From 8897a50119ec60ff11648cfd5ba05dbd9539d49e Mon Sep 17 00:00:00 2001 From: Thomas Weber Date: Wed, 26 Jun 2024 12:16:21 +0000 Subject: [PATCH] Add mock data and update GH actions --- .github/workflows/main_test.yaml | 187 +++++++++--------- .../config/simple_config_ashleys.yaml | 0 .../config/simple_config_mosaicatcher.yaml | 0 .../config/slurm_config/config.yaml | 0 .../bam/BM510x04_PE20301.sort.mdup.bam | 0 .../bam/BM510x04_PE20302.sort.mdup.bam | 0 .../bam/BM510x04_PE20303.sort.mdup.bam | 0 .../bam/BM510x04_PE20304.sort.mdup.bam | 0 .../bam/BM510x04_PE20305.sort.mdup.bam | 0 .../bam/BM510x04_PE20306.sort.mdup.bam | 0 .../bam/BM510x04_PE20307.sort.mdup.bam | 0 .../bam/BM510x04_PE20308.sort.mdup.bam | 0 .../bam/BM510x04_PE20309.sort.mdup.bam | 0 .../bam/BM510x04_PE20310.sort.mdup.bam | 0 .../bam/BM510x04_PE20311.sort.mdup.bam | 0 .../bam/BM510x04_PE20312.sort.mdup.bam | 0 .../bam/BM510x04_PE20313.sort.mdup.bam | 0 .../bam/BM510x04_PE20314.sort.mdup.bam | 0 .../bam/BM510x04_PE20316.sort.mdup.bam | 0 .../bam/BM510x04_PE20317.sort.mdup.bam | 0 .../bam/BM510x04_PE20318.sort.mdup.bam | 0 .../bam/BM510x04_PE20319.sort.mdup.bam | 0 .../fastq/BM510x04_PE20301.1.fastq.gz | 0 .../fastq/BM510x04_PE20301.2.fastq.gz | 0 .../fastq/BM510x04_PE20302.1.fastq.gz | 0 .../fastq/BM510x04_PE20302.2.fastq.gz | 0 .../fastq/BM510x04_PE20303.1.fastq.gz | 0 .../fastq/BM510x04_PE20303.2.fastq.gz | 0 .../fastq/BM510x04_PE20304.1.fastq.gz | 0 .../fastq/BM510x04_PE20304.2.fastq.gz | 0 .../fastq/BM510x04_PE20305.1.fastq.gz | 0 .../fastq/BM510x04_PE20305.2.fastq.gz | 0 .../fastq/BM510x04_PE20306.1.fastq.gz | 0 .../fastq/BM510x04_PE20306.2.fastq.gz | 0 .../fastq/BM510x04_PE20307.1.fastq.gz | 0 .../fastq/BM510x04_PE20307.2.fastq.gz | 0 .../fastq/BM510x04_PE20308.1.fastq.gz | 0 .../fastq/BM510x04_PE20308.2.fastq.gz | 0 .../fastq/BM510x04_PE20309.1.fastq.gz | 0 .../fastq/BM510x04_PE20309.2.fastq.gz | 0 .../fastq/BM510x04_PE20310.1.fastq.gz | 0 .../fastq/BM510x04_PE20310.2.fastq.gz | 0 .../fastq/BM510x04_PE20311.1.fastq.gz | 0 .../fastq/BM510x04_PE20311.2.fastq.gz | 0 .../fastq/BM510x04_PE20312.1.fastq.gz | 0 .../fastq/BM510x04_PE20312.2.fastq.gz | 0 .../fastq/BM510x04_PE20313.1.fastq.gz | 0 .../fastq/BM510x04_PE20313.2.fastq.gz | 0 .../fastq/BM510x04_PE20314.1.fastq.gz | 0 .../fastq/BM510x04_PE20314.2.fastq.gz | 0 .../fastq/BM510x04_PE20316.1.fastq.gz | 0 .../fastq/BM510x04_PE20316.2.fastq.gz | 0 .../fastq/BM510x04_PE20317.1.fastq.gz | 0 .../fastq/BM510x04_PE20317.2.fastq.gz | 0 .../fastq/BM510x04_PE20318.1.fastq.gz | 0 .../fastq/BM510x04_PE20318.2.fastq.gz | 0 .../fastq/BM510x04_PE20319.1.fastq.gz | 0 .../fastq/BM510x04_PE20319.2.fastq.gz | 0 .../scNOVA_input_user/input_subclonality.txt | 0 .../data_CHR17/config/config_df.tsv | 0 .../.tests-mock/external_data/chr17.fa | 0 .../.tests-mock/external_data/chr17.fa.amb | 0 .../.tests-mock/external_data/chr17.fa.ann | 0 .../.tests-mock/external_data/chr17.fa.bwt | 0 .../.tests-mock/external_data/chr17.fa.fai | 0 .../.tests-mock/external_data/chr17.fa.gzi | 0 .../.tests-mock/external_data/chr17.fa.pac | 0 .../.tests-mock/external_data/chr17.fa.sa | 0 68 files changed, 94 insertions(+), 93 deletions(-) create mode 100644 github-actions-runner/.tests-mock/config/simple_config_ashleys.yaml create mode 100644 