Nextflow Registry | nf-core/openmsthirdparty/cometadapter@0.0.0-0c7146d

nf-core/openmsthirdparty/cometadapter @ 0.0.0-0c7146d

Annotates MS/MS spectra using Comet.

search engine fasta mzml openms proteomics

Latest version: 0.0.0-0c7146d

Total downloads: 1

Source: nf-core/modules

Authors: @jonasscheid

Maintainers: @jonasscheid

Annotates MS/MS spectra using Comet.

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

include { OPENMSTHIRDPARTY_COMETADAPTER } from 'nf-core/openmsthirdparty/cometadapter'

MIT License

Process

`Name`	`OPENMSTHIRDPARTY_COMETADAPTER`

Input 1 channel

#1 tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'sample1', single_end:false ]`
`mzml` file	File containing mass spectra in mzML format `*.{mzML}`
`fasta` file	Protein sequence database containing targets and decoys `*.{fasta}`

Output 4 channels

#1 pin tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'sample1', single_end:false ]`
`*.tsv` file	TSV file tailored as Percolator input (pin) file `*.{tsv}`

#2 idxml tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'sample1', single_end:false ]`
`*.idXML` file	File containing target and decoy hits in idXML format `*.{idXML}`

#3 versions_comet tuple

`${task.process}` string	The name of the process
`Comet` string	The name of the tool
`comet 2>&1 \| sed -n 's/.Comet version " $.$"./\1/p'` eval	The expression to obtain the version of the tool

#4 versions_cometadapter tuple

`${task.process}` string	The name of the process
`CometAdapter` string	The name of the tool
`CometAdapter --help 2>&1 \| sed -nE 's/^Version: ([0-9.]+).*/\1/p'` eval	The expression to obtain the version of the tool

Tool	Description	Homepage
openms	OpenMS is an open-source software C++ library for LC-MS data management and analyses	https://openms.de
CometAdapter	Annotates MS/MS spectra using Comet.	https://openms.de
Comet	Comet is an open source tandem mass spectrometry (MS/MS) sequence database search tool.	http://comet-ms.sourceforge.net/

Version	0.0.0-0c7146d
Commit ID	135d883a43b1a2324b4112cd270cf22e20835533
Release Date	08 Apr 2026 19:00:01 (UTC)
Download URL	https://registry-stage.nextflow.io/api/v1/modules/nf-core%2Fopenmsthirdparty%2Fcometadapter/0.0.0-0c7146d/download
OCI Store URL	https://public.cr.stage-seqera.io/v2/nextflow/plugin-stage/modules/nf-core/openmsthirdparty/cometadapter/blobs/sha256:42dbb2a0e9d85471fa97f304ebb9fc240af2f6726d278c2b8c01ebdf94d0b56b
Size	3.7 KB
Checksum	sha256:42dbb2a0e9d85471fa97f304ebb9fc240af2f6726d278c2b8c01ebdf94d0b56b
Downloads	1

Version	Date	Status	Downloads	Size	Diff
0.0.0-0c7146d	08 Apr 2026 19:00:01 (UTC)		1	3.7 KB	-