modules/tailfindr

Estimating poly(A)-tail lengths from basecalled fast5 files produced by Nanopore sequencing of RNA and DNA

polya tailfast5nanopore

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

Description

Estimating poly(A)-tail lengths from basecalled fast5 files produced by Nanopore sequencing of RNA and DNA

Input

name:type

description

pattern

`meta`
`:map`

Groovy Map containing sample information e.g. [ id:‘test’ ]

`fast5`
`:file`

fast5 file

*.fast5

Output

name:type

description

pattern

`csv_gz`

`meta`
`:map`

Groovy Map containing sample information e.g. [ id:‘test’ ]

`*.csv.gz`
`:file`

Compressed csv file

*.csv.gz

`versions_tailfindr`

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

The name of the process

`tailfindr`
`:string`

The name of the tool

`Rscript -e "cat(paste(packageVersion('tailfindr'), collapse='.'))"`
`:eval`

The expression to obtain the version of the tool

`versions_ont_fast5_api`

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

The name of the process

`ont-fast5-api`
`:string`

The name of the tool

`python -c "import ont_fast5_api; print(ont_fast5_api.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

`tailfindr`
`:string`

The name of the tool

`Rscript -e "cat(paste(packageVersion('tailfindr'), collapse='.'))"`
`:eval`

The expression to obtain the version of the tool

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

The name of the process

`ont-fast5-api`
`:string`

The name of the tool

`python -c "import ont_fast5_api; print(ont_fast5_api.version)"`
`:eval`

The expression to obtain the version of the tool

Tools

tailfindr
AGPL v3

An R package for estimating poly(A)-tail lengths in Oxford Nanopore RNA and DNA reads.

github.com/adnaniazi/tailfindr github.com/adnaniazi/tailfindr/blob/master/README.md https://github.com/adnaniazi/tailfindr 10.1261/rna.071332.119

modules/tailfindr

Description

Input

`meta`
`:map`

`fast5`
`:file`

Output

`csv_gz`

`meta`
`:map`

`*.csv.gz`
`:file`

`versions_tailfindr`

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

`tailfindr`
`:string`

`Rscript -e "cat(paste(packageVersion('tailfindr'), collapse='.'))"`
`:eval`

`versions_ont_fast5_api`

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

`ont-fast5-api`
`:string`

`python -c "import ont_fast5_api; print(ont_fast5_api.version)"`
`:eval`

Topics

`versions`

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

`tailfindr`
`:string`

`Rscript -e "cat(paste(packageVersion('tailfindr'), collapse='.'))"`
`:eval`

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

`ont-fast5-api`
`:string`

`python -c "import ont_fast5_api; print(ont_fast5_api.version)"`
`:eval`

Tools

tailfindr
AGPL v3

maintainer

get in touch

modules/tailfindr

Description

Input

meta:map

fast5:file

Output

csv_gz

meta:map

*.csv.gz:file

versions_tailfindr

${task.process}:string

tailfindr:string

Rscript -e "cat(paste(packageVersion('tailfindr'), collapse='.'))":eval

versions_ont_fast5_api

${task.process}:string

ont-fast5-api:string

python -c "import ont_fast5_api; print(ont_fast5_api.__version__)":eval

Topics

versions

${task.process}:string

tailfindr:string

Rscript -e "cat(paste(packageVersion('tailfindr'), collapse='.'))":eval

${task.process}:string

ont-fast5-api:string

python -c "import ont_fast5_api; print(ont_fast5_api.__version__)":eval

Tools

tailfindr AGPL v3

maintainer

get in touch

`meta`
`:map`

`fast5`
`:file`

`csv_gz`

`meta`
`:map`

`*.csv.gz`
`:file`

`versions_tailfindr`

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

`tailfindr`
`:string`

`Rscript -e "cat(paste(packageVersion('tailfindr'), collapse='.'))"`
`:eval`

`versions_ont_fast5_api`

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

`ont-fast5-api`
`:string`

`python -c "import ont_fast5_api; print(ont_fast5_api.version)"`
`:eval`

`versions`

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

`tailfindr`
`:string`

`Rscript -e "cat(paste(packageVersion('tailfindr'), collapse='.'))"`
`:eval`

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

`ont-fast5-api`
`:string`

`python -c "import ont_fast5_api; print(ont_fast5_api.version)"`
`:eval`

tailfindr
AGPL v3