github-actions-runner/.tests-mock/config/simple_config_mosaicatcher.yaml create mode 100644 github-actions-runner/.tests-mock/config/slurm_config/config.yaml create mode 100644 github-actions-runner/.tests-mock/data_CHR17/RPE-BM510/bam/BM510x04_PE20301.sort.mdup.bam create mode 100644 github-actions-runner/.tests-mock/data_CHR17/RPE-BM510/bam/BM510x04_PE20302.sort.mdup.bam create mode 100644 github-actions-runner/.tests-mock/data_CHR17/RPE-BM510/bam/BM510x04_PE20303.sort.mdup.bam create mode 100644 github-actions-runner/.tests-mock/data_CHR17/RPE-BM510/bam/BM510x04_PE20304.sort.mdup.bam create mode 100644 github-actions-runner/.tests-mock/data_CHR17/RPE-BM510/bam/BM510x04_PE20305.sort.mdup.bam create mode 100644 github-actions-runner/.tests-mock/data_CHR17/RPE-BM510/bam/BM510x04_PE20306.sort.mdup.bam create mode 100644 github-actions-runner/.tests-mock/data_CHR17/RPE-BM510/bam/BM510x04_PE20307.sort.mdup.bam create mode 100644 github-actions-runner/.tests-mock/data_CHR17/RPE-BM510/bam/BM510x04_PE20308.sort.mdup.bam create mode 100644 github-actions-runner/.tests-mock/data_CHR17/RPE-BM510/bam/BM510x04_PE20309.sort.mdup.bam create mode 100644 github-actions-runner/.tests-mock/data_CHR17/RPE-BM510/bam/BM510x04_PE20310.sort.mdup.bam create mode 100644 github-actions-runner/.tests-mock/data_CHR17/RPE-BM510/bam/BM510x04_PE20311.sort.mdup.bam create mode 100644 github-actions-runner/.tests-mock/data_CHR17/RPE-BM510/bam/BM510x04_PE20312.sort.mdup.bam create mode 100644 github-actions-runner/.tests-mock/data_CHR17/RPE-BM510/bam/BM510x04_PE20313.sort.mdup.bam create mode 100644 github-actions-runner/.tests-mock/data_CHR17/RPE-BM510/bam/BM510x04_PE20314.sort.mdup.bam create mode 100644 github-actions-runner/.tests-mock/data_CHR17/RPE-BM510/bam/BM510x04_PE20316.sort.mdup.bam create mode 100644 github-actions-runner/.tests-mock/data_CHR17/RPE-BM510/bam/BM510x04_PE20317.sort.mdup.bam create mode 100644 github-actions-runner/.tests-mock/data_CHR17/RPE-BM510/bam/BM510x04_PE20318.sort.mdup.bam create mode 100644 github-actions-runner/.tests-mock/data_CHR17/RPE-BM510/bam/BM510x04_PE20319.sort.mdup.bam create mode 100644 github-actions-runner/.tests-mock/data_CHR17/RPE-BM510/fastq/BM510x04_PE20301.1.fastq.gz create mode 100644 github-actions-runner/.tests-mock/data_CHR17/RPE-BM510/fastq/BM510x04_PE20301.2.fastq.gz create mode 100644 github-actions-runner/.tests-mock/data_CHR17/RPE-BM510/fastq/BM510x04_PE20302.1.fastq.gz create mode 100644 github-actions-runner/.tests-mock/data_CHR17/RPE-BM510/fastq/BM510x04_PE20302.2.fastq.gz create mode 100644 github-actions-runner/.tests-mock/data_CHR17/RPE-BM510/fastq/BM510x04_PE20303.1.fastq.gz create mode 100644 github-actions-runner/.tests-mock/data_CHR17/RPE-BM510/fastq/BM510x04_PE20303.2.fastq.gz create mode 100644 github-actions-runner/.tests-mock/data_CHR17/RPE-BM510/fastq/BM510x04_PE20304.1.fastq.gz create mode 100644 github-actions-runner/.tests-mock/data_CHR17/RPE-BM510/fastq/BM510x04_PE20304.2.fastq.gz create mode 100644 github-actions-runner/.tests-mock/data_CHR17/RPE-BM510/fastq/BM510x04_PE20305.1.fastq.gz create mode 100644 github-actions-runner/.tests-mock/data_CHR17/RPE-BM510/fastq/BM510x04_PE20305.2.fastq.gz create mode 100644 github-actions-runner/.tests-mock/data_CHR17/RPE-BM510/fastq/BM510x04_PE20306.1.fastq.gz