nf-core/skesa @ 0.0.0-0c7146d
Summary
Assemble microbial genomes from short-read FASTQ files into contigs in FASTA format using SKESA.
Get started
Add the following snippet to your workflow script to include this module.
include { SKESA } from 'nf-core/skesa'
License
MIT License
Process
Name
|
SKESA |
|---|
Input
1 channel
#1
tuple
meta
map
|
Groovy Map containing sample information e.g. |
|---|---|
fastq
file
|
One or more input FASTQ files containing sequencing reads for assembly. Provide a single file for single-end data and one or more files for paired-end data. *.{fastq,fq,fastq.gz,fq.gz}
|
Output
2 channels
#1
fasta
tuple
meta
map
|
Groovy Map containing sample information e.g. |
|---|---|
*.fa
file
|
Assembled contigs in FASTA format *.fa
|
#2
versions_skesa
tuple
${task.process}
string
|
The name of the process |
|---|---|
skesa
string
|
The name of the tool |
skesa --version 2>&1 | sed -n 's/^SKESA //p'
eval
|
The command used to obtain the version of the tool |
| Tool | Description | Homepage |
|---|---|---|
| skesa | SKESA is a de-novo sequence read assembler for microbial genomes based on DeBruijn graphs. | https://github.com/ncbi/SKESA |
| Version | 0.0.0-0c7146d |
|---|---|
| Commit ID | 6c4ed3a220310b905a1fc9d04f05be2e0837142b |
| Release Date | 08 Apr 2026 19:38:59 (UTC) |
| Download URL | https://registry.nextflow.io/api/v1/modules/nf-core%2Fskesa/0.0.0-0c7146d/download |
| OCI Store URL | https://public.cr.seqera.io/v2/nextflow/plugin/modules/nf-core/skesa/blobs/sha256:cc9899ec9fbe92391181702998acf2135c984ba1a07e8f83d7b6f5f26ae93e44 |
| Size | 2.5 KB |
| Checksum | sha256:cc9899ec9fbe92391181702998acf2135c984ba1a07e8f83d7b6f5f26ae93e44 |
| Downloads | 1 |
| Version | Date | Status | Downloads | Size |
|---|---|---|---|---|
| 0.0.0-6c4ed3a | 23 Apr 2026 15:46:23 (UTC) | 1 | 2.5 KB | |
| 0.0.0-3fc6d40 | 22 Apr 2026 15:32:03 (UTC) | 1 | 2.5 KB | |
| 0.0.0-0c7146d | 08 Apr 2026 19:38:59 (UTC) | 1 | 2.5 KB |