Nextflow Registry | nf-core/proteus/readproteingroups@0.0.0-c4ed7fd

nf-core/proteus/readproteingroups @ 0.0.0-c4ed7fd

reads a maxQuant proteinGroups file with Proteus

proteomics proteus readproteingroups

Latest version: 0.0.0-c4ed7fd

Total downloads: 9

Source: nf-core/modules

Authors: @WackerO

Maintainers: @WackerO

reads a maxQuant proteinGroups file with Proteus

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

include { PROTEUS_READPROTEINGROUPS } from 'nf-core/proteus/readproteingroups'

MIT License

Process

`Name`	`PROTEUS_READPROTEINGROUPS`

Input 1 channel

#1 tuple

`meta` map	Groovy Map containing contrast information, e.g. [ variable:'treatment', reference:'treated', control:'saline', blocking:'' ]
`samplesheet` file	CSV or TSV format sample sheet with sample metadata; check here for specifications: https://rdrr.io/github/bartongroup/Proteus/man/readProteinGroups.html
`intensities` file	proteinGroups TXT file with protein intensities information from maxQuant; check here for specifications: https://rdrr.io/github/bartongroup/Proteus/man/readProteinGroups.html

Output 10 channels

#1 raw_tab tuple

`meta` file	PNG file; dendrogram of the normalized samples hierarchically clustered by their intensities
`*raw_proteingroups_tab.tsv` file	TSV-format intensities table from Proteus, contains raw protein intensities

#2 norm_tab tuple

`meta` file	PNG file; dendrogram of the normalized samples hierarchically clustered by their intensities
`*normalized_proteingroups_tab.tsv` file	TSV-format intensities table from Proteus, contains normalized protein intensities

#3 versions

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

#4 raw_rdata tuple

`meta` file	PNG file; dendrogram of the normalized samples hierarchically clustered by their intensities
`*raw_proteingroups.rds` file	RDS file of a proteinGroups object from Proteus, contains raw protein intensities and additional info

#5 norm_rdata tuple

`meta` file	PNG file; dendrogram of the normalized samples hierarchically clustered by their intensities
`*normalized_proteingroups.rds` file	RDS file of a proteinGroups object from Proteus, contains normalized protein intensities and additional info

#6 dendro_plot tuple

`meta` file	PNG file; dendrogram of the normalized samples hierarchically clustered by their intensities
`*dendrogram.png` file	PNG file; dendrogram of the normalized samples hierarchically clustered by their intensities

#7 session_info tuple

`meta` file	PNG file; dendrogram of the normalized samples hierarchically clustered by their intensities
`*R_sessionInfo.log` file	LOG file of the R sessionInfo from the module run

#8 mean_var_plot tuple

`meta` file	PNG file; dendrogram of the normalized samples hierarchically clustered by their intensities
`*mean_variance_relationship.png` file	PNG file; plot of the log-intensity variance vs log-intensity mean of each condition in the normalized samples

#9 raw_dist_plot tuple

`meta` file	PNG file; dendrogram of the normalized samples hierarchically clustered by their intensities
`*raw_distributions.png` file	PNG file; plot of the intensity/ratio distributions of the raw samples

#10 norm_dist_plot tuple

`meta` file	PNG file; dendrogram of the normalized samples hierarchically clustered by their intensities
`*normalized_distributions.png` file	PNG file; plot of the intensity/ratio distributions of the normalized samples

Tool	Description	Homepage
proteus	R package for analysing proteomics data	https://github.com/bartongroup/Proteus

Version	0.0.0-c4ed7fd
Commit ID	c4ed7fdd281d290c622c5d93fa173effc0217fdb