Nextflow Registry | nf-core/pypolca/run@0.0.0-0c7146d

nf-core/pypolca/run @ 0.0.0-0c7146d

Short read polisher for long read assemblies

polish python genomics

Latest version: 0.0.0-0c7146d

Total downloads: 1

Source: nf-core/modules

Authors: @dwells-eit

Maintainers: @dwells-eit

Short read polisher for long read assemblies

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

include { PYPOLCA_RUN } from 'nf-core/pypolca/run'

MIT License

Process

`Name`	`PYPOLCA_RUN`

Input 2 channels

#1 tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'sample1' ]`
`reads` file	List of short reads for assembly polishing. Length 1 for single-end and 2 for paired-end `*.{fastq,fq}.gz`

#2 tuple

`meta2` map	Groovy Map containing sample information e.g. `[ id:'sample1' ]`
`contigs` file	Genome assembly from long reads `*.{fa,fasta,fna}`

Output 4 channels

#1 vcf tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'sample1' ]`
`${prefix}/*.vcf` file	variant calls `*.vcf`

#2 report tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'sample1' ]`
`${prefix}/*.report` file	Pypolca report `*.report`

#3 polished tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'sample1' ]`
`${prefix}/*_corrected.fasta` file	Polished assembly `*.{fasta}`

#4 versions_pypolca tuple

`${task.process}` string	The name of the process
`pypolca` string	The name of the tool
`pypolca --version` eval	The expression to obtain the version of the tool

Tool	Description	Homepage
pypolca	Standalone Python re-implementation of the POLCA polisher from MaSuRCA	https://github.com/gbouras13/pypolca

Version	0.0.0-0c7146d
Commit ID	135d883a43b1a2324b4112cd270cf22e20835533
Release Date	08 Apr 2026 19:06:18 (UTC)
Download URL	https://registry-stage.nextflow.io/api/v1/modules/nf-core%2Fpypolca%2Frun/0.0.0-0c7146d/download
OCI Store URL	https://public.cr.stage-seqera.io/v2/nextflow/plugin-stage/modules/nf-core/pypolca/run/blobs/sha256:9b8cd286a4a3e961b8d479f615a3b851ff5808dbdbb059ea5e97fbe0aec570fe
Size	2.6 KB
Checksum	sha256:9b8cd286a4a3e961b8d479f615a3b851ff5808dbdbb059ea5e97fbe0aec570fe
Downloads	1

Version	Date	Status	Downloads	Size	Diff
0.0.0-0c7146d	08 Apr 2026 19:06:18 (UTC)		1	2.6 KB	-