nf-core/mhcquant
Identify and quantify MHC eluted peptides from mass spectrometry raw data
Version history
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
andOPENMS_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 -
#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 toMAP_ALIGNMENT
to indicate that the alignment (and the complementing processes) of the different maps happens here -
POST_QUANTIFICATION
is renamed toPROCESS_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
andOPENMS_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
Added
-
#206 Updated the workflow picture
-
Adjustments of the
PRE_QUANTIFICATION
subworkflow:OPENMS_FALSEDISCOVERYRATE
,OPENMS_IDFILTER_FOR_ALIGNMENT
, andOPENMS_TEXTEXPORTER_PSMS
-
Included
OPENMS_TEXTEXPORTER_UNQUANTIFIED
to write a combined FDR filtered output file for unquantified data -
Included
pipeline summary
and increment thedocumentation
paragraph -
#195 Updated parameter documentation
-
#189 Added backslashes in Quick Start in README
-
#188 Added reference links to README
Fixed
-
Typo in previous release date
-
#208 - nf-core template update (version 2.3.2)
-
#199 Fixes some typos and stuff in the output documentation
-
#192 Fixed samplesheet format in usage.md
-
#184 Fix parsing for VEP annotated VCF files
Dependencies
| Dependency | Old version | New version |
| ---------- | ----------- | ----------- |
| MultiQC
| 1.11 | 1.12 |
Deprecated
- #191 Removed the table of contents from usage.md
Added
-
Included the newest nf-core template (version 2.2)
-
Adjustment of the README, including all contributors
-
Inclusion of the PSMs files (tsv format) per replicates in
results/PSMs
-
Include check-in WorkflowMhcquant, to determine if the allele and vcf sheet has been provided under specific circumstances
Fixed
-
Changed parameters in the nextflow_schema.json to be in coherence with the nextflow.config
-
Error that was raised in generate_proteins_from_vcf
-
Problems that were detected in predict_possible_class1_neoepitopes and predict_possible_class2_neoepitopes
-
Error that occurred in mhcnuggets_predictneoepitopesclass2 (faulty container set up)
Dependencies
| Dependency | Old version | New version |
| --------------------- | ----------- | ----------- |
| fred2
| 2.0.6 | 2.0.7 |
Added
-
Inclusion of
assets/schema_input.json
-
Added the MultiQC again to report the versions
-
MHCquant parameters are now directly assigned to the argument of the process
Fixed
-
Fixed typos
-
Change the version annotation
-
Renaming of various processes (functionality remained the same)
-
#165 - Raise memory requirements of
FeatureFinderIdentification
step -
#176 - Pipeline crashes when setting the
--skip_quantification
flag
Dependencies
| Dependency | Old version | New version |
| --------------------- | ----------- | ----------- |
| openms
| 2.5.0 | 2.6.0 |
| openms-thirdparty
| 2.5.0 | 2.6.0 |
| thermorawfileparser
| 1.2.3 | 1.3.4 |
Enhancements
-
DSL1 to DSL2 conversion
-
Different processes based on a unique step in the pipeline
-
Inclusion of one sub-workflow: refine FDR on a predicted subset
-
The process: openms_cometadapter includes commented lines (which could be used as a reference for future module development)
-
MHCquant pipeline runs from workflows/mhcquant.nf instead of the main
-
Template update to nf-core/tools 2.1
Added
-
Template update to 1.10.2
-
Added parameter json schema
-
Added full size AWS test profile
-
Included new parameters for Neutral loss and precursor ion inclusion
Fixed
- Changed trigger for AWS tests
Bugfix release:
-
optimal cluster configuration
-
fixed duplication of ids/mixing of channels
-
raise OpenMS version to 2.5
-
adapt workflow accordingly with new options
-
integrate sample, allele and vcf sheets instead of file dirs
-
remove specifying input as file directorys eg. "data/*.mzML"
-
branched mzML/raw input
-
introduce param to skip quantification
Template Update
Raw File Reading
Quantification FDR
Retention Time Prediction
MHCFlurry, MHCNugget, Percolator version increase
v1.2.6 nf-core/mhcquant "Golden Eagle" - 2019/03/05
Fixed
linear retention time alignment
refine_fdr README
v1.2.5 nf-core/mhcquant "Golden Eagle" - 2019/03/04
Fixed
sort channels by basename
fixed psm-level-fdrs
v1.2.4 nf-core/mhcquant "Golden Eagle" - 2019/02/06
Fixed
fixed refine_fdr_on_predicted_subset float error
v1.2.3 nf-core/mhcquant "Golden Eagle" - 2019/02/02
Fixed
filter out uncommon aminoacids U,X,B,J,Z
v1.2.2 nf-core/mhcquant "Golden Eagle" - 2019/01/28
Fixed
default params to false
change on centroidisation parameter
small changes on docu
v1.2.1 nf-core/mhcquant "Golden Eagle" - 2019/01/24
Fixed
process identical names bug
v1.2.0 nf-core/mhcquant "Golden Eagle" - 2019/01/19
Added
-
Subset FDR refinement option
-
Fred2 dependency
-
vcf parser and translation to proteins
Updates since 1.0.0:
* mhcflurry conda package added
* mhcflurry predictions added
* peak picking preprocessing added
* minor changes in default parameters
* few arguments added eg. min_peptide_len, max_peptide_len
This is the initial pipeline release of nf-core/mhcquant "Naked Chicken"!
nfcore/mhcquant is a bioinformatics analysis pipeline used for quantitative processing of data dependant (DDA) peptidomics data.
It was specifically designed to analyse immunopeptidomics data, which deals with the analysis of affinity purified, unspecifically cleaved peptides that have recently been discussed intensively in the context of cancer vaccines. (https://www.nature.com/articles/ncomms13404)
The workflow is based on the OpenMS C++ framework for computational mass spectrometry. RAW files (mzML) serve as inputs and a database search (Comet) is performed based on a given input protein database. FDR rescoring is applied using Percolator 3.0 based on a competitive target-decoy approach (reversed decoys). For label free quantification all input files undergo identification based retention time alignment (MapAlignerIdentification), and targeted feature extraction matching ids between runs (FeatureFinderIdentification).
The pipeline is built using Nextflow, a workflow tool to run tasks across multiple compute infrastructures in a very portable manner. It comes with docker / singularity containers making installation trivial and results highly reproducible.