Merge pull request #16 from friendsofstrandseq/dev

Genecore mode: Version 1.8.2

.github/workflows/conda.yaml

@@ -0,0 +1,238 @@
+name: MosaiCatcher conda checks
+
+on:
+  push:
+    branches:
+      - dev
+
+jobs:
+  # WORK
+
+  Testing_norm_disabled:
+    runs-on: ubuntu-latest
+    # needs:
+    #   - Linting
+    #   - Formatting
+    steps:
+      - uses: actions/checkout@v2
+      - name: Testing data
+        uses: snakemake/[email protected]
+        with:
+          directory: .
+          snakefile: ./workflow/Snakefile
+          stagein: "conda config --set channel_priority flexible"
+          args: "--cores 1 --use-conda --configfile .tests/config/simple_config.yaml --config normalized_counts=False --conda-frontend mamba -p --verbose --debug"
+      - name: Testing report
+        uses: snakemake/[email protected]
+        with:
+          directory: .
+          snakefile: ./workflow/Snakefile
+          args: "--cores 1 --use-conda --configfile .tests/config/simple_config.yaml --config normalized_counts=False --conda-frontend mamba --report report.zip"
+
+  Linting_ashleys:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v2
+      - name: Linting
+        uses: snakemake/[email protected]
+        with:
+          directory: .
+          snakefile: ./workflow/Snakefile
+          args: "--lint --config ashleys_pipeline=True"
+  Testing_ashleys:
+    runs-on: ubuntu-latest
+    # needs:
+    #   - Linting
+    #   - Formatting
+    steps:
+      - uses: actions/checkout@v2
+      - name: Testing data
+        uses: snakemake/[email protected]
+        with:
+          directory: .
+          snakefile: ./workflow/Snakefile
+          stagein: "conda config --set channel_priority flexible"
+          args: "--cores 1 --use-conda --configfile .tests/config/simple_config.yaml --config ashleys_pipeline=True use_light_data=True --conda-frontend mamba -p --verbose --debug"
+      - name: Testing report
+        uses: snakemake/[email protected]
+        with:
+          directory: .
+          snakefile: ./workflow/Snakefile
+          args: "--cores 1 --use-conda --configfile .tests/config/simple_config.yaml --config ashleys_pipeline=True use_light_data=True --conda-frontend mamba --report report.zip"
+
+  Testing_ashleys_norm_counts_disabled:
+    runs-on: ubuntu-latest
+    # needs:
+    #   - Linting
+    #   - Formatting
+    steps:
+      - uses: actions/checkout@v2
+      - name: Testing data
+        uses: snakemake/[email protected]
+        with:
+          directory: .
+          snakefile: ./workflow/Snakefile
+          stagein: "conda config --set channel_priority flexible"
+          args: "--cores 1 --use-conda --configfile .tests/config/simple_config.yaml --config ashleys_pipeline=True use_light_data=True normalized_counts=False --conda-frontend mamba -p --verbose --debug"
+      - name: Testing report
+        uses: snakemake/[email protected]
+        with:
+          directory: .
+          snakefile: ./workflow/Snakefile
+          args: "--cores 1 --use-conda --configfile .tests/config/simple_config.yaml --config ashleys_pipeline=True use_light_data=True normalized_counts=False --conda-frontend mamba --report report.zip"
+  Testing_ashleys_norm_enabled_GC_correction:
+    runs-on: ubuntu-latest
+    # needs:
+    #   - Linting
+    #   - Formatting
+    steps:
+      - uses: actions/checkout@v2
+      - name: Testing data
+        uses: snakemake/[email protected]
+        with:
+          directory: .
+          snakefile: ./workflow/Snakefile
+          stagein: "conda config --set channel_priority flexible"
+          args: "--cores 1 --use-conda --config chromosomes=[chr17] ashleys_pipeline=True normalized_counts=True GC_analysis=True use_light_data=True  --conda-frontend mamba -p --verbose --debug"
+      - name: Testing report
+        uses: snakemake/[email protected]
+        with:
+          directory: .
+          snakefile: ./workflow/Snakefile
+          args: "--cores 1 --use-conda --config chromosomes=[chr17] ashleys_pipeline=True normalized_counts=True GC_analysis=True use_light_data=True  --conda-frontend mamba --report report.zip"
+  Testing_ashleys_jup_nb:
+    runs-on: ubuntu-latest
+    # needs:
+    #   - Linting
+    #   - Formatting
+    steps:
+      - uses: actions/checkout@v2
+      - name: Testing data
+        uses: snakemake/[email protected]
+        with:
+          directory: .
+          snakefile: ./workflow/Snakefile
+          stagein: "conda config --set channel_priority flexible"
+          args: "--cores 1 --use-conda --configfile .tests/config/simple_config.yaml --config ashleys_pipeline=True use_light_data=True hand_selection=True --conda-frontend mamba -p --verbose --debug"
+      - name: Testing report
+        uses: snakemake/[email protected]
+        with:
+          directory: .
