mhcquant 2.4.0 - Maroon Gold Boxer

Added

• Additional output from CometAdapter (generated with the parameter --pin_out)
• Folder structure within the intermediate_results folder to retrace the outcome files easier
• OPENMS_FALSEDISCOVERYRATE and OPENMS_IDFILTER_FOR_ALIGNMENT are now included in the first quantification step
• Altered the outcome content with the inclusion of the different folder structure
• Updated the mhcquant_web.png in the assets folder
• #229 Add ion annotation feature requested in #220
• #235 Add the annotate_ions parameter to enable/disable the ion annotation feature (default is false)

Fixed

• Resolved issues with SAMPLESHEET_CHECK
• Fix for the peakpickerhires, mzml files generated from input raw files are now seen as input for this step as well
• PRE_QUANTIFICATION is renamed to MAP_ALIGNMENT to indicate that the alignment (and the complementing processes) of the different maps happens here
• POST_QUANTIFICATION is renamed to PROCESS_FEATURE since the feature identification and processing is done here
• Outcome of OPENMS_FEATUREFINDERIDENTIFICATION got lost during one of the previous updates, this is reintroduced
• OPENMS_TEXTEXPORTER_UNQUANTIFIED and OPENMS_TEXTEXPORTER_QUANTIFIED return only significant hits again
• #226 - nf-core template update (version 2.6)
• #230 - Issue with OPENMS_MZTABEXPORTER_QUANT
• #236 - Resolved issue with PYOPENMS_IONANNOTATOR
• Fix for an inconsistent mzml channel issue
• #241 - Fix of the HLA allele annotation in the help of the allele_sheet parameter

Dependencies

• Updated the multiQC module

Dependency	Old version	New version
MultiQC	1.11	1.12
OpenMS	2.6.0	2.8.0
OpenMS thirdparty	2.6.0	2.8.0
pyOpenMS	-	2.8
thermorawfileparser	1.3.4	1.4.0

Deprecated

• OPENMS_TEXTEXPORTER_PSMS was removed due to the outcome of the comet adapter step