Welcome to pluto’s documentation!¶
Utilities module for pluto-cwl and helix_filters_01 repos, with helper classes and methods for working with CWL files.
pluto¶
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Wrapper class to locate the full path to a cwl file more conveniently |
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class for running a CWL File |
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An all-in-one unittest.TestCase wrapper class that includes a tmpdir, CWLRunner, and other helper functions, to make it easier to create and run unit tests and integration tests for CWL workflows |
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Handler for reading a table with comments |
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Helper function to run a shell command easier |
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Run the CWL with cwltool / cwl-runner |
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Run a CWL using Toil |
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Parse a file with comments in its header to return the comments and the line number to start reader from. |
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Load the mutations from a tabular .maf file |
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Write a table to a temp location |
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Helper function to convert a list of dicts into a list of lines to use with write_table create a list of line parts to pass for write_table |
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Get md5sum of a file by reading it in small chunks. |