snakemake-github-action/action.yml at master · snakemake/snakemake-github-action · GitHub

1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
name: snakemake

description: Run Snakemake on the repository

branding:
  icon: git-pull-request
  color: green

inputs:
  directory:
    description: Working directory for the execution
    required: true
    default: .test
  snakefile:
    description: Snakefile containing the workflow description
    default: Snakefile
  args:
    description: Additional Snakemake arguments to use
    required: false
    default: ""
  stagein:
    description: Additional steps to prepare the workflow for execution
    required: false
    default: ""
  task:
    description: Whether to run Snakemake or to generate a container image specification.
    required: false
    default: "run"
  show-disk-usage-on-error:
    description: Whether to return the used disk space on failing.
    required: false
    default: "false"
  snakemake-version:
    description: |
      Snakemake version to use. If not specified, uses latest version. Pin a specific version (e.g., '8.25.5') for reproducibility.
    required: false
    default: "*"
  snakemake-branch:
    description: |
      Optional Snakemake git branch to install from https://github.com/snakemake/snakemake.
      If set, this takes precedence over snakemake-version and Snakemake is installed via pip.
    required: false
    default: ""
  install-apptainer:
    description: Install Apptainer (true/false)
    required: false
    default: "false"
  containerize-args:
    description: Additional arguments for --containerize, can be one of 'dockerfile', 'apptainer' or '' (defaults to dockerfile)
    required: false
    default: ""

runs:
  using: "composite"
  steps:
    - name: Validate inputs
      if: ${{ ! (inputs.task == 'containerize' || inputs.task == 'run' )}}
      shell: bash -el {0}
      run: |
        echo 'Invalid value for "task": "${{ inputs.task }}". Options: "containerize", "run".'
        exit 1

    - name: Install Apptainer
      if: ${{ inputs.install-apptainer == 'true' }}
      shell: bash -el {0}
      run: |
        if ! command -v apt-get &> /dev/null; then
          echo "Error: This action currently supports Apptainer installation only on Ubuntu runners"
          exit 1
        fi
        sudo add-apt-repository -y ppa:apptainer/ppa
        sudo apt-get update
        sudo apt-get install -y apptainer

    - name: Prepare .snakemake.environment.yaml
      shell: bash -el {0}
      run: |
        cat <<EOF > .snakemake.environment.yaml
        channels:
          - conda-forge
          - bioconda
          - nodefaults
        dependencies:
          - snakemake ==${{ inputs.snakemake-version }}

    - name: Setup conda
      uses: conda-incubator/setup-miniconda@v3
      with:
        channels: conda-forge,bioconda
        channel-priority: strict
        miniforge-version: latest
        environment-file: .snakemake.environment.yaml
        activate-environment: snakemake

    - name: Install snakemake from git branch
      if: ${{ inputs.snakemake-branch != '' }}
      shell: bash -el {0}
      run: |
        pip install "git+https://github.com/snakemake/snakemake@${{ inputs.snakemake-branch }}"

    - name: Display snakemake version
      shell: bash -el {0}
      run: snakemake --version

    - name: Run snakemake
      if: ${{ inputs.task == 'run' }}
      shell: bash -el {0}
      run: |
        ${{ inputs.stagein }}
        snakemake --directory ${{ inputs.directory }} --snakefile ${{ inputs.snakefile }} --show-failed-logs ${{ inputs.args }}
        if [[ "$?" -ne 0 ]]; then
          if [[ ${{ inputs.show-disk-usage-on-error }} = true ]]; then
              # return disk usage and space on failing
              df -h
              printf "disk usage working directory"
              du -h -d3 ${{ inputs.directory }}
          fi
          exit 1
        fi

    - name: Containerize snakemake
      if: ${{ inputs.task == 'containerize' }}
      shell: bash -el {0}
      run: |
        if [[ "${{ inputs.containerize-args }}" == "apptainer" ]]; then
          recipe="apptainer.def"
        else
          recipe="Dockerfile"
        fi
        snakemake --directory ${{ inputs.directory }} --snakefile ${{ inputs.snakefile }} --show-failed-logs ${{ inputs.args }} --containerize ${{ inputs.containerize-args }} > $recipe