+          snakefile: ./workflow/Snakefile
+          args: "--cores 1 --use-conda --configfile .tests/config/simple_config.yaml --config ashleys_pipeline=True use_light_data=True hand_selection=True  --conda-frontend mamba --report report.zip"
+
+  Testing_ashleys_norm_enabled_hg19:
+    runs-on: ubuntu-latest
+    # needs:
+    #   - Linting
+    #   - Formatting
+    steps:
+      - uses: actions/checkout@v2
+      - name: Testing data
+        uses: snakemake/[email protected]
+        with:
+          directory: .
+          snakefile: ./workflow/Snakefile
+          stagein: "conda config --set channel_priority flexible"
+          args: "--cores 1 --use-conda --config ashleys_pipeline=True use_light_data=True chromosomes=[chr17] normalized_counts=True reference=hg19 --conda-frontend mamba -p --verbose --debug"
+      - name: Testing report
+        uses: snakemake/[email protected]
+        with:
+          directory: .
+          snakefile: ./workflow/Snakefile
+          args: "--cores 1 --use-conda --config ashleys_pipeline=True use_light_data=True chromosomes=[chr17] normalized_counts=True reference=hg19 --conda-frontend mamba --report report.zip"
+  Testing_ashleys_norm_enabled_hg38_full:
+    runs-on: ubuntu-latest
+    # needs:
+    #   - Linting
+    #   - Formatting
+    steps:
+      - uses: actions/checkout@v2
+      - name: Testing data
+        uses: snakemake/[email protected]
+        with:
+          directory: .
+          snakefile: ./workflow/Snakefile
+          stagein: "conda config --set channel_priority flexible"
+          args: "--cores 1 --use-conda --config ashleys_pipeline=True use_light_data=True chromosomes=[chr17] normalized_counts=True reference=hg38 --conda-frontend mamba -p --verbose --debug"
+      - name: Testing report
+        uses: snakemake/[email protected]
+        with:
+          directory: .
+          snakefile: ./workflow/Snakefile
+          args: "--cores 1 --use-conda --config ashleys_pipeline=True use_light_data=True chromosomes=[chr17] normalized_counts=True reference=hg38 --conda-frontend mamba --report report.zip"
+  Testing_ashleys_norm_enabled_T2T:
+    runs-on: ubuntu-latest
+    # needs:
+    #   - Linting
+    #   - Formatting
+    steps:
+      - uses: actions/checkout@v2
+      - name: Testing data
+        uses: snakemake/[email protected]
+        with:
+          directory: .
+          snakefile: ./workflow/Snakefile
+          stagein: "conda config --set channel_priority flexible"
+          args: "--cores 1 --use-conda --config ashleys_pipeline=True use_light_data=True chromosomes=[chr17] normalized_counts=True reference=T2T --conda-frontend mamba -p --verbose --debug"
+      - name: Testing report
+        uses: snakemake/[email protected]
+        with:
+          directory: .
+          snakefile: ./workflow/Snakefile
+          args: "--cores 1 --use-conda --config ashleys_pipeline=True use_light_data=True chromosomes=[chr17] normalized_counts=True reference=T2T --conda-frontend mamba --report report.zip"
+
+  Downloading_example_data:
+    runs-on: ubuntu-latest
+    # needs:
+    #   - Linting
+    #   - Formatting
+    steps:
+      - uses: actions/checkout@v2
+      - name: Downloading_example_data
+        uses: snakemake/[email protected]
+        with:
+          directory: .
+          snakefile: ./workflow/Snakefile
+          stagein: "mamba install -c conda-forge unzip"
+          args: "--cores 1 --config dl_bam_example=True -p --verbose --debug"
+  Downloading_hg19:
+    runs-on: ubuntu-latest
+    # needs:
+    #   - Linting
+    #   - Formatting
+    steps:
+      - uses: actions/checkout@v2
+      - name: Downloading_hg19
+        uses: snakemake/[email protected]
+        with:
+          directory: .
+          snakefile: ./workflow/Snakefile
+          args: "--cores 1 --config dl_external_files=True reference=hg19 -p --verbose --debug"
+  Downloading_hg38:
+    runs-on: ubuntu-latest
+    # needs:
+    #   - Linting
+    #   - Formatting
+    steps:
+      - uses: actions/checkout@v2
+      - name: Downloading_hg38
+        uses: snakemake/[email protected]
+        with:
+          directory: .
+          snakefile: ./workflow/Snakefile
+          args: "--cores 1 --config dl_external_files=True reference=hg38 -p --verbose --debug"
+  Downloading_installing_T2T:
+    runs-on: ubuntu-latest
+    # needs:
+    #   - Linting
+    #   - Formatting
+    steps:
+      - uses: actions/checkout@v2
+      - name: Downloading_T2T
+        uses: snakemake/[email protected]
+        with:
+          directory: .
+          snakefile: ./workflow/Snakefile
+          stagein: "conda config --set channel_priority flexible"
+          args: "--cores 1  --use-conda --conda-frontend mamba --config dl_external_files=True reference=T2T -p --verbose --debug"

