Nextflow Registry | nf-core/percolator@0.0.0-e2d3f0d

nf-core/percolator @ 0.0.0-e2d3f0d

Rescore peptide-spectrum matches and estimate false discovery rates using the Percolator semi-supervised learning algorithm.

Latest version: 0.0.0-e2d3f0d

Total downloads: 1

Source: nf-core/modules

Authors: @julianu

Maintainers: @julianu

Rescore peptide-spectrum matches and estimate false discovery rates using the Percolator semi-supervised learning algorithm.

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

include { PERCOLATOR } from 'nf-core/percolator'

MIT License

Process

`Name`	`PERCOLATOR`

Input 1 channel

#1 tuple

`meta` map	Groovy Map containing sample information. e.g. `[ id:'sample1' ]`
`peptide_identification` file	peptide identifications as PIN (Percolator input) file `*.pin`

Output 11 channels

#1 weights tuple

`meta` map	Groovy Map containing sample information. e.g. `[ id:'sample1' ]`
`${prefix}.weights.tsv` file	TSV file containing the final feature weights `*.weights.tsv`

#2 pout_xml tuple

`meta` map	Groovy Map containing sample information. e.g. `[ id:'sample1' ]`
`${prefix}.pout.xml` file	Percolator output in XML format containing all PSM-level results `*.pout.xml`

#3 decoy_psms tuple

`meta` map	Groovy Map containing sample information. e.g. `[ id:'sample1' ]`
`${prefix}.psm.decoy.pout` file	Decoy PSM-level results in tab separated format (pout) `*.psm.decoy.pout`

#4 pout_pepxml tuple

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

#5 target_psms tuple

`meta` map	Groovy Map containing sample information. e.g. `[ id:'sample1' ]`
`${prefix}.psm.target.pout` file	Target PSM-level results in tab separated format (pout) `*.psm.target.pout`

#6 features_pin tuple

`meta` map	Groovy Map containing sample information. e.g. `[ id:'sample1' ]`
`${prefix}.features.pin` file	Tab-separated file with rescored features (PIN format) `*.features.pin`

#7 decoy_peptides tuple

`meta` map	Groovy Map containing sample information. e.g. `[ id:'sample1' ]`
`${prefix}.pep.decoy.pout` file	Decoy peptide-level results in tab separated format (pout) `*.pep.decoy.pout`

#8 decoy_proteins tuple

`meta` map	Groovy Map containing sample information. e.g. `[ id:'sample1' ]`
`${prefix}.protein.decoy.pout` file	Decoy protein-level results in tab separated format (pout) `*.protein.decoy.pout`

#9 target_peptides tuple

`meta` map	Groovy Map containing sample information. e.g. `[ id:'sample1' ]`
`${prefix}.pep.target.pout` file	Target peptide-level results in tab separated format (pout) `*.pep.target.pout`

#10 target_proteins tuple

`meta` map	Groovy Map containing sample information. e.g. `[ id:'sample1' ]`
`${prefix}.protein.target.pout` file	Target protein-level results in tab separated format (pout) `*.protein.target.pout`

#11 versions_percolator tuple


`${task.process}` string	The name of the process