mspipelines 0.3.3

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.

mspipelines 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.

mspipelines 0.3.1

Breaking changes

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

Breaking changes

• 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.

mspipelines 0.3.0

Added components:

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

Minor changes:

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

• convert/thermo_to_mzml: Added unit test.

mspipelines 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.

mspipelines 0.1.0

Initial release of mspipeline

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.