile b/Dockerfile
@@ -20,6 +20,21 @@ LABEL io.github.snakemake.conda_env_hash="7a57714fe74eb25255d53b45e2095cd8a4dd4f
 RUN mkdir -p /conda-envs/c243bde7dc056785a077f6c33e56e8d6
 COPY workflow/envs/NGmerge.yaml /conda-envs/c243bde7dc056785a077f6c33e56e8d6/environment.yaml
 
+# Conda environment:
+#   source: workflow/envs/bbmap_samtools_htslib.yaml
+#   prefix: /conda-envs/575ebc82fb464fb2d0748323abbd3a13
+# ---
+# channels:
+#   - bioconda
+#   - conda-forge
+#   - defaults
+# dependencies:
+#   - bbmap
+#   - samtools
+#   - htslib
+RUN mkdir -p /conda-envs/575ebc82fb464fb2d0748323abbd3a13
+COPY workflow/envs/bbmap_samtools_htslib.yaml /conda-envs/575ebc82fb464fb2d0748323abbd3a13/environment.yaml
+
 # Conda environment:
 #   source: workflow/envs/bwa_samtools_picard_htslib.yaml
 #   prefix: /conda-envs/f354d1f7a8fd64abb8ea8902ec91d399
@@ -151,6 +166,7 @@ COPY workflow/envs/quarto.yaml /conda-envs/b8e51d222ab0d9caac2206a127729b1c/envi
 # Step 2: Generate conda environments
 
 RUN mamba env create --prefix /conda-envs/c243bde7dc056785a077f6c33e56e8d6 --file /conda-envs/c243bde7dc056785a077f6c33e56e8d6/environment.yaml
+RUN mamba env create --prefix /conda-envs/575ebc82fb464fb2d0748323abbd3a13 --file /conda-envs/575ebc82fb464fb2d0748323abbd3a13/environment.yaml
 RUN mamba env create --prefix /conda-envs/f354d1f7a8fd64abb8ea8902ec91d399 --file /conda-envs/f354d1f7a8fd64abb8ea8902ec91d399/environment.yaml
 RUN mamba env create --prefix /conda-envs/9444545a0ebc79ec516fa74514742720 --file /conda-envs/9444545a0ebc79ec516fa74514742720/environment.yaml
 RUN mamba env create --prefix /conda-envs/dc242c7dafc90db387bc0290c31dc7ae --file /conda-envs/dc242c7dafc90db387bc0290c31dc7ae/environment.yaml

diff --git a/profiles/default/config.yaml b/profiles/default/config.yaml
@@ -130,7 +130,7 @@ set-resources:
     mem: 15G
 
   assigned_counts_combine_replicates_barcode_output:
-    runtime: 20
+    runtime: 60
     mem: 30G
     slurm_partition: medium
 
@@ -143,15 +143,15 @@ set-resources:
   ########################
 
   statistic_counts_frequent_umis:
-    runtime: 240
+    runtime: 480
     slurm_partition: medium
 
   statistic_counts_barcode_base_composition:
     runtime: 1440
     slurm_partition: medium
     mem: 20G
   statistic_counts_table:
-    runtime: 120
+    runtime: 240
     slurm_partition: medium
 
   #############################

diff --git a/release-please-config.json b/release-please-config.json
@@ -0,0 +1,15 @@
+{
+    "$schema": "https://raw.githubusercontent.com/googleapis/release-please/main/schemas/config.json",
+    "release-type": "simple",
+    "pull-request-title-pattern": "chore${scope}: release${component} ${version}",
+    "packages": {
+        ".": {
+            "package-name": "MPRAsnakeflow",
+            "release-type": "simple",
+            "bump-minor-pre-major": true,
+            "bump-patch-for-minor-pre-major": true,
+            "draft": true,
+            "prerelease": true
+        }
+    }
+}
diff --git a/version.txt b/version.txt
@@ -0,0 +1 @@
+0.1.0