modules/opt_flip

flip corrects probes that are aligning to the opposite strand of their intended target genes by reverse complementing them

optopt fliptranscriptsoff-target probesalign probes

https://github.com/nf-core/modules/[...]/modules/nf-core/opt/flip

Description

flip corrects probes that are aligning to the opposite strand of their intended target genes by reverse complementing them

Input

name:type

description

pattern

`meta`
`:map`

Groovy Map containing sample information of the probe panel sequences used for the xenium experiment e.g. [ id:'breast_cancer_probe_panel_sequences' ]

`probes_fasta`
`:file`

Fasta file for the probe sequences used in the xenium experiment

*.fasta

`meta2`
`:map`

Groovy Map containing the information of the genomic features and fasta files used as references e.g. [ id:'gencode_references' ]

`ref_annot_gff`
`:file`

Reference annotations in gff format

*.gff

`ref_annot_fa`
`:file`

Reference annotations in fasta format

*.fa

Output

name:type

description

pattern

`fwd_oriented_fa`

`meta`
`:map`

Groovy Map containing information of the forward oriented fasta generated with the probes panel sequences ‘opt flip’ e.g. [ id:'breast_cancer_probe_panel_sequences' ]

`${prefix}/fwd_oriented.fa`
`:file`

Fasta file for the forward oriented probe sequences generated with ‘opt flip’

*fwd_oriented.fa

`versions_opt`

`${task.process}`
`:string`

The name of the process

`opt`
`:string`

The name of the tool

`opt --version`
`:eval`

The expression to obtain the version of the tool

Topics

name:type

description

pattern

`versions`

`${task.process}`
`:string`

The name of the process

`opt`
`:string`

The name of the tool

`opt --version`
`:eval`

The expression to obtain the version of the tool

Tools

opt
GPL-3.0 license

opt is a simple program that aligns probe sequences to transcript sequences to detect potential off-target probe activity

github.com/JEFworks-Lab/off-target-probe-tracker github.com/JEFworks-Lab/off-target-probe-tracker/blob/main/README.md https://github.com/JEFworks-Lab/off-target-probe-tracker

modules/opt_flip

Description

Input

`meta`
`:map`

`probes_fasta`
`:file`

`meta2`
`:map`

`ref_annot_gff`
`:file`

`ref_annot_fa`
`:file`

Output

`fwd_oriented_fa`

`meta`
`:map`

`${prefix}/fwd_oriented.fa`
`:file`

`versions_opt`

`${task.process}`
`:string`

`opt`
`:string`

`opt --version`
`:eval`

Topics

`versions`

`${task.process}`
`:string`

`opt`
`:string`

`opt --version`
`:eval`

Tools

opt
GPL-3.0 license

included in

maintainer

get in touch

modules/opt_flip

Description

Input

meta:map

probes_fasta:file

meta2:map

ref_annot_gff:file

ref_annot_fa:file

Output

fwd_oriented_fa

meta:map

${prefix}/fwd_oriented.fa:file

versions_opt

${task.process}:string

opt:string

opt --version:eval

Topics

versions

${task.process}:string

opt:string

opt --version:eval

Tools

opt GPL-3.0 license

included in

maintainer

get in touch

`meta`
`:map`

`probes_fasta`
`:file`

`meta2`
`:map`

`ref_annot_gff`
`:file`

`ref_annot_fa`
`:file`

`fwd_oriented_fa`

`meta`
`:map`

`${prefix}/fwd_oriented.fa`
`:file`

`versions_opt`

`${task.process}`
`:string`

`opt`
`:string`

`opt --version`
`:eval`

`versions`

`${task.process}`
`:string`

`opt`
`:string`

`opt --version`
`:eval`

opt
GPL-3.0 license