nf-core/pypolca/run @ 0.0.0-3fc6d40
Summary
Short read polisher for long read assemblies
Get started
Add the following snippet to your workflow script to include this module.
include { PYPOLCA_RUN } from 'nf-core/pypolca/run'
License
MIT License
Process
Name
|
PYPOLCA_RUN |
|---|
Input
2 channels
#1
tuple
meta
map
|
Groovy Map containing sample information e.g. |
|---|---|
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. |
|---|---|
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. |
|---|---|
${prefix}/*.vcf
file
|
variant calls *.vcf
|
#2
report
tuple
meta
map
|
Groovy Map containing sample information e.g. |
|---|---|
${prefix}/*.report
file
|
Pypolca report *.report
|
#3
polished
tuple
meta
map
|
Groovy Map containing sample information e.g. |
|---|---|
${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 | 0.0.0-3fc6d40 |
|---|---|
| Commit ID | 6c4ed3a220310b905a1fc9d04f05be2e0837142b |
| Release Date | 22 Apr 2026 15:28:02 (UTC) |
| Download URL | https://registry.nextflow.io/api/v1/modules/nf-core%2Fpypolca%2Frun/0.0.0-3fc6d40/download |
| OCI Store URL | https://public.cr.seqera.io/v2/nextflow/plugin/modules/nf-core/pypolca/run/blobs/sha256:df857e06811028879de0e2513b534be5dbdbb7c9ffe7a147a85f6f89f273acb1 |
| Size | 2.7 KB |
| Checksum | sha256:df857e06811028879de0e2513b534be5dbdbb7c9ffe7a147a85f6f89f273acb1 |
| Downloads | 3 |
| Version | Date | Status | Downloads | Size |
|---|---|---|---|---|
| 0.0.0-6c4ed3a | 23 Apr 2026 15:39:12 (UTC) | 3 | 2.6 KB | |
| 0.0.0-3fc6d40 | 22 Apr 2026 15:28:02 (UTC) | 3 | 2.7 KB | |
| 0.0.0-0c7146d | 08 Apr 2026 19:29:36 (UTC) | 2 | 2.6 KB |