Running snakemake till spades fails

.github/workflows/test_pipeline.yml

@@ -11,7 +11,6 @@ on:
 jobs:
   Test-QCD-Pipeline:
     runs-on: ubuntu-latest
-    #runs-on: self-hosted
     steps:
       # - run: echo "🎉 The job was automatically triggered by a ${{ github.event_name }} event."
       # - run: echo "🐧 This job is now running on a ${{ runner.os }} server hosted by GitHub!"
@@ -29,36 +28,24 @@ jobs:
       - name: Get working directory
         run: |
           pwd
-
       - name: Set up Miniconda
         uses: conda-incubator/setup-miniconda@v2
-        # env:
-        #   CONDA: "/Users/Dhatrib/miniconda3" 
         with:
-          #miniconda-version: "latest"
           python-version: '3.10'
           auto-update-conda: true
           activate-environment: 'qcd_env_test'
-          environment-file: 'qcd_environment_shr.yaml'
+          environment-file: 'qcd_environment.yaml'
           use-channel-priority: true
-
-      # - name: SSh into Actions
-      #   uses: actions/checkout@v4
-      # - name: Setup tmate session
-      #   uses: mxschmitt/action-tmate@v3
-
+
       - name: Install pip dependencies
         run: |
-          #source /Users/Dhatrib/miniconda3/etc/profile.d/conda.sh
-          #conda init
           source $CONDA/bin/activate
           conda activate qcd_env_test
           pip install --requirement .test/requirements.txt
           pip install dropbox
           pip install --upgrade tabulate
           pip install --upgrade snakemake
-          #source $CONDA/bin/activate
-          #source ~/.bash_profile  
+        
       # - name: Install singularity
       #   run: |
       #     sudo apt-get install -y \
@@ -88,41 +75,10 @@ jobs:
            # ./mconfig --without-suid && \
            # make -C ./builddir && \
            # make -C ./builddir install
-      # - name: Install Go
-      #   run: |
-      #     brew install go
-      #     go version
-
-      # - name: Install dependencies using Homebrew
-      #   run: |
-      #     brew install wget
-      #     brew install go 
-      #     brew install squashfs
-
-      # - name: Download Singularity
-      #   run: |
-      #     wget https://github.com/sylabs/singularity/archive/refs/tags/v3.8.3.tar.gz
-      #     tar -xzf singularity-3.8.3.tar.gz
-
-      # - name: Install Singularity
-      #   run: |
-      #     cd singularity
-      #     ./mconfig
-      #     make -C builddir
-      #     sudo make -C builddir install
-
-      # - name: Verify Singularity installation
-      #   run: singularity --version
-
-        #https://github.com/sylabs/singularity/archive/refs/tags/v3.8.3.tar.gz    
       - name: Install singularity
         uses: eWaterCycle/setup-singularity@v7
         with:
           singularity-version: 3.8.3
-      - name: Configure Singularity
-        run: |
-          singularity config global --set "allow setuid = no"
-          singularity config global --set "enable overlay = yes"
       # - name: Export Singularity Path
       #   run: |
       #     export PATH=/home/runner/go/src/github.com/hpcng/singularity-3.8.3/prefix/bin:$PATH
@@ -159,11 +115,14 @@ jobs:
         env:
           DROPBOX_ACCESS_TOKEN: ${{ secrets.DROPBOX_ACCESS_TOKEN }}
         run: |
-          #source /Users/Dhatrib/miniconda3/etc/profile.d/conda.sh
           source $CONDA/bin/activate
           conda activate qcd_env_test
           export DROPBOX_ACCESS_TOKEN=${DROPBOX_ACCESS_TOKEN}
           python3 download_fastqs.py
+      # - name: SSh into Actions
+      #   uses: actions/checkout@v4
+      # - name: Setup tmate session
+      #   uses: mxschmitt/action-tmate@v3
 
       - name: Create necessary directories
         run: |
@@ -181,7 +140,7 @@ jobs:
         run: |
           source $CONDA/bin/activate
           conda activate qcd_env_test
-          snakemake -s QCD.smk -p --use-conda --use-singularity --conda-frontend conda --configfile .test/config/config.yaml --latency-wait 1000 --cores 2 
+          snakemake -s QCD.smk -p --use-conda --use-singularity --conda-frontend conda --configfile .test/config/config.yaml --latency-wait 1000 --cores 4 
         # uses: snakemake/[email protected]
         # with:
         #   directory: '.'