nf-core/picard/collectvariantcallingmetrics @ 0.0.0-6c4ed3a
Summary
Collects per-sample and aggregate (spanning all samples) metrics from the provided VCF file
Get started
Add the following snippet to your workflow script to include this module.
include { PICARD_COLLECTVARIANTCALLINGMETRICS } from 'nf-core/picard/collectvariantcallingmetrics'
License
MIT License
Name
|
PICARD_COLLECTVARIANTCALLINGMETRICS |
|---|
meta
map
|
Groovy Map containing sample information e.g. |
|---|---|
vcf
file
|
Input VCF file for analysis *.{vcf,vcf.gz}
|
index
file
|
Index file for the input VCF file *.{idx,tbi}
|
intervals_file
file
|
Optional BED file specifying target intervals *.{bed,bed.gz,intervals_list}
|
fasta
file
|
Reference sequence file *.{fasta,fa,fasta.gz,fa.gz}
|
dict
file
|
Reference sequence dictionary file *.{dict}
|
dbsnp
file
|
Reference dbSNP file in dbSNP or VCF format *.{vcf,vcf.gz}
|
dbsnp_index
file
|
Reference dbSNP file in dbSNP or VCF format *.{idx,tbi}
|
detail_metrics
tuple
meta
map
|
Groovy Map containing sample information e.g. |
|---|---|
*.variant_calling_detail_metrics
file
|
Detailed variant calling metrics file *.variant_calling_detail_metrics
|
summary_metrics
tuple
meta
map
|
Groovy Map containing sample information e.g. |
|---|---|
*.variant_calling_summary_metrics
file
|
Summary variant calling metrics file *.variant_calling_summary_metrics
|
versions_picard
tuple
${task.process}
string
|
The process the versions were collected from |
|---|---|
picard
string
|
The tool name |
picard CollectVariantCallingMetrics --version 2>&1 | sed -n 's/.*Version://p'
string
|
The command used to generate the version of the tool |
| Tool | Description | Homepage |
|---|---|---|
| picard | A set of command line tools (in Java) for manipulating high-throughput sequencing (HTS) data and formats such as SAM/BAM/CRAM and VCF. | https://broadinstitute.github.io/picard/ |
| Version | 0.0.0-6c4ed3a |
|---|---|
| Commit ID | 6c4ed3a220310b905a1fc9d04f05be2e0837142b |
| Release Date | 23 Apr 2026 15:35:59 (UTC) |
| Download URL | https://registry.nextflow.io/api/v1/modules/nf-core%2Fpicard%2Fcollectvariantcallingmetrics/0.0.0-6c4ed3a/download |
| OCI Store URL | https://public.cr.seqera.io/v2/nextflow/plugin/modules/nf-core/picard/collectvariantcallingmetrics/blobs/sha256:9204e4feb8c966c680c7205e5bdb91c5231ba2d7c2d94e4064ce73a002aefa48 |
| Size | 3.2 KB |
| Checksum | sha256:9204e4feb8c966c680c7205e5bdb91c5231ba2d7c2d94e4064ce73a002aefa48 |
| Downloads | 3 |
| Version | Date | Status | Downloads | Size |
|---|---|---|---|---|
| 0.0.0-6c4ed3a | 23 Apr 2026 15:35:59 (UTC) | 3 | 3.2 KB | |
| 0.0.0-3fc6d40 | 22 Apr 2026 15:25:40 (UTC) | 3 | 3.2 KB | |
| 0.0.0-0c7146d | 08 Apr 2026 19:25:34 (UTC) | 3 | 3.2 KB |