create mode 100644 github-actions-runner/.tests-mock/data_CHR17/RPE-BM510/fastq/BM510x04_PE20306.2.fastq.gz create mode 100644 github-actions-runner/.tests-mock/data_CHR17/RPE-BM510/fastq/BM510x04_PE20307.1.fastq.gz create mode 100644 github-actions-runner/.tests-mock/data_CHR17/RPE-BM510/fastq/BM510x04_PE20307.2.fastq.gz create mode 100644 github-actions-runner/.tests-mock/data_CHR17/RPE-BM510/fastq/BM510x04_PE20308.1.fastq.gz create mode 100644 github-actions-runner/.tests-mock/data_CHR17/RPE-BM510/fastq/BM510x04_PE20308.2.fastq.gz create mode 100644 github-actions-runner/.tests-mock/data_CHR17/RPE-BM510/fastq/BM510x04_PE20309.1.fastq.gz create mode 100644 github-actions-runner/.tests-mock/data_CHR17/RPE-BM510/fastq/BM510x04_PE20309.2.fastq.gz create mode 100644 github-actions-runner/.tests-mock/data_CHR17/RPE-BM510/fastq/BM510x04_PE20310.1.fastq.gz create mode 100644 github-actions-runner/.tests-mock/data_CHR17/RPE-BM510/fastq/BM510x04_PE20310.2.fastq.gz create mode 100644 github-actions-runner/.tests-mock/data_CHR17/RPE-BM510/fastq/BM510x04_PE20311.1.fastq.gz create mode 100644 github-actions-runner/.tests-mock/data_CHR17/RPE-BM510/fastq/BM510x04_PE20311.2.fastq.gz create mode 100644 github-actions-runner/.tests-mock/data_CHR17/RPE-BM510/fastq/BM510x04_PE20312.1.fastq.gz create mode 100644 github-actions-runner/.tests-mock/data_CHR17/RPE-BM510/fastq/BM510x04_PE20312.2.fastq.gz create mode 100644 github-actions-runner/.tests-mock/data_CHR17/RPE-BM510/fastq/BM510x04_PE20313.1.fastq.gz create mode 100644 github-actions-runner/.tests-mock/data_CHR17/RPE-BM510/fastq/BM510x04_PE20313.2.fastq.gz create mode 100644 github-actions-runner/.tests-mock/data_CHR17/RPE-BM510/fastq/BM510x04_PE20314.1.fastq.gz create mode 100644 github-actions-runner/.tests-mock/data_CHR17/RPE-BM510/fastq/BM510x04_PE20314.2.fastq.gz create mode 100644 github-actions-runner/.tests-mock/data_CHR17/RPE-BM510/fastq/BM510x04_PE20316.1.fastq.gz create mode 100644 github-actions-runner/.tests-mock/data_CHR17/RPE-BM510/fastq/BM510x04_PE20316.2.fastq.gz create mode 100644 github-actions-runner/.tests-mock/data_CHR17/RPE-BM510/fastq/BM510x04_PE20317.1.fastq.gz create mode 100644 github-actions-runner/.tests-mock/data_CHR17/RPE-BM510/fastq/BM510x04_PE20317.2.fastq.gz create mode 100644 github-actions-runner/.tests-mock/data_CHR17/RPE-BM510/fastq/BM510x04_PE20318.1.fastq.gz create mode 100644 github-actions-runner/.tests-mock/data_CHR17/RPE-BM510/fastq/BM510x04_PE20318.2.fastq.gz create mode 100644 github-actions-runner/.tests-mock/data_CHR17/RPE-BM510/fastq/BM510x04_PE20319.1.fastq.gz create mode 100644 github-actions-runner/.tests-mock/data_CHR17/RPE-BM510/fastq/BM510x04_PE20319.2.fastq.gz create mode 100644 github-actions-runner/.tests-mock/data_CHR17/RPE-BM510/scNOVA_input_user/input_subclonality.txt create mode 100644 github-actions-runner/.tests-mock/data_CHR17/config/config_df.tsv create mode 100644 github-actions-runner/.tests-mock/external_data/chr17.fa create mode 100644 github-actions-runner/.tests-mock/external_data/chr17.fa.amb create mode 100644 github-actions-runner/.tests-mock/external_data/chr17.fa.ann create mode 100644 github-actions-runner/.tests-mock/external_data/chr17.fa.bwt create mode 100644 