diff --git a/.devcontainer/devcontainer.json b/.devcontainer/devcontainer.json index 4ecfbfe3..4a9bc5c7 100644 --- a/.devcontainer/devcontainer.json +++ b/.devcontainer/devcontainer.json @@ -18,11 +18,11 @@ "python.linting.flake8Path": "/opt/conda/bin/flake8", "python.linting.pycodestylePath": "/opt/conda/bin/pycodestyle", "python.linting.pydocstylePath": "/opt/conda/bin/pydocstyle", - "python.linting.pylintPath": "/opt/conda/bin/pylint" + "python.linting.pylintPath": "/opt/conda/bin/pylint", }, // Add the IDs of extensions you want installed when the container is created. - "extensions": ["ms-python.python", "ms-python.vscode-pylance", "nf-core.nf-core-extensionpack"] - } - } + "extensions": ["ms-python.python", "ms-python.vscode-pylance", "nf-core.nf-core-extensionpack"], + }, + }, } diff --git a/docs/images/id_pipeline.png b/docs/images/id_pipeline.png index b4c9a7f4..7ac1c07b 100644 Binary files a/docs/images/id_pipeline.png and b/docs/images/id_pipeline.png differ diff --git a/docs/images/id_pipeline.svg b/docs/images/id_pipeline.svg index b2939b96..7f226118 100644 --- a/docs/images/id_pipeline.svg +++ b/docs/images/id_pipeline.svg @@ -1,1420 +1,4 @@ - - - - - - - - - - - - - - - - - - ID Comet - - - - ID Comet - - - - - - - - - - - mix - - - - mix - - - - - - - - - - - if multi-engine - - - - - if multi-engine - - - - - - - - - - - if single-engine - - - - - if single-engine - - - - - - - - - merge - - - - merge - - - - - - - - - - - Percolator - - - - Percolator - - - - - - - - - - - ID MSGF - - - - ID MSGF - - - - - - - - - - - FDR - - - - FDR - - - - - - - - - - - Distribution-based PEP - - - - Distribution-basedPEP - - - - - - - - - - - ConsensusID - - - - ConsensusID - - - - - - - - - Luciphor - - - - Luciphor - - - - - - - - - - - combined FDR - - - - combined FDR - - - - - - - - - - - Switch to q-value/FDR - - - - Switch toq-value/FDR - - - - - - - - - - - IDFilter - - - - IDFilter - - - - - - - - - - - Raw file conversion/Indexing - - - - Raw fileconversion/... - - - - - - - - - - - - - - - - - - if !multi-engine - - - - - if !multi-engine - - - - - - - - - - - - - if localize - - - - - - if localize - - - - - - - - - - if necessary - - - - - if necessary - - - - - - - - - Decoy generation - - - - Decoy generation - - - - - - - - - - if requested - - - - - if requested - - - - - - - - - Database - - - - Database - - - - - - - - - - Input - - - - Input - - - - - - - - - + - - - - + - - - - Design - - - - - - - - - Spectra - - - - - Spectra - - - - - - - - - - or - - - - or - - - - - - - - - - Viewer does not support full SVG 1.1 - - - + + + +
ID Comet
ID Comet
mix
mix
if multi-engine
if multi-engine
if single-engine
if single-engine
merge
merge
Percolator
Percolator
ID MSGF
ID MSGF
FDR
FDR
Distribution-based PEP
Distribution-based P...
ConsensusID
ConsensusID
Luciphor
Luciphor
combined FDR
combined FDR
Quantification +
Inference and experiment-wide FDR filter
Quantification +...
Switch to q-value/FDR
Switch to q-value/FDR
IDFilter
IDFilter
MSstats
MSstats
Raw file conversion/Indexing
Raw file conversion/...
if !multi-engine
if !multi-engine
if localize
if localize
if necessary
if necessary
Decoy generation
Decoy generation
if requested
if requested
Database
Database
Input
Input
+
+Design
Spectra
Spectra
or
or
or
or
ID SAGE
ID SAGEText is not SVG - cannot display \ No newline at end of file diff --git a/docs/images/quantms.png b/docs/images/quantms.png index 2a0fc055..b3498dbd 100644 Binary files a/docs/images/quantms.png and b/docs/images/quantms.png differ diff --git a/docs/images/quantms.svg b/docs/images/quantms.svg index 2d4066c1..6cf881d3 100644 --- a/docs/images/quantms.svg +++ b/docs/images/quantms.svg @@ -4,7 +4,7 @@ rawMS-GF+, Comet, Percolator, ConsesusIDMS-GF+, SAGE, CometPercolator, ConsesusID + viewBox="0 0 1283 603" style="enable-background:new 0 0 1283 603;" xml:space="preserve"> - + + + - - - + + + - Search engines(at least one) - - - - - - - - - - - - - - Rescoring(exactly one) - - - - - - - - - Search engines + (at least one) + + + - + + + - - - + + + + + + - ThermoRawFileParser - - - - - - - - + Rescoring + (exactly one) + + + + + + + + + + + + + - Comet - - + ThermoRaw + FileParser + + + + + + + - MSGF+ - - - - - - + Comet + + + + + + - ConsensusID + ConsensusID - - - + + + - Distributionfitting - - - - - - + Distribution + fitting + + + + + + - FDRcontrol + FDR + control - + - IsobaricAnalyzer - - - - - - - - - + Isobaric + Analyzer + + + + + + + + + - Mod.localization + Mod. + localization - + - Percolator + FDR - - - - - - - - + Percolator + FDR + + + + + + + + - Legend + Legend - - - + + + - DDA-LFQ + DDA-LFQ - DDA-ISO + DDA-ISO - DIA-LFQ + DIA-LFQ - Parallel step + Parallel step - - - + + + - IDMapper + IDMapper - + - Proteininference + Protein + inference - - - + + + - nf-core/quantms v1.1Example analysis pathways + nf-core/quantms v1.2 + Example analysis pathways - - mzMLindexing + mzML + indexing - - + + - DIA-NN insilico lib. predict + DIA-NN + insilico lib. predict - - + - DIA-NNpreanalysis + preanalysis - - DIA-NNempirical lib. gen. + DIA-NN + empirical lib. gen. - + - Adddecoys - - - - - - + Add + decoys + + + + + + - ProteomicsLFQ + Proteomics + LFQ - + - mzTab + mzTab - + - ProteinQuantifier + Protein + Quantifier - - + + - Triqler + Triqler - - + + - MSstats + MSstats - + - DIA-NNsummary + DIA-NN + summary - - + + - DIA-NNindividual final analysis + DIA-NN + individual final analysis - + + + MSGF+ + + + + + + - - - - - -Job n -In Parallel - -Job 1 -...... + + + + + +Job n +In Parallel + +Job 1 +...... - - - - - - - - - - mzML - + + + + + + + + + + + + mzML + + + - - - - - - - - - - raw - + + + + + + + + + + + + raw + + + - - - - - - - - - - fasta - + + + + + + + + + + + + fasta + + + - - - - - - - - - - tsv - + + + + + + + + + + + + tsv + + + - - - - - - - - - - mzTab - + + + + + + + + + + + + mzTab + + + - - - - - - - - - - tsv - + + + + + + + + + + + + tsv + + + - - - -Job 1 -...... -Job n - In Parallel - + + + +Job 1 +...... +Job n + In Parallel + + + + + + + + + + + + + + + + + Sage + + + + + + + + + + + + +speclib +skip diff --git a/docs/images/quantms_metro.png b/docs/images/quantms_metro.png index f1f5d155..90685839 100644 Binary files a/docs/images/quantms_metro.png and b/docs/images/quantms_metro.png differ