Nextflow Registry | nf-core/gedi/price@0.0.0-eac429d

nf-core/gedi/price @ 0.0.0-eac429d

Identify translated ORFs from Ribo-seq BAMs using the PRICE algorithm

riboseq orf price gedi translation

Latest version: 0.0.0-eac429d

Total downloads: 0

Source: nf-core/modules

Authors: @pinin4fjords

Maintainers: @pinin4fjords

Identify translated ORFs from Ribo-seq BAMs using the PRICE algorithm

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

include { GEDI_PRICE } from 'nf-core/gedi/price'

MIT License

Process

`Name`	`GEDI_PRICE`

Input 2 channels

#1 tuple

`meta` map	Groovy Map identifying the cohort of Ribo-seq BAMs analysed together. PRICE is run jointly across all BAMs in this tuple. e.g. `[ id:'all_samples' ]`
`bams` file	One or more sorted Ribo-seq BAM files. Staged under `bams/` so PRICE discovers them via a generated bamlist. `*.{bam}`
`bais` file	Index files matching the input BAMs. `*.{bai}`

#2 tuple

`meta2` map	Groovy Map containing reference information. `meta2.id` must match the base name used when the index was built (`<id>.oml` lives inside the index directory). e.g. `[ id:'homo_sapiens' ]`
`index` directory	GEDI genome index directory produced by GEDI_INDEXGENOME. `price_index`

Output 8 channels

#1 model tuple

`meta` map	Groovy Map identifying the analysed cohort.
`${prefix}.model` file	PRICE model parameters fit during the run. `*.model`

#2 param tuple

`meta` map	Groovy Map identifying the analysed cohort.
`${prefix}.param` file	PRICE run parameters file. `*.param`

#3 signal tuple

`meta` map	Groovy Map identifying the analysed cohort.
`${prefix}.signal.tsv` file	Tab-delimited per-position signal summary. `*.signal.tsv`

#4 orfs_cit tuple

`meta` map	Groovy Map identifying the analysed cohort.
`${prefix}.orfs.cit` file	GEDI binary CIT file of called ORFs. `*.orfs.cit`

#5 orfs_tsv tuple

`meta` map	Groovy Map identifying the analysed cohort.
`${prefix}.orfs.tsv` file	Tab-delimited table of predicted translated ORFs with start codon, location, p-value and supporting read counts. `*.orfs.tsv`

#6 codons_cit tuple

`meta` map	Groovy Map identifying the analysed cohort.
`${prefix}.codons.cit` file	GEDI binary CIT file of per-codon signal. `*.codons.cit`

#7 orfs_metadata tuple

`meta` map	Groovy Map identifying the analysed cohort.
`${prefix}.orfs.cit.metadata.json` file	JSON metadata accompanying the ORF CIT file. `*.orfs.cit.metadata.json`

#8 versions_gedi tuple

`${task.process}` string	The name of the process
`gedi` string	The name of the tool
`gedi -e Version 2>&1 \| sed -n 's/.Gedi version $[^ ]$.*/\1/p' \| head -n 1` eval	The expression to obtain the version of the tool

Tool	Description	Homepage
gedi	Gedi is a Java software platform for working with genomic data (sequencing reads, sequences, per-base numeric values, annotations). It provides the PRICE algorithm (Probabilistic Inference of Codon Activities by an EM algorithm) for ribosome profiling ORF discovery with near-cognate start codon detection.	https://github.com/erhard-lab/gedi

Version	0.0.0-eac429d
Commit ID	eac429d4c67ac5114ce7d4287d460d8f05fd9fab