nf-core/checkm/lineagewf @ 0.0.0-0c7146d
Summary
CheckM provides a set of tools for assessing the quality of genomes recovered from isolates, single cells, or metagenomes.
Get started
Add the following snippet to your workflow script to include this module.
include { CHECKM_LINEAGEWF } from 'nf-core/checkm/lineagewf'
License
MIT License
Name
|
CHECKM_LINEAGEWF |
|---|
meta
map
|
Groovy Map containing sample information e.g. [ id:'test', single_end:false ] |
|---|---|
fasta
file
|
One or a list of multiple FASTA files of each bin, with extension defined with the fasta_ext value *.{$fasta_ext}
|
fasta_ext
string
|
The file-type extension suffix of the input FASTA files (e.g., fasta, fna, fa, fas) |
|---|
db
directory
|
Optional directory pointing to checkM database to prevent re-downloading |
|---|
checkm_tsv
tuple
meta
map
|
Groovy Map containing sample information e.g. [ id:'sample', bin:'1' ] |
|---|---|
${prefix}.tsv
file
|
CheckM summary completeness statistics table *.tsv
|
marker_file
tuple
meta
map
|
Groovy Map containing sample information e.g. [ id:'sample', bin:'1' ] |
|---|---|
${prefix}/lineage.ms
file
|
Lineage file *.ms
|
checkm_output
tuple
meta
map
|
Groovy Map containing sample information e.g. [ id:'sample', bin:'1' ] |
|---|---|
${prefix}
directory
|
CheckM output directory */
|
versions_checkm
tuple
${task.process}
string
|
The name of the process |
|---|---|
checkm
string
|
The name of the tool |
checkm 2>&1 | grep '...:::' | sed 's/.*CheckM v//;s/ .*//'
eval
|
The expression to obtain the version of the tool |
| Tool | Description | Homepage |
|---|---|---|
| checkm | Assess the quality of microbial genomes recovered from isolates, single cells, and metagenomes. | https://ecogenomics.github.io/CheckM/ |
| Version | 0.0.0-0c7146d |
|---|---|
| Commit ID | 135d883a43b1a2324b4112cd270cf22e20835533 |
| Release Date | 08 Apr 2026 18:30:19 (UTC) |
| Download URL | https://registry-stage.nextflow.io/api/v1/modules/nf-core%2Fcheckm%2Flineagewf/0.0.0-0c7146d/download |
| OCI Store URL | https://public.cr.stage-seqera.io/v2/nextflow/plugin-stage/modules/nf-core/checkm/lineagewf/blobs/sha256:fb9b4a2b69d1562a6a396c73a2880c50c640babc435d524e64a428a705f476df |
| Size | 3.1 KB |
| Checksum | sha256:fb9b4a2b69d1562a6a396c73a2880c50c640babc435d524e64a428a705f476df |
| Downloads | 1 |
| Version | Date | Status | Downloads | Size | Diff |
|---|---|---|---|---|---|
| 0.0.0-0c7146d | 08 Apr 2026 18:30:19 (UTC) | 1 | 3.1 KB | - |