Nextflow Registry | nf-core/ribotish/predict@0.0.0-6c4ed3a

nf-core/ribotish/predict @ 0.0.0-6c4ed3a

Quality control of riboseq bam data

riboseq predict bam

Latest version: 0.0.0-6c4ed3a

Total downloads: 9

Source: nf-core/modules

Authors: @pinin4fjords

Maintainers: @pinin4fjords

Quality control of riboseq bam data

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

include { RIBOTISH_PREDICT } from 'nf-core/ribotish/predict'

MIT License

Process

`Name`	`RIBOTISH_PREDICT`

Input 6 channels

#1 tuple

`meta` map	Groovy Map containing riboseq sample information e.g. `[ id:'sample1', single_end:false ]
`bam_ribo` file	Sorted riboseq BAM file(s) `*.{bam}`
`bai_ribo` file	Index for sorted riboseq bam file(s) `*.{bai}`

#2 tuple

`meta2` map	Groovy Map containing TI-Seq sample information e.g. `[ id:'sample1', single_end:false ]`
`bam_ti` file	Sorted TI-Seq BAM file(s) `*.{bam}`
`bai_ti` file	Index for sorted TI-Seq BAM file(s) `*.{bai}`

#3 tuple

`meta3` map	Groovy Map containing reference information e.g. `[ id:'Ensembl human v.111' ]`
`fasta` file	Fasta-format sequence file for reference sequences used in the bam file `*.gtf`
`gtf` file	GTF-format annotation file for reference sequences used in the bam file `*.gtf`

#4 tuple

`meta4` map	Groovy Map containing information on candidate ORFs
`candidate_orfs` file	3-column (transIDstarttstop) candidate ORFs file `*.txt`

#5 tuple

`meta5` map	Groovy Map containing information on riboseq P-site offset parameter files
`para_ribo` file	Input P-site offset parameter files for riboseq bam files `*.py`

#6 tuple

`meta6` map	Groovy Map containing information on TI-seq P-site offset parameter files
`para_ti` file	Input P-site offset parameter files for TI-seq bam files `*.py`

Output 4 channels

#1 all tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'sample1', single_end:false ]`
`*_all.txt` file	txt file similar to the predictions but do not use FDR (q-value) cutoff `*.{txt}`

#2 versions

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

#3 predictions tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'sample1', single_end:false ]`
`*_pred.txt` file	txt file all possible ORF results that fit the thresholds `*.{txt}`

#4 transprofile tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'sample1', single_end:false ]`
`*_transprofile.py` file	Output RPF P-site profile for each transcript. The profile data is in python dict format, recording non-zero read counts at different positions on transcript. `*.{py}`

Tool	Description	Homepage
ribotish	Ribo TIS Hunter (Ribo-TISH) identifies translation activities using ribosome profiling data.	https://github.com/zhpn1024/ribotish