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Merge branch 'release/1.1.0'
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‎.github/workflows/validate_cwls.yml‎

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name: Validate CWL Files
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on:
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push:
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branches: [master, develop]
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pull_request:
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branches: [master, develop]
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jobs:
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validate_cwls:
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runs-on: macos-latest
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strategy:
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fail-fast: false
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matrix:
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python-version: [3.6, 3.7]
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steps:
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- uses: actions/checkout@v2
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with:
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submodules: recursive
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- name: Set up Python ${{ matrix.python-version }}
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uses: actions/setup-python@v2
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with:
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python-version: ${{ matrix.python-version }}
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- name: Install cwltool
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run: |
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python -m pip install toil[cwl]==4.2.0
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- uses: actions/checkout@v2
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- name: Validate
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run: |
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pip install cwltool
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find . -name '*.cwl' | xargs -n 1 -P 8 cwltool --validate

‎alignment/alignment__packed.cwl‎

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"boolean"
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],
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"https://www.sevenbridges.com/x": 319.15625,
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"https://www.sevenbridges.com/y": 852.0390625
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"https://www.sevenbridges.com/y": 958.8671875
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},
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{
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"id": "#output_file_name",
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"string"
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],
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"https://www.sevenbridges.com/x": 319.15625,
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"https://www.sevenbridges.com/y": 745.2109375
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"https://www.sevenbridges.com/y": 852.0390625
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},
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{
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"id": "#read_group_description",
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"string"
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],
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"https://www.sevenbridges.com/x": 0,
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"https://www.sevenbridges.com/y": 1388.765625
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"https://www.sevenbridges.com/y": 1495.59375
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},
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{
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"id": "#read_group_identifier",
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"type": "string",
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"https://www.sevenbridges.com/x": 0,
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"https://www.sevenbridges.com/y": 1281.9375
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"https://www.sevenbridges.com/y": 1388.765625
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},
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{
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"id": "#read_group_library",
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"type": "string",
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"https://www.sevenbridges.com/x": 0,
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"https://www.sevenbridges.com/y": 1175.109375
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"https://www.sevenbridges.com/y": 1281.9375
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},
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{
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"id": "#read_group_platform_unit",
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"type": "string",
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"https://www.sevenbridges.com/x": 0,
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"https://www.sevenbridges.com/y": 1068.28125
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"https://www.sevenbridges.com/y": 1175.109375
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},
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{
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"id": "#read_group_run_date",
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"string"
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],
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"https://www.sevenbridges.com/x": 0,
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"https://www.sevenbridges.com/y": 961.453125
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"https://www.sevenbridges.com/y": 1068.28125
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},
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{
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"id": "#read_group_sample_name",
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"type": "string",
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"https://www.sevenbridges.com/x": 0,
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"https://www.sevenbridges.com/y": 854.625
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"https://www.sevenbridges.com/y": 961.453125
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},
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{
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"id": "#read_group_sequencing_center",
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"type": "string",
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"https://www.sevenbridges.com/x": 0,
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"https://www.sevenbridges.com/y": 747.796875
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"https://www.sevenbridges.com/y": 854.625
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},
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{
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"id": "#read_group_sequencing_platform",
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"type": "string",
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"https://www.sevenbridges.com/x": 0,
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"https://www.sevenbridges.com/y": 640.96875
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"https://www.sevenbridges.com/y": 747.796875
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},
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{
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"id": "#sort_order",
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"string"
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],
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"https://www.sevenbridges.com/x": 0,
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"https://www.sevenbridges.com/y": 320.484375
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"https://www.sevenbridges.com/y": 427.3125
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},
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{
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"id": "#validation_stringency",
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{
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"id": "#reference",
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"type": "File",
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"secondaryFiles": [
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".amb",
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".fai",
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".sa",
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"^.dict",
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".ann",
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".bwt",
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".pac"
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],
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"https://www.sevenbridges.com/x": 0,
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"https://www.sevenbridges.com/y": 427.3125
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"https://www.sevenbridges.com/y": 534.140625
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},
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{
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"id": "#reads",
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"items": "File"
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},
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"https://www.sevenbridges.com/x": 0,
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"https://www.sevenbridges.com/y": 534.140625
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"https://www.sevenbridges.com/y": 640.96875
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},
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{
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"id": "#output",
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"string"
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],
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"https://www.sevenbridges.com/x": 0,
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"https://www.sevenbridges.com/y": 1602.421875
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"https://www.sevenbridges.com/y": 1709.25
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},
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{
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"id": "#P",
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"boolean"
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],
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"https://www.sevenbridges.com/x": 0,
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"https://www.sevenbridges.com/y": 1495.59375
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"https://www.sevenbridges.com/y": 1602.421875
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},
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{
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"id": "#M",
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"boolean"
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],
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"https://www.sevenbridges.com/x": 0,
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"https://www.sevenbridges.com/y": 1709.25
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"https://www.sevenbridges.com/y": 1816.078125
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},
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{
