modules/comet

Comet is an open source tandem mass spectrometry (MS/MS) sequence database search tool

spectrum identificationsearch engineproteomicsfastamzml

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

Description

Comet is an open source tandem mass spectrometry (MS/MS) sequence database search tool

Input

name:type

description

pattern

`meta`
`:map`

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

`mzml`
`:file`

File containing mass spectra in mzML format

*.{mzML}

`fasta`
`:file`

Protein sequence database containing targets and decoys

*.{fasta}

`comet_params`
`:file`

Comet params file containing the search parameters

*.{comet.params}

Output

name:type

description

pattern

`params`

`meta`
`:map`

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

`${prefix}*.comet.params`
`:file`

The parameter file used for the Comet search (for reproducibility)

*.comet.params

`sqt`

`meta`
`:map`

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

`${prefix}*.sqt`
`:file`

Search results in SQT format

*.sqt

`txt`

`meta`
`:map`

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

`${prefix}*.txt`
`:file`

Search results in simple TXT format

*.txt

`pepxml`

`meta`
`:map`

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

`${prefix}*.pep.xml`
`:file`

Search results in pepXML format

*.pep.xml

`mzid`

`meta`
`:map`

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

`${prefix}*.mzid`
`:file`

Search results in mzIdentML format

*.mzid

`pin`

`meta`
`:map`

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

`${prefix}*.pin`
`:file`

Search results in Percolator input format (pin)

*.pin

`versions_comet`

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

The name of the process

`comet`
`:string`

The name of the tool

`comet 2>&1 | head -2 | tail -1 | sed 's;."$.$.*";\1;g'`
`:eval`

The expression to obtain the version of the tool

Topics

name:type

description

pattern

`versions`

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

The name of the process

`comet`
`:string`

The name of the tool

`comet 2>&1 | head -2 | tail -1 | sed 's;."$.$.*";\1;g'`
`:eval`

The expression to obtain the version of the tool

Tools

comet
Apache License 2.0

Comet is an open source tandem mass spectrometry (MS/MS) sequence database search tool.

uwpr.github.io/Comet https://github.com/UWPR/Comet 10.1002/pmic.201200439

modules/comet

Description

Input

`meta`
`:map`

`mzml`
`:file`

`fasta`
`:file`

`comet_params`
`:file`

Output

`params`

`meta`
`:map`

`${prefix}*.comet.params`
`:file`

`sqt`

`meta`
`:map`

`${prefix}*.sqt`
`:file`

`txt`

`meta`
`:map`

`${prefix}*.txt`
`:file`

`pepxml`

`meta`
`:map`

`${prefix}*.pep.xml`
`:file`

`mzid`

`meta`
`:map`

`${prefix}*.mzid`
`:file`

`pin`

`meta`
`:map`

`${prefix}*.pin`
`:file`

`versions_comet`

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

`comet`
`:string`

`comet 2>&1 | head -2 | tail -1 | sed 's;."\(.\).*";\1;g'`
`:eval`

Topics

`versions`

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

`comet`
`:string`

`comet 2>&1 | head -2 | tail -1 | sed 's;."\(.\).*";\1;g'`
`:eval`

Tools

comet
Apache License 2.0

included in

maintainer

get in touch

modules/comet

Description

Input

meta:map

mzml:file

fasta:file

comet_params:file

Output

params

meta:map

${prefix}*.comet.params:file

sqt

meta:map

${prefix}*.sqt:file

txt

meta:map

${prefix}*.txt:file

pepxml

meta:map

${prefix}*.pep.xml:file

mzid

meta:map

${prefix}*.mzid:file

pin

meta:map

${prefix}*.pin:file

versions_comet

${task.process}:string

comet:string

comet 2>&1 | head -2 | tail -1 | sed 's;.*"\(.*\).*";\1;g':eval

Topics

versions

${task.process}:string

comet:string

comet 2>&1 | head -2 | tail -1 | sed 's;.*"\(.*\).*";\1;g':eval

Tools

comet Apache License 2.0

included in

maintainer

get in touch

`meta`
`:map`

`mzml`
`:file`

`fasta`
`:file`

`comet_params`
`:file`

`params`

`meta`
`:map`

`${prefix}*.comet.params`
`:file`

`sqt`

`meta`
`:map`

`${prefix}*.sqt`
`:file`

`txt`

`meta`
`:map`

`${prefix}*.txt`
`:file`

`pepxml`

`meta`
`:map`

`${prefix}*.pep.xml`
`:file`

`mzid`

`meta`
`:map`

`${prefix}*.mzid`
`:file`

`pin`

`meta`
`:map`

`${prefix}*.pin`
`:file`

`versions_comet`

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

`comet`
`:string`

`comet 2>&1 | head -2 | tail -1 | sed 's;."\(.\).*";\1;g'`
`:eval`

`versions`

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

`comet`
`:string`

`comet 2>&1 | head -2 | tail -1 | sed 's;."\(.\).*";\1;g'`
`:eval`

comet
Apache License 2.0