nf-core/varlociraptor/estimatealignmentproperties @ 0.0.0-0c7146d
Summary
In order to judge about candidate indel and structural variants, Varlociraptor needs to know about certain properties of the underlying sequencing experiment in combination with the used read aligner.
Get started
Add the following snippet to your workflow script to include this module.
include { VARLOCIRAPTOR_ESTIMATEALIGNMENTPROPERTIES } from 'nf-core/varlociraptor/estimatealignmentproperties'
License
MIT License
Process
Name
|
VARLOCIRAPTOR_ESTIMATEALIGNMENTPROPERTIES |
|---|
Input
1 channel
#1
tuple
meta
map
|
Groovy Map containing sample information e.g. [ id:'test', single_end:false ] |
|---|---|
bam
file
|
Sorted BAM/CRAM/SAM file *.{bam,cram,sam}
|
bai
file
|
Index of sorted BAM/CRAM/SAM file *.{bai,crai,sai}
|
fasta
file
|
Reference fasta file *.{fasta}
|
fai
file
|
Index for reference fasta file (must be with samtools index) *.{fai}
|
Output
2 channels
#1
versions_varlociraptor
tuple
${task.process}
string
|
The process the versions were collected from |
|---|---|
varlociraptor
string
|
The tool name |
varlociraptor --version | sed 's/^varlociraptor //'
string
|
The command used to generate the version of the tool |
#2
alignment_properties_json
tuple
meta
map
|
Groovy Map containing sample information e.g. [ id:'test', single_end:false ] |
|---|---|
*.alignment-properties.json
file
|
File containing alignment properties *.alignment-properties.json
|
| Tool | Description | Homepage |
|---|---|---|
| varlociraptor | Flexible, uncertainty-aware variant calling with parameter free filtration via FDR control. | https://varlociraptor.github.io/docs/estimating/ |
| Version | 0.0.0-0c7146d |
|---|---|
| Commit ID | 135d883a43b1a2324b4112cd270cf22e20835533 |
| Release Date | 08 Apr 2026 19:21:18 (UTC) |
| Download URL | https://registry-stage.nextflow.io/api/v1/modules/nf-core%2Fvarlociraptor%2Festimatealignmentproperties/0.0.0-0c7146d/download |
| OCI Store URL | https://public.cr.stage-seqera.io/v2/nextflow/plugin-stage/modules/nf-core/varlociraptor/estimatealignmentproperties/blobs/sha256:9fdf0e8da41e740f6cd9a2ef7cfc8c52565c3e9060d935b0e96d164988464483 |
| Size | 2.8 KB |
| Checksum | sha256:9fdf0e8da41e740f6cd9a2ef7cfc8c52565c3e9060d935b0e96d164988464483 |
| Downloads | 1 |
| Version | Date | Status | Downloads | Size | Diff |
|---|---|---|---|---|---|
| 0.0.0-0c7146d | 08 Apr 2026 19:21:18 (UTC) | 1 | 2.8 KB | - |