fix: remove checkpoint in dorado_demux to speed up workflow, closes #32

.github/workflows/deploy_apptainer.yml

@@ -20,12 +20,6 @@ jobs:
         with:
           fetch-depth: 0
 
-      - name: add apptainer source
-        shell: bash
-        run: |
-          sudo add-apt-repository -y ppa:apptainer/ppa
-          sudo apt-get update
-
       - name: create dockerfile
         uses: snakemake/snakemake-github-action@v2
         with:

.github/workflows/main.yml

@@ -1,20 +1,19 @@
-name: CI
+name: Tests
 
 on:
   push:
-    branches: [main, dev]
+    branches: [main]
   pull_request:
-    branches: [main, dev]
+    branches: [main]
 
 jobs:
   Formatting:
     runs-on: ubuntu-latest
-    if: ${{ github.actor != 'github-actions[bot]' }}
     steps:
       - uses: actions/checkout@v4
         with:
           fetch-depth: 0
-      - name: Test formatting
+      - name: Formatting
         uses: super-linter/super-linter@v7
         env:
           VALIDATE_ALL_CODEBASE: false
@@ -25,33 +24,33 @@ jobs:
 
   Linting:
     runs-on: ubuntu-latest
-    if: ${{ github.actor != 'github-actions[bot]' }}
     steps:
       - uses: actions/checkout@v4
-      - name: Test linting workflow
-        uses: snakemake/snakemake-github-action@v2.0.0
+      - name: Lint workflow
+        uses: snakemake/snakemake-github-action@v2
         with:
           directory: .
           snakefile: workflow/Snakefile
           args: "--lint"
 
   Testing:
     runs-on: ubuntu-latest
-    if: ${{ github.actor != 'github-actions[bot]' }}
     needs:
+      - Linting
       - Formatting
     steps:
       - uses: actions/checkout@v4
-      - name: Test run workflow
-        uses: snakemake/snakemake-github-action@v2.0.0
+
+      - name: Test workflow
+        uses: snakemake/snakemake-github-action@v2
         with:
           directory: .test
           snakefile: workflow/Snakefile
-          args: "--sdm conda --show-failed-logs --cores 3 --conda-cleanup-pkgs cache -n"
+          args: "--sdm conda --show-failed-logs --cores 2 --conda-cleanup-pkgs cache -n"
 
       - name: Test report
-        uses: snakemake/snakemake-github-action@v2.0.0
+        uses: snakemake/snakemake-github-action@v2
         with:
           directory: .test
           snakefile: workflow/Snakefile
-          args: "--cores 3 --report report.zip -n"
+          args: "--cores 2 --report report.zip"

.github/workflows/release-please.yml

@@ -17,4 +17,4 @@ jobs:
       - uses: googleapis/release-please-action@v4
         with:
           token: ${{ secrets.GITHUB_TOKEN }}
-          release-type: simple
+          release-type: go # just keep a changelog, no version anywhere outside of git tags

README.md

@@ -67,8 +67,6 @@ conda activate snakemake-ont-basecalling
 This step creates all conda environments specified in the snakemake rules. This step is optional.
 
 ```bash
-# activate new environment
-conda activate snakemake-ont-basecalling
 snakemake -c 1 --sdm conda --conda-create-envs-only --conda-cleanup-pkgs cache --directory .test
 ```
 
@@ -118,7 +116,7 @@ snakemake --cores 3 --sdm conda apptainer --directory .test --apptainer-args "--
 To run the workflow with test files on a **slurm cluster**, adjust the slurm-specific profile `workflow/profiles/slurm/config.yaml` file and run:
 
 ```bash
-snakemake --sdm conda --workflow-profile workflow/profiles/slurm/ --directory .test
+snakemake --cores 3 --sdm conda --workflow-profile workflow/profiles/slurm/ --directory .test
 ```
 
 **Note:**

config/README.md

@@ -44,7 +44,7 @@ snakemake --cores 3 --sdm conda apptainer --directory .test --apptainer-args "--
 To run the workflow with test files on a **slurm cluster**, adjust the slurm-specific profile `workflow/profiles/slurm/config.yaml` file and run:
 
 ```bash
-snakemake --sdm conda --workflow-profile workflow/profiles/slurm/ --directory .test
+snakemake --cores 3 --sdm conda --workflow-profile workflow/profiles/slurm/ --directory .test
 ```
 
 **Note:**