modules/pypolca_run

Short read polisher for long read assemblies

polishpythongenomics

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

Description

Short read polisher for long read assemblies

Input

name:type

description

pattern

`meta`
`:map`

Groovy Map containing sample information e.g. [ id:'sample1' ]

`contigs`
`:file`

Genome assembly from long reads

*.{fa,fasta,fna}

`reads`
`:file`

List of short reads for assembly polishing. Length 1 for single-end and 2 for paired-end

*.{fastq,fq}.gz

Output

name:type

description

pattern

`polished`

`meta`
`:map`

Groovy Map containing sample information e.g. [ id:'sample1' ]

`${prefix}/*_corrected.fasta`
`:file`

Polished assembly

*.{fasta}

`vcf`

`meta`
`:map`

Groovy Map containing sample information e.g. [ id:'sample1' ]

`${prefix}/*.vcf`
`:file`

variant calls

*.vcf

`report`

`meta`
`:map`

Groovy Map containing sample information e.g. [ id:'sample1' ]

`${prefix}/*.report`
`:file`

Pypolca report

*.report

`versions_pypolca`

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

The name of the process

`pypolca`
`:string`

The name of the tool

`pypolca --version | sed 's/^pypolca, 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

`pypolca`
`:string`

The name of the tool

`pypolca --version | sed 's/^pypolca, version //'`
`:eval`

The expression to obtain the version of the tool

Tools

pypolca
MIT

Standalone Python re-implementation of the POLCA polisher from MaSuRCA

github.com/gbouras13/pypolca github.com/gbouras13/pypolca?tab=readme-ov-file#usage 10.1099/mgen.0.001254

modules/pypolca_run

Description

Input

`meta`
`:map`

`contigs`
`:file`

`reads`
`:file`

Output

`polished`

`meta`
`:map`

`${prefix}/*_corrected.fasta`
`:file`

`vcf`

`meta`
`:map`

`${prefix}/*.vcf`
`:file`

`report`

`meta`
`:map`

`${prefix}/*.report`
`:file`

`versions_pypolca`

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

`pypolca`
`:string`

`pypolca --version | sed 's/^pypolca, version //'`
`:eval`

Topics

`versions`

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

`pypolca`
`:string`

`pypolca --version | sed 's/^pypolca, version //'`
`:eval`

Tools

pypolca
MIT

included in

maintainer

get in touch

modules/pypolca_run

Description

Input

meta :map

contigs :file

reads :file

Output

polished

meta :map

${prefix}/*_corrected.fasta :file

vcf

meta :map

${prefix}/*.vcf :file

report

meta :map

${prefix}/*.report :file

versions_pypolca

${task.process} :string

pypolca :string

pypolca --version | sed 's/^pypolca, version //' :eval

Topics

versions

${task.process} :string

pypolca :string

pypolca --version | sed 's/^pypolca, version //' :eval

Tools

pypolcaMIT

included in

maintainer

get in touch

`meta`
`:map`

`contigs`
`:file`

`reads`
`:file`

`polished`

`meta`
`:map`

`${prefix}/*_corrected.fasta`
`:file`

`vcf`

`meta`
`:map`

`${prefix}/*.vcf`
`:file`

`report`

`meta`
`:map`

`${prefix}/*.report`
`:file`

`versions_pypolca`

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

`pypolca`
`:string`

`pypolca --version | sed 's/^pypolca, version //'`
`:eval`

`versions`

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

`pypolca`
`:string`

`pypolca --version | sed 's/^pypolca, version //'`
`:eval`

pypolca
MIT