Nextflow Registry | nf-core/gprofiler2/gost@0.0.0-6c4ed3a

nf-core/gprofiler2/gost @ 0.0.0-6c4ed3a

runs a functional enrichment analysis with gprofiler2

gene set analysis enrichment gprofiler2 gost gene set

Latest version: 0.0.0-6c4ed3a

Total downloads: 7

Source: nf-core/modules

Authors: @WackerO

runs a functional enrichment analysis with gprofiler2

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

include { GPROFILER2_GOST } from 'nf-core/gprofiler2/gost'

MIT License

Process

`Name`	`GPROFILER2_GOST`

Input 3 channels

#1 tuple

`meta` map	Groovy Map containing contrast information, e.g. [ variable:'treatment', reference:'treated', control:'saline', blocking:'' ]
`de_file` file	CSV or TSV-format tabular file with differential analysis outputs `*.{csv,tsv}`

#2 tuple

`meta2` map	Groovy map
`gmt_file` file	Path to a GMT file downloaded from g:profiler that should be queried instead of the online databases `*.gmt`

#3 tuple

`meta3` map	Groovy map
`background_file` file	Path to a CSV/TSV/TXT file listing gene IDs that should be used as the background (will override count_file). This can be an expression matrix (see also background_column parameter); if so, will only consider those genes with an expression value > 0 in at least one sample. Alternatively, this can be a TXT file containing only a list of gene IDs. `*.{csv,tsv,txt}`

Output 9 channels

#1 rds tuple

`meta` map	Groovy Map containing contrast information, e.g. [ variable:'treatment', reference:'treated', control:'saline', blocking:'' ]
`*.gprofiler2.gost_results.rds` file	RDS file; R object containing the results of the gost query `gprofiler2.gost_results.rds`

#2 plot_png tuple

`meta` map	Groovy Map containing contrast information, e.g. [ variable:'treatment', reference:'treated', control:'saline', blocking:'' ]
`*.gprofiler2.gostplot.png` file	PNG file; Manhattan plot of all enriched pathways `gprofiler2.gostplot.png`

#3 sub_plot tuple

`meta` map	Groovy Map containing contrast information, e.g. [ variable:'treatment', reference:'treated', control:'saline', blocking:'' ]
`.gprofiler2..sub_enriched_pathways.png` file	PNG file; bar plot showing the fraction of genes that were found enriched in each pathway `gprofiler2.sub_enriched_pathways.png`

#4 versions

`versions.yml` file	YAML file containing versions of tools used in the module `versions.yml`

#5 plot_html tuple

`meta` map	Groovy Map containing contrast information, e.g. [ variable:'treatment', reference:'treated', control:'saline', blocking:'' ]
`*.gprofiler2.gostplot.html` file	HTML file; interactive Manhattan plot of all enriched pathways `gprofiler2.gostplot.html`

#6 all_enrich tuple

`meta` map	Groovy Map containing contrast information, e.g. [ variable:'treatment', reference:'treated', control:'saline', blocking:'' ]
`*.gprofiler2.all_enriched_pathways.tsv` file	TSV file; table listing all enriched pathways that were found. This table will always be created (empty if no enrichment was found), the other output files are only created if enriched pathways were found `gprofiler2.all_enriched_pathways.tsv`

#7 sub_enrich tuple

`meta` map	Groovy Map containing contrast information, e.g. [ variable:'treatment', reference:'treated', control:'saline', blocking:'' ]
`.gprofiler2..sub_enriched_pathways.tsv` file	TSV file; table listing enriched pathways that were found from one particular source `gprofiler2.sub_enriched_pathways.tsv`

#8 filtered_gmt tuple

`meta` map	Groovy Map containing contrast information, e.g. [ variable:'treatment', reference:'treated', control:'saline', blocking:'' ]
`*ENSG_filtered.gmt` file	GMT file that was provided as input or that was downloaded from g:profiler if no input GMT file was given; filtered for the selected datasources `*ENSG_filtered.gmt`

#9 session_info tuple

`meta` map	Groovy Map containing contrast information, e.g. [ variable:'treatment', reference:'treated', control:'saline', blocking:'' ]
`*R_sessionInfo.log` file	Log file containing information about the R session that was run for this module