Nextflow Registry | nf-core/sageproteomics/sage@0.0.0-0c7146d

nf-core/sageproteomics/sage @ 0.0.0-0c7146d

sage is a search software for proteomics data

proteomics sage mass spectrometry

Latest version: 0.0.0-0c7146d

Total downloads: 1

Source: nf-core/modules

Authors: @dgemperline-lilly

Maintainers: @dgemperline-lilly

sage is a search software for proteomics data

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

include { SAGEPROTEOMICS_SAGE } from 'nf-core/sageproteomics/sage'

MIT License

Process

`Name`	`SAGEPROTEOMICS_SAGE`

Input 3 channels

#1 tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'sample1']`
`*.mzML` file	mzML files for proteomics search `*.mzML`

#2 tuple

`meta2` map	Groovy Map containing information about fasta_proteome e.g. `[ id:'sample1']`
`fasta_proteome` file	proteome database in fasta format `*.{fasta,fasta.gz}`

#3 tuple

`meta3` map	Groovy Map containing information about base_config e.g. `[ id:'sample1']`
`base_config` file	sage configuration json `*.json`

Output 6 channels

#1 lfq_tsv tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'sample1']`
`lfq.tsv` file	label free quantification `lfq.tsv`

#2 tmt_tsv tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'sample1']`
`tmt.tsv` file	tandem mass tag quantification `tmt.tsv`

#3 versions

`versions.yml` file	File containing software versions `versions.yml`

#4 results_pin tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'sample1']`
`results.sage.pin` file	pin format output results `results.sage.pin`

#5 results_tsv tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'sample1']`
`results.sage.tsv` file	tsv output results `results.sage.tsv`

#6 results_json tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'sample1']`
`results.json` file	json output results `results.json`

Tool	Description	Homepage
sageproteomics	Proteomics searching so fast it feels like magic.	https://lazear.github.io/sage/

Version	0.0.0-0c7146d
Commit ID	135d883a43b1a2324b4112cd270cf22e20835533
Release Date	08 Apr 2026 19:09:10 (UTC)
Download URL	https://registry-stage.nextflow.io/api/v1/modules/nf-core%2Fsageproteomics%2Fsage/0.0.0-0c7146d/download
OCI Store URL	https://public.cr.stage-seqera.io/v2/nextflow/plugin-stage/modules/nf-core/sageproteomics/sage/blobs/sha256:1a24f1ccac35c8d71894cc01914560dfeef644a2a0748f33ccb6c7019ae16b70
Size	2.7 KB
Checksum	sha256:1a24f1ccac35c8d71894cc01914560dfeef644a2a0748f33ccb6c7019ae16b70
Downloads	1

Version	Date	Status	Downloads	Size	Diff