github-actions-runner/.tests-mock/external_data/chr17.fa.fai create mode 100644 github-actions-runner/.tests-mock/external_data/chr17.fa.gzi create mode 100644 github-actions-runner/.tests-mock/external_data/chr17.fa.pac create mode 100644 github-actions-runner/.tests-mock/external_data/chr17.fa.sa diff --git a/.github/workflows/main_test.yaml b/.github/workflows/main_test.yaml index 76c38a8..ff642cc 100644 --- a/.github/workflows/main_test.yaml +++ b/.github/workflows/main_test.yaml @@ -6,7 +6,6 @@ on: - "**" jobs: - Formatting: runs-on: ubuntu-latest steps: @@ -21,36 +20,27 @@ jobs: GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} VALIDATE_SNAKEMAKE_SNAKEFMT: true - Linting: runs-on: ubuntu-latest steps: - - name: Checkout repository with submodules + - name: Checkout repository without submodules uses: actions/checkout@v4 - with: - submodules: 'recursive' # Ensures all submodules are checked out - lfs: true # Ensures LFS objects for the main repo are pulled - - - name: Pull LFS objects in submodules - run: | - git submodule foreach --recursive 'git lfs pull' + # with: + # submodules: "recursive" # Ensures all submodules are checked out + # lfs: true # Ensures LFS objects for the main repo are pulled - - name: List contents of .tests - run: | - tree -h .tests - - - name: List contents of workflow/data - run: | - tree -h workflow/data + # - name: Pull LFS objects in submodules + # run: | + # git submodule foreach --recursive 'git pull origin main' - - name: List contents of snakemake_profiles + - name: List contents of .tests-mock run: | - tree -h workflow/snakemake_profiles + tree -h github-actions-runner/.tests-mock - name: Setup Python - uses: actions/setup-python@v5 + uses: actions/setup-python@v5 with: - python-version: '3.12' + python-version: "3.12" - name: Add Conda to system path run: | @@ -66,27 +56,29 @@ jobs: - name: Run Snakemake Lint run: | - snakemake --lint + snakemake --config data_location=github-actions-runner/.tests-mock/data_CHR17 --lint Testing-basic: runs-on: ubuntu-latest - # needs: + # needs: # - Formatting # - Linting steps: - - name: Checkout repository with submodules and LFS + - name: Checkout repository with submodules uses: actions/checkout@v4 with: submodules: recursive - lfs: true - - name: Pull LFS objects in submodules - run: git submodule foreach --recursive 'git lfs pull' + # Update references + - name: Git Submodule Update + run: | + git pull --recurse-submodules + git submodule update --remote --recursive - name: Setup Python - uses: actions/setup-python@v5 + uses: actions/setup-python@v5 with: - python-version: '3.12' + python-version: "3.12" - name: List contents of .tests run: | @@ -120,7 +112,7 @@ jobs: # Testing-basic-with-slurm: # runs-on: ubuntu-latest - # needs: + # needs: # - Formatting # - Linting # - Testing-basic @@ -156,9 +148,9 @@ jobs: # tree -h workflow/data # - name: Setup Python - # uses: actions/setup-python@v5 + # uses: actions/setup-python@v5 # with: - # python-version: '3.12' + # python-version: '3.12' # - name: Add Conda to system path # run: echo "$CONDA/bin" >> $GITHUB_PATH @@ -176,24 +168,26 @@ jobs: Testing-with-MultiQC: runs-on: ubuntu-latest - needs: - - Formatting - - Linting - - Testing-basic + needs: + - Formatting + - Linting + - Testing-basic steps: - - name: Checkout repository with submodules and LFS + - name: Checkout repository with submodules uses: actions/checkout@v4 with: submodules: recursive - lfs: true - - name: Pull LFS objects in submodules - run: git submodule foreach --recursive 'git lfs pull' + # Update references + - name: Git Submodule Update + run: | + git pull --recurse-submodules + git submodule update --remote --recursive - name: Setup Python - uses: actions/setup-python@v5 + uses: actions/setup-python@v5 with: - python-version: '3.12' + python-version: "3.12" - name: Add Conda to system path run: echo "$CONDA/bin" >> $GITHUB_PATH @@ -215,24 +209,26 @@ jobs: Testing-with-ms-norm: runs-on: ubuntu-latest - needs: - - Formatting - - Linting - - Testing-basic + needs: + - Formatting + - Linting + - Testing-basic steps: - - name: Checkout repository with submodules and LFS + - name: Checkout repository with submodules uses: actions/checkout@v4 with: submodules: recursive - lfs: true - - name: Pull LFS objects in submodules - run: git submodule foreach --recursive 'git lfs pull' + # Update references + - name: Git Submodule Update + run: | + git pull --recurse-submodules + git submodule update --remote --recursive - name: Setup Python - uses: actions/setup-python@v5 + uses: actions/setup-python@v5 with: - python-version: '3.12' + python-version: "3.12" - name: Add Conda to system path run: echo "$CONDA/bin" >> $GITHUB_PATH @@ -254,25 +250,27 @@ jobs: Testing-with-hg38: runs-on: ubuntu-latest - needs: - - Formatting - - Linting - - Testing-basic + needs: + - Formatting + - Linting + - Testing-basic # - Testing-basic-with-slurm steps: - - name: Checkout repository with submodules and LFS + - name: Checkout repository with submodules uses: actions/checkout@v4 with: submodules: recursive - lfs: true - - name: Pull LFS objects in submodules - run: git submodule foreach --recursive 'git lfs pull' + # Update references + - name: Git Submodule Update + run: | + git pull --recurse-submodules + git submodule update --remote --recursive - name: Setup Python - uses: actions/setup-python@v5 + uses: actions/setup-python@v5 with: - python-version: '3.12' + python-version: "3.12" - name: Add Conda to system path run: echo "$CONDA/bin" >> $GITHUB_PATH @@ -290,29 +288,31 @@ jobs: - name: Run workflow run: | snakemake --cores 1 --use-conda --config reference=hg38 use_light_data=True chromosomes=[chr17] \ - --conda-frontend mamba -p --verbose --debug --snakefile workflow/Snakefile + --conda-frontend mamba -p --verbose --debug --snakefile workflow/Snakefile Testing-with-hg19: runs-on: ubuntu-latest - needs: - - Formatting - - Linting - - Testing-basic + needs: + - Formatting + - Linting + - Testing-basic # - Testing-basic-with-slurm steps: - - name: Checkout repository with submodules and LFS + - name: Checkout repository with submodules uses: actions/checkout@v4 with: submodules: recursive - lfs: true - - name: Pull LFS objects in submodules - run: git submodule foreach --recursive 'git lfs pull' + # Update references + - name: Git Submodule Update + run: | + git pull --recurse-submodules + git submodule update --remote --recursive - name: Setup Python - uses: actions/setup-python@v5 + uses: actions/setup-python@v5 with: - python-version: '3.12' + python-version: "3.12" - name: Add Conda to system path run: echo "$CONDA/bin" >> $GITHUB_PATH @@ -330,14 +330,14 @@ jobs: - name: Run workflow run: | snakemake --cores 1 --use-conda --config reference=hg19 use_light_data=True chromosomes=[chr17] \ - --conda-frontend mamba -p --verbose --debug --snakefile workflow/Snakefile + --conda-frontend mamba -p --verbose --debug --snakefile workflow/Snakefile Testing-with-T2T: runs-on: ubuntu-latest - needs: - - Formatting - - Linting - - Testing-basic + needs: + - Formatting + - Linting + - Testing-basic # - Testing-basic-with-slurm steps: - name: Checkout repository with submodules and LFS @@ -350,9 +350,9 @@ jobs: run: git submodule foreach --recursive 'git lfs pull' - name: Setup Python - uses: actions/setup-python@v5 + uses: actions/setup-python@v5 with: - python-version: '3.12' + python-version: "3.12" - name: Add Conda to system path run: echo "$CONDA/bin" >> $GITHUB_PATH @@ -370,29 +370,31 @@ jobs: - name: Run workflow run: | snakemake --cores 1 --use-conda --config reference=T2T use_light_data=True chromosomes=[chr17] \ - --conda-frontend mamba -p --verbose --debug --snakefile workflow/Snakefile + --conda-frontend mamba -p --verbose --debug --snakefile workflow/Snakefile Testing-with-mm10: runs-on: ubuntu-latest - needs: - - Formatting - - Linting - - Testing-basic + needs: + - Formatting + - Linting + - Testing-basic # - Testing-basic-with-slurm steps: - - name: Checkout repository with submodules and LFS + - name: Checkout repository with submodules uses: actions/checkout@v4 with: submodules: recursive - lfs: true - - name: Pull LFS objects in submodules - run: git submodule foreach --recursive 'git lfs pull' + # Update references + - name: Git Submodule Update + run: | + git pull --recurse-submodules + git submodule update --remote --recursive - name: Setup Python - uses: actions/setup-python@v5 + uses: actions/setup-python@v5 with: - python-version: '3.12' + python-version: "3.12" - name: Add Conda to system path run: echo "$CONDA/bin" >> $GITHUB_PATH @@ -410,9 +412,8 @@ jobs: - name: Run workflow run: | snakemake --cores 1 --use-conda --config reference=T2T use_light_data=True chromosomes=[chr17] \ - --conda-frontend mamba -p --verbose --debug --snakefile workflow/Snakefile + --conda-frontend mamba -p --verbose --debug --snakefile workflow/Snakefile - # Testing_publishdir: # runs-on: ubuntu-latest # steps: diff --git a/github-actions-runner/.tests-mock/config/simple_config_ashleys.yaml b/github-actions-runner/.tests-mock/config/simple_config_ashleys.yaml new file mode 100644 index 0000000..e69de29 diff --git a/github-actions-runner/.tests-mock/config/simple_config_mosaicatcher.yaml b/github-actions-runner/.tests-mock/config/simple_config_mosaicatcher.yaml new file mode 100644 index 0000000..e69de29 diff --git a/github-actions-runner/.tests-mock/config/slurm_config/config.yaml b/github-actions-runner/.tests-mock/config/slurm_config/config.yaml new file mode 100644 index 0000000..e69de29 diff --git a/github-actions-runner/.tests-mock/data_CHR17/RPE-BM510/bam/BM510x04_PE20301.sort.mdup.bam b/github-actions-runner/.tests-mock/data_CHR17/RPE-BM510/bam/BM510x04_PE20301.sort.mdup.bam new file mode 100644 index 0000000..e69de29 diff --git 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