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CHANGELOG.md

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mspipeline 0.3.3

Minor changes

  • convert/maxquant_to_h5ad: Converted script to python and implemented a (preliminary) unit test.

  • maxquant/maxquant: Added parameters:

    • --input_experiment: Set the experiment label for a given input. Must be undefined or of the same length as --input.
    • --input_fraction: Set the fraction for a given input. Must be undefined or of the same length as --input.
    • --input_ptm: Set the PTM value for a given input. Must be undefined or of the same length as --input.
    • --dia_library_type: Which type of DIA library to use. Must be "MaxQuant" or "tsv".
    • --dia_library: Path to the DIA library.

Bug fixes

  • maxquant/maxquant: Fix issue where lfq_mode was not being passed to the jinja template.

mspipeline 0.3.2

New functionality

  • proteomics/fastadl: Generates a FASTA sequence database for a given taxonomy using UniProtKB

Minor changes

  • msdial/msdial_gcms: Use parallel processing for processing input files.

  • msdial/msdial_lcms: Use parallel processing for processing input files.

  • maxquant/maxquant: The mqpar.xml is now generated by a jinja template instead of a lot of Python code.

  • maxquant/maxquant: Added parameters:

    • --ref_identifier_rule: The identifier parsing regex for the provided reference fastas. Length must be 1 or match that of the --reference argument.
    • --ref_description_rule: The description parsing regex for the provided reference fastas. Length must be 1 or match that of the --reference argument.
    • --ref_taxonomy_rule: The taxonomy parsing regex for the provided reference fastas. Length must be 1 or match that of the --reference argument.
    • --peptides_for_quantification: Specify how the protein ratios will be calculated.
    • --main_search_max_combinations: The maximum combinations during the main search.

mspipeline 0.3.1

Breaking changes

  • msdial/msdial_gcms: Now only accepts one or more input files. Directories are no longer accepted.

New functionality

  • msdial/msdial_lcms: Added MSDial LC/MS DDA/DIA component.

Major changes

  • msdial/msdial_gcms: Added support for setting the name, type, class_id, batch, analytical_order and inject_volume of input files.

Minor changes

  • convert/thermo_to_mzml: Revert being able to process input directories. Only allow processing individual input files.

Bug fixes

  • maxquant/maxquant: Fix refactoring error in script.

mspipeline 0.3.0

Added components:

  • msdial/msdial_gcms: Added MSDial GC/MS component.

Major changes:

  • maxquant/maxquant: Refactored Bash script into a Python script.

  • maxquant/maxquant: Added parameters to tweak the analysis.

Minor changes:

  • convert/thermo_to_mzml: Allow also processing whole directories instead of individual raw files.

  • convert/thermo_to_mzml: Added unit test.

mspipeline 0.2.0

Added components:

  • convert/thermo_to_mzml: Convert a Thermo raw file to mzML.
  • qc/rawbeans: Perform QC analysis on mzML file.

Major changes:

  • Pipeline maxquant: Added rawbeans to pipeline.

mspipeline 0.1.0

Initial release of mspipeline.

Added components:

  • maxquant/maxquant: Running a MaxQuant analysis with mostly default parameters.
  • convert/maxquant_to_h5ad: Converting a MaxQuant output folder to an AnnData file.
  • download/sync_resources_test: Download testing resources from S3 to the resources_test/ directory.

Nextflow workflows:

  • maxquant: Starting from Thermo Raw files, run MaxQuant and convert the outputs to AnnData.