.github/workflows/docker.yaml

@@ -1,10 +1,10 @@
-name: Build container
+name: Build & Push docker container
 
 on:
   pull_request:
     types: [closed]
-    branches:
-      - master
+#     branches:
+#       - master
 
 # on:
 #   push:
@@ -27,14 +27,14 @@ jobs:
           directory: .
           snakefile: ./workflow/Snakefile
           stagein: "conda config --set channel_priority flexible"
-          args: "--cores 2 --use-conda --configfile .tests/config/simple_config.yaml --config chromosomes=[chr17] ashleys_pipeline=True normalized_counts=True GC_analysis=True use_light_data=True  --conda-frontend mamba -p"
+          args: "--cores 1 --use-conda --config chromosomes=[chr17] ashleys_pipeline=True normalized_counts=True GC_analysis=True use_light_data=True  --conda-frontend mamba -p --verbose --debug"
       - name: Create container file
         uses: snakemake/[email protected]
         with:
           snakefile: ./workflow/Snakefile
           directory: .
           task: "containerize"
-          args: "--cores 1 --use-conda --configfile .tests/config/simple_config.yaml --config chromosomes=[chr17] ashleys_pipeline=True normalized_counts=True GC_analysis=True use_light_data=True"
+          args: "--cores 1 --use-conda --config chromosomes=[chr17] ashleys_pipeline=True normalized_counts=True GC_analysis=True use_light_data=True  --conda-frontend mamba -p --verbose --debug"
       - name: Print Dockerfile
         run: |
           cat Dockerfile
@@ -89,3 +89,45 @@ jobs:
           registry: docker.io/weber8thomas
           username: ${{ secrets.DOCKER_USERNAME }}
           password: ${{ secrets.DOCKER_TOKEN }}
+
+  # Test_singularity:
+  #   name: Snakemake x Singularity
+  #   runs-on: ubuntu-latest
+
+  #   # needs:
+  #   #   - create_dockerfile
+  #   #   - build_and_push_image
+
+  #   defaults:
+  #     run:
+  #       shell: bash -l {0}
+
+  #   steps:
+  #     - name: checkout repository
+  #       uses: actions/checkout@v2
+
+  #     - uses: eWaterCycle/setup-singularity@v7
+  #       with:
+  #         singularity-version: 3.8.3
+
+  #     - name: create environment with mamba
+  #       uses: conda-incubator/setup-miniconda@v2
+  #       with:
+  #         mamba-version: "*"
+  #         channels: conda-forge,bioconda,defaults
+  #         auto-activate-base: false
+  #         activate-environment: snakemake_env
+  #         environment-file: ./workflow/envs/snakemake.yaml
+
+  #     # - name: check solution
+  #     #   run: |
+  #     #     mamba env export
+
+  #     - name: test snakemake
+  #       run: |
+  #         which snakemake
+  #         snakemake --version
+
+  #     - name: Testing data
+  #       run: |
+  #         snakemake --cores 1 --use-singularity --singularity-args '-B /etc:/etc -B /home:/home' --use-conda --configfile .tests/config/simple_config.yaml --conda-frontend mamba -p --verbose --debug