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"id": "#T",
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"int"
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],
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"https://www.sevenbridges.com/x": 0,
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"https://www.sevenbridges.com/y": 213.65625
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"https://www.sevenbridges.com/y": 320.484375
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},
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{
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"id": "#Y",
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"int"
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],
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"https://www.sevenbridges.com/x": 0,
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"https://www.sevenbridges.com/y": 1816.078125
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"https://www.sevenbridges.com/y": 1922.90625
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},
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{
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"id": "#bwa_number_of_threads",
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"int"
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],
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"https://www.sevenbridges.com/x": 0,
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"https://www.sevenbridges.com/y": 1922.90625
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"https://www.sevenbridges.com/y": 2029.734375
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},
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{
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"id": "#temporary_directory",
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"type": [
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"null",
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"string"
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],
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"https://www.sevenbridges.com/x": 0,
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"https://www.sevenbridges.com/y": 213.65625
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}
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],
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"outputs": [
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"#picard_add_or_replace_read_groups_4_1_8_1/picard_add_or_replace_read_groups_bam"
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],
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"type": "File",
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"https://www.sevenbridges.com/x": 1379.46142578125,
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"https://www.sevenbridges.com/y": 961.453125
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"secondaryFiles": [
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"^.bai"
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],
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"https://www.sevenbridges.com/x": 1389.239501953125,
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"https://www.sevenbridges.com/y": 1014.8671875
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}
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],
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"steps": [
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{
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"id": "#picard_add_or_replace_read_groups_4_1_8_1/create_bam_index",
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"source": "#create_bam_index"
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},
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{
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"id": "#picard_add_or_replace_read_groups_4_1_8_1/temporary_directory",
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"source": "#temporary_directory"
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}
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],
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"out": [
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"run": "#picard_add_or_replace_read_groups_4.1.8.1.cwl",
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"label": "picard_add_or_replace_read_groups_4.1.8.1",
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"https://www.sevenbridges.com/x": 737.3328857421875,
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"https://www.sevenbridges.com/y": 870.453125
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"https://www.sevenbridges.com/y": 923.8671875
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},
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{
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"id": "#bwa_mem_0_7_17",
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"run": "#bwa_mem_0.7.17.cwl",
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"label": "bwa_mem_0.7.17",
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"https://www.sevenbridges.com/x": 319.15625,
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"https://www.sevenbridges.com/y": 1014.8671875
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"https://www.sevenbridges.com/y": 1121.6953125
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}
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],
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"requirements": [],
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"requirements": [
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{
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"class": "ResourceRequirement",
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"ramMin": "${ if(inputs.memory_per_job && inputs.memory_overhead) { return inputs.memory_per_job + inputs.memory_overhead } else if (inputs.memory_per_job && !inputs.memory_overhead){ return inputs.memory_per_job + 2000 } else if(!inputs.memory_per_job && inputs.memory_overhead){ return 32000 + inputs.memory_overhead } else { return 32000 } }",
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"coresMin": "${ if (inputs.number_of_threads) { return inputs.number_of_threads } else { return 16 } }"
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"ramMin": 34000,
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"coresMin": 16
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},
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{
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"class": "DockerRequirement",
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"dockerPull": "mskaccess/bwa_mem_0.7.17:0.1.0"
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"dockerPull": "ghcr.io/msk-access/bwa:0.7.17"
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},
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{
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"class": "InlineJavascriptRequirement"
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"prefix": "--CREATE_INDEX"
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},
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"doc": "Whether to create a BAM index when writing a coordinate-sorted BAM file. Default value:false. This option can be set to 'null' to clear the default value. Possible values:{true, false}"
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},
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{
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"id": "#picard_add_or_replace_read_groups_4.1.8.1.cwl/temporary_directory",
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"type": [
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"null",
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"string"
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],
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"doc": "Default value: null. This option may be specified 0 or more times."
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}
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],
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"outputs": [
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},
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{
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"position": 0,
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"valueFrom": "-XX:-UseGCOverheadLimit",
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"shellQuote": false
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"prefix": "-Djava.io.tmpdir=",
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"separate": false,
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"valueFrom": "${\n if(inputs.temporary_directory)\n return inputs.temporary_directory;\n return runtime.tmpdir\n}"
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},
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{
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"position": 0,
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"valueFrom": "-Djava.io.tmpdir=$(runtime.tmpdir)",
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"shellQuote": false
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"shellQuote": false,
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"valueFrom": "-XX:-UseGCOverheadLimit"
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},
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{
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"position": 0,
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{
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"position": 0,
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"prefix": "--TMP_DIR",
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"valueFrom": "$(runtime.tmpdir)"
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"valueFrom": "${\n if(inputs.temporary_directory)\n return inputs.temporary_directory;\n return runtime.tmpdir\n}"
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},
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{
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"position": 0,
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}
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],
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"requirements": [
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{
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"class": "ShellCommandRequirement"
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},
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{
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"class": "ResourceRequirement",
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"ramMin": 25000,
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"ramMin": 17000,
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"coresMin": 2
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},
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{
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"class": "DockerRequirement",
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"dockerPull": "broadinstitute/gatk:4.1.8.1"
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"dockerPull": "ghcr.io/msk-access/gatk:4.1.8.1"
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},
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{
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"class": "InlineJavascriptRequirement"
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],
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"cwlVersion": "v1.0",
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"$schemas": [
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"http://schema.org/version/9.0/schemaorg-current-http.rdf"
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"http://schema.org/version/latest/schemaorg-current-http.rdf"
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]
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}

