nf-core/checkm/qa @ 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_QA } from 'nf-core/checkm/qa'
License
MIT License
Name
|
CHECKM_QA |
|---|
meta
map
|
Groovy Map containing sample information e.g. [ id:'test', single_end:false ] |
|---|---|
analysis_dir
file
|
Directory containing output of checkm/analyze or checkm/lineage_wf etc. *
|
marker_file
file
|
Marker file specified during checkm/analyze or produced by checkm/{lineage,taxonomy}_wf *.ms
|
coverage_file
file
|
File containing coverage of each sequence (generated by checkm coverage) |
exclude_marker_file
file
|
File specifying markers to exclude from marker sets |
|---|
db
directory
|
CheckM database directory |
|---|
fasta
tuple
meta
map
|
Groovy Map containing sample information e.g. [ id:'test', single_end:false ] |
|---|---|
${prefix}.fasta
file
|
Output in fasta format (only if --out_format 9) *.fasta
|
output
tuple
meta
map
|
Groovy Map containing sample information e.g. [ id:'test', single_end:false ] |
|---|---|
${prefix}.txt
file
|
Default completeness statistics in various formats, as specified with --out_format (excluding option: 9) *.txt
|
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 18:30:22 (UTC) |
| Download URL | https://registry-stage.nextflow.io/api/v1/modules/nf-core%2Fcheckm%2Fqa/0.0.0-0c7146d/download |
| OCI Store URL | https://public.cr.stage-seqera.io/v2/nextflow/plugin-stage/modules/nf-core/checkm/qa/blobs/sha256:345edea6b2e2ca40a4c0974d9bc8f5d01ac43ddb29187d4865d901c2cb415258 |
| Size | 3.1 KB |
| Checksum | sha256:345edea6b2e2ca40a4c0974d9bc8f5d01ac43ddb29187d4865d901c2cb415258 |
| Downloads | 1 |
| Version | Date | Status | Downloads | Size | Diff |
|---|---|---|---|---|---|
| 0.0.0-0c7146d | 08 Apr 2026 18:30:22 (UTC) | 1 | 3.1 KB | - |