Nextflow Registry | nf-core/anota2seq/anota2seqrun@0.0.0-6c4ed3a

nf-core/anota2seq/anota2seqrun @ 0.0.0-6c4ed3a

Generally applicable transcriptome-wide analysis of translational efficiency using anota2seq

riboseq rnaseq translation differential

Latest version: 0.0.0-6c4ed3a

Total downloads: 9

Source: nf-core/modules

Authors: @pinin4fjords

Maintainers: @pinin4fjords

Generally applicable transcriptome-wide analysis of translational efficiency using anota2seq

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

include { ANOTA2SEQ_ANOTA2SEQRUN } from 'nf-core/anota2seq/anota2seqrun'

MIT License

Process

`Name`	`ANOTA2SEQ_ANOTA2SEQRUN`

Input 2 channels

#1 tuple

`meta` map	Groovy Map containing contrast information. e.g. [ id:'contrast1', blocking:'patient' ]
`sample_treatment_col` string	The column in the sample sheet that should be used to define groups for comparison
`reference` string	The value within the contrast_variable column of the sample sheet that should be used to derive the reference samples
`target` string	The value within the contrast_variable column of the sample sheet that should be used to derive the target samples

#2 tuple

`meta2` map	Groovy map containing study-wide metadata related to the sample sheet and matrix
`samplesheet` file	CSV or TSV format sample sheet with sample metadata
`counts` file	Raw TSV or CSV format expression matrix

Output 16 channels

#1 rdata tuple

`meta` map	Groovy Map containing contrast information. e.g. [ id:'contrast1', blocking:'patient' ]
`*.Anota2seqDataSet.rds` file	Serialised Anota2seqDataSet object `.Anota2seqDataSet.rds`

#2 buffering tuple

`meta` map	Groovy Map containing contrast information. e.g. [ id:'contrast1', blocking:'patient' ]
`*.buffering.anota2seq.results.tsv` file	anota2seq results for the 'translated mRNA' analysis, describing buffering across conditions, being stable levels of translated RNA (from riboseq samples) across conditions, despite changes in total mRNA. See https://rdrr.io/bioc/anota2seq/man/anota2seqGetOutput.html for description of output columns. `.buffering.anota2seq.results.tsv`

#3 total_mrna tuple

`meta` map	Groovy Map containing contrast information. e.g. [ id:'contrast1', blocking:'patient' ]
`*.total_mRNA.anota2seq.results.tsv` file	anota2seq results for the 'translated mRNA' analysis, describing differences in RNA levels across conditions for RNA-seq samples. See https://rdrr.io/bioc/anota2seq/man/anota2seqGetOutput.html for description of output columns. `.total_mRNA.anota2seq.results.tsv`

#4 translation tuple

`meta` map	Groovy Map containing contrast information. e.g. [ id:'contrast1', blocking:'patient' ]
`*.translation.anota2seq.results.tsv` file	anota2seq results for the 'translated mRNA' analysis, describing differences in translation across conditions, being differences in translated RNA levels not explained by total RNA levels. See https://rdrr.io/bioc/anota2seq/man/anota2seqGetOutput.html for description of output columns. `.translation.anota2seq.results.tsv`

#5 session_info tuple

`meta` map	Groovy Map containing contrast information. e.g. [ id:'contrast1', blocking:'patient' ]
`*.R_sessionInfo.log` file	dump of R SessionInfo `*.log`

#6 mrna_abundance tuple

`meta` map	Groovy Map containing contrast information. e.g. [ id:'contrast1', blocking:'patient' ]
`*.mRNA_abundance.anota2seq.results.tsv` file	anota2seq results for the 'mRNA abunance' analysis, describing changes across conditions consistent between total mRNA and translated RNA (RNA-seq and Riboseq samples). See https://rdrr.io/bioc/anota2seq/man/anota2seqGetOutput.html for description of output columns. `.mRNA_abundance.anota2seq.results.tsv`

#7 translated_mrna tuple

`meta` map	Groovy Map containing contrast information. e.g. [ id:'contrast1', blocking:'patient' ]
`*.translated_mRNA.anota2seq.results.tsv` file	anota2seq results for the 'translated mRNA' analysis, describing differences in RNA levels across conditions for Ribo-seq samples. See https://rdrr.io/bioc/anota2seq/man/anota2seqGetOutput.html for description of output columns. `.translated_mRNA.anota2seq.results.tsv`

#8 fold_change_plot tuple


`meta` map	Groovy Map containing contrast information. e.g. [ id:'contrast1', blocking:'patient' ]