‎bam_qc_stats/README.md‎

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---
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description: Specifications for performing Indel Re-alignment on a BAM file.
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---
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## Indel Re-alignment sub-workflow specification - abra_fx.cwl
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### Tools used:
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- [bedtools genomecov](https://msk-access.gitbook.io/command-line-tools-cwl/bedtools/bedtools_genomecov_v2.28.0_cv2)
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- [bedtools merge](https://msk-access.gitbook.io/command-line-tools-cwl/bedtools/bedtools_merge_v2.28.0_cv2)
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- [ABRA2](https://msk-access.gitbook.io/command-line-tools-cwl/abra2/abra2_2.22)
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- [GATK - FixMateInformation](https://msk-access.gitbook.io/command-line-tools-cwl/picard-tools/picard_fix_mate_information_4.1.8.1)
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### Usage
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```bash
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usage: indel_realignment.cwl [-h] [--window_size WINDOW_SIZE]
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[--soft_clip_contig SOFT_CLIP_CONTIG]
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[--scoring_gap_alignments SCORING_GAP_ALIGNMENTS]
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--reference_fasta REFERENCE_FASTA [--no_sort]
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[--maximum_mixmatch_rate MAXIMUM_MIXMATCH_RATE]
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[--maximum_average_depth MAXIMUM_AVERAGE_DEPTH]
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[--ignore_bad_assembly]
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[--contig_anchor CONTIG_ANCHOR]
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[--consensus_sequence] [--bam_index]
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[--number_of_threads NUMBER_OF_THREADS]
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[--option_bedgraph] [--no_edge_complex_indel]
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[--distance_between_features DISTANCE_BETWEEN_FEATURES]
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[job_order]
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positional arguments:
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job_order Job input json file
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optional arguments:
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-h, --help show this help message and exit
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--window_size WINDOW_SIZE
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--soft_clip_contig SOFT_CLIP_CONTIG
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--scoring_gap_alignments SCORING_GAP_ALIGNMENTS
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--reference_fasta REFERENCE_FASTA
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--no_sort
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--maximum_mixmatch_rate MAXIMUM_MIXMATCH_RATE
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--maximum_average_depth MAXIMUM_AVERAGE_DEPTH
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--ignore_bad_assembly
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--contig_anchor CONTIG_ANCHOR
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--consensus_sequence
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--bam_index
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--number_of_threads NUMBER_OF_THREADS
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--option_bedgraph
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--no_edge_complex_indel
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--distance_between_features DISTANCE_BETWEEN_FEATURES
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```

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