Nextflow Registry | nf-core/ribotricer/detectorfs@0.0.0-6c4ed3a

nf-core/ribotricer/detectorfs @ 0.0.0-6c4ed3a

Accurate detection of short and long active ORFs using Ribo-seq data

riboseq orf genomics

Latest version: 0.0.0-6c4ed3a

Total downloads: 9

Source: nf-core/modules

Authors: @pinin4fjords

Maintainers: @pinin4fjords

Accurate detection of short and long active ORFs using Ribo-seq data

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

include { RIBOTRICER_DETECTORFS } from 'nf-core/ribotricer/detectorfs'

MIT License

Process

`Name`	`RIBOTRICER_DETECTORFS`

Input 2 channels

#1 tuple

`meta` map	Map containing riboseq sample information e.g. `[ id:'sample1', single_end:false, strandedness: 'single' ]
`bam` file	BAM/CRAM/SAM file `*.{bam,cram,sam}`
`bai` file	Index for sorted BAM/CRAM/SAM file `*.{bai}`

#2 tuple

`meta2` map	Map containing reference information for the candidate ORFs e.g. `[ id:'Ensembl human v.111' ]`
`candidate_orfs` file	TSV file with candidate ORFs from 'ribotricer prepareorfs' `*.tsv`

Output 11 channels

#1 orfs tuple

`meta` map	Groovy Map containing riboseq sample information e.g. `[ id:'sample1', single_end:false ]
`*_translating_ORFs.tsv` file	"TSV with ORFs assessed as translating in this BAM file. You can output all ORFs regardless of the translation status with option --report_all" `*_translating_ORFs.tsv`

#2 neg_wig tuple

`meta` map	Groovy Map containing riboseq sample information e.g. `[ id:'sample1', single_end:false ]
`*_neg.wig` file	Negative strand WIG file for visualization in Genome Browser `*_neg.wig`

#3 pos_wig tuple

`meta` map	Groovy Map containing riboseq sample information e.g. `[ id:'sample1', single_end:false ]
`*_pos.wig` file	Positive strand WIG file for visualization in Genome Browser `*_pos.wig`

#4 protocol tuple

`meta` map	Groovy Map containing riboseq sample information e.g. `[ id:'sample1', single_end:false ]
`*_protocol.txt` file	txt file containing inferred protocol if it was inferred (not supplied as input) `*_protocol.txt`

#5 versions

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

#6 bam_summary tuple

`meta` map	Groovy Map containing riboseq sample information e.g. `[ id:'sample1', single_end:false ]
`*_bam_summary.txt` file	Text summary of reads found in the BAM `*_bam_summary.txt`

#7 psite_offsets tuple

`meta` map	Groovy Map containing riboseq sample information e.g. `[ id:'sample1', single_end:false ]
`*_psite_offsets.txt` file	"If the P-site offsets are not provided, txt file containing the derived relative offsets" `*_psite_offsets.txt`

#8 metagene_plots tuple

`meta` map	Groovy Map containing riboseq sample information e.g. `[ id:'sample1', single_end:false ]
`*_metagene_plots.pdf` file	Metagene plots for quality control `*_metagene_plots.pdf`

#9 read_length_dist tuple

`meta` map	Groovy Map containing riboseq sample information e.g. `[ id:'sample1', single_end:false ]
`*_read_length_dist.pdf` file	PDF-format read length distribution as quality control `*_read_length_dist.pdf`

#10 metagene_profile_3p tuple

`meta` map	Groovy Map containing riboseq sample information e.g. `[ id:'sample1', single_end:false ]
`*_metagene_profiles_3p.tsv` file	Metagene profile aligning with the stop codon `*_metagene_profiles_3p.tsv`

#11 metagene_profile_5p