Nextflow Registry | nf-core/comet@0.0.0-0c7146d

nf-core/comet @ 0.0.0-0c7146d

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

spectrum identification search engine proteomics fasta mzml

Latest version: 0.0.0-0c7146d

Total downloads: 1

Source: nf-core/modules

Authors: @julianu

Maintainers: @julianu

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

Add the following snippet to your workflow script to include this module.

include { COMET } from 'nf-core/comet'

MIT License

Process

`Name`	`COMET`

Input 1 channel

#1 tuple

`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 7 channels

#1 pin tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'sample1' ]`
`${prefix}*.pin` file	Search results in Percolator input format (pin) `*.pin`

#2 sqt tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'sample1' ]`
`${prefix}*.sqt` file	Search results in SQT format `*.sqt`

#3 txt tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'sample1' ]`
`${prefix}*.txt` file	Search results in simple TXT format `*.txt`

#4 mzid tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'sample1' ]`
`${prefix}*.mzid` file	Search results in mzIdentML format `*.mzid`

#5 params tuple

`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`

#6 pepxml tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'sample1' ]`
`${prefix}*.pep.xml` file	Search results in pepXML format `*.pep.xml`

#7 versions_comet tuple

`${task.process}` string	The name of the process
`comet` string	The name of the tool
`comet 2>&1 \| head -2 \| tail -1 \| sed 's;."$.$.*";\1;g'` eval	The expression to obtain the version of the tool

Tool	Description	Homepage
comet	Comet is an open source tandem mass spectrometry (MS/MS) sequence database search tool.	https://uwpr.github.io/Comet/

Version	0.0.0-0c7146d
Commit ID	135d883a43b1a2324b4112cd270cf22e20835533
Release Date	08 Apr 2026 18:32:16 (UTC)
Download URL	https://registry-stage.nextflow.io/api/v1/modules/nf-core%2Fcomet/0.0.0-0c7146d/download
OCI Store URL	https://public.cr.stage-seqera.io/v2/nextflow/plugin-stage/modules/nf-core/comet/blobs/sha256:da24ecaf604a4f78a25407aab0f61b329d360723b983d24cd54b395d51e9296d
Size	6.2 KB