modules/easypqp_convert

Convert peptide identifications (pepXML or idXML) and the matching spectra (mzML, mzXML or MGF) into EasyPQP PSM and peak pickle files for spectral library generation.

proteomicsspectral librarydiapepxmlidxmlmzml

https://github.com/nf-core/modules/[...]/modules/nf-core/easypqp/convert

Description

Convert peptide identifications (pepXML or idXML) and the matching spectra (mzML, mzXML or MGF) into EasyPQP PSM and peak pickle files for spectral library generation.

Input

name:type

description

pattern

`meta`
`:map`

Groovy Map containing sample information e.g. [ id:'sample1' ]

`id_file`
`:file`

Peptide identifications for one MS run. Either a pepXML file (*.pep.xml, e.g. interact-*.pep.xml from the Trans-Proteomic Pipeline; PSMs without PeptideProphet/iProphet probabilities are ignored) or an OpenMS idXML file (*.idXML, any score type; a q-value or PEP score is used when present). The idXML route is used by nf-core/mhcquant with Comet/Percolator results.

*.{pep.xml,pepxml,idXML}

`spectra`
`:file`

Spectra of the same MS run in mzML, mzXML or MGF (timsTOF) format. The output pickles are named after the basename of this file.

*.{mzML,mzXML,mgf}

`unimod`
`:file`

Optional UniMod XML file used to annotate modifications. EasyPQP’s bundled UniMod is used when omitted.

*.xml

Output

name:type

description

pattern

`psmpkl`

`meta`
`:map`

Groovy Map containing sample information e.g. [ id:'sample1' ]

`*.psmpkl`
`:file`

Pickled pandas DataFrame with the parsed PSMs. Named after the spectra file basename, which easypqp library uses to pair PSMs and peaks.

*.psmpkl

`peakpkl`

`meta`
`:map`

Groovy Map containing sample information e.g. [ id:'sample1' ]

`*.peakpkl`
`:file`

Pickled pandas DataFrame with the annotated fragment ion peaks. Named after the spectra file basename, which easypqp library uses to pair PSMs and peaks.

*.peakpkl

`versions_easypqp`

`${task.process}`
`:string`

The name of the process

`easypqp`
`:string`

The name of the tool

`easypqp --version | sed 's/.*version //'`
`:eval`

The expression to obtain the version of the tool

Topics

name:type

description

pattern

`versions`

`${task.process}`
`:string`

The name of the process

`easypqp`
`:string`

The name of the tool

`easypqp --version | sed 's/.*version //'`
`:eval`

The expression to obtain the version of the tool

Tools

easypqp
BSD-3-Clause

Python package to generate spectral libraries for data-independent acquisition (DIA) proteomics from DDA search results.

github.com/grosenberger/easypqp

modules/easypqp_convert

Description

Input

`meta`
`:map`

`id_file`
`:file`

`spectra`
`:file`

`unimod`
`:file`

Output

`psmpkl`

`meta`
`:map`

`*.psmpkl`
`:file`

`peakpkl`

`meta`
`:map`

`*.peakpkl`
`:file`

`versions_easypqp`

`${task.process}`
`:string`

`easypqp`
`:string`

`easypqp --version | sed 's/.*version //'`
`:eval`

Topics

`versions`

`${task.process}`
`:string`

`easypqp`
`:string`

`easypqp --version | sed 's/.*version //'`
`:eval`

Tools

easypqp
BSD-3-Clause

maintainer

get in touch

modules/easypqp_convert

Description

Input

meta :map

id_file :file

spectra :file

unimod :file

Output

psmpkl

meta :map

*.psmpkl :file

peakpkl

meta :map

*.peakpkl :file

versions_easypqp

${task.process} :string

easypqp :string

easypqp --version | sed 's/.*version //' :eval

Topics

versions

${task.process} :string

easypqp :string

easypqp --version | sed 's/.*version //' :eval

Tools

easypqpBSD-3-Clause

maintainer

get in touch

`meta`
`:map`

`id_file`
`:file`

`spectra`
`:file`

`unimod`
`:file`

`psmpkl`

`meta`
`:map`

`*.psmpkl`
`:file`

`peakpkl`

`meta`
`:map`

`*.peakpkl`
`:file`

`versions_easypqp`

`${task.process}`
`:string`

`easypqp`
`:string`

`easypqp --version | sed 's/.*version //'`
`:eval`

`versions`

`${task.process}`
`:string`

`easypqp`
`:string`

`easypqp --version | sed 's/.*version //'`
`:eval`

easypqp
BSD-3-Clause