nf-core/ataqv/ataqv @ 0.0.0-6c4ed3a
Summary
ataqv function of a corresponding ataqv tool
Get started
Add the following snippet to your workflow script to include this module.
include { ATAQV_ATAQV } from 'nf-core/ataqv/ataqv'
License
MIT License
Name
|
ATAQV_ATAQV |
|---|
meta
map
|
Groovy Map containing sample information e.g. [ id:'test', single_end:false ] |
|---|---|
bam
file
|
BAM file *.bam
|
bai
file
|
BAM index file with the same prefix as bam file. Required if tss_file input is provided. *.bam.bai
|
peak_file
file
|
A BED file of peaks called for alignments in the BAM file *.bed
|
organism
string
|
The subject of the experiment, which determines the list of autosomes (see "Reference Genome Configuration" section at https://github.com/ParkerLab/ataqv). |
|---|
mito_name
string
|
Name of the mitochondrial sequence. |
|---|
tss_file
file
|
A BED file of transcription start sites for the experiment organism. If supplied, a TSS enrichment score will be calculated according to the ENCODE data standards. This calculation requires that the BAM file of alignments be indexed. *.bed
|
|---|
excl_regs_file
file
|
A BED file containing excluded regions. Peaks or TSS overlapping these will be ignored. *.bed
|
|---|
autosom_ref_file
file
|
A file containing autosomal reference names, one per line. The names must match the reference names in the alignment file exactly, or the metrics based on counts of autosomal alignments will be wrong. |
|---|
json
tuple
meta
map
|
Groovy Map containing sample information e.g. [ id:'test', single_end:false ] |
|---|---|
*.ataqv.json
file
|
The JSON file to which metrics will be written. |
problems
tuple
meta
map
|
Groovy Map containing sample information e.g. [ id:'test', single_end:false ] |
|---|---|
*.problems
file
|
If given, problematic reads will be logged to a file per read group, with names derived from the read group IDs, with ".problems" appended. If no read groups are found, the reads will be written to one file named after the BAM file. *.problems
|
versions_ataqv
tuple
${task.process}
string
|
The name of the process |
|---|---|
ataqv
string
|
The name of the tool |
echo \$(ataqv --version)
eval
|
The expression to obtain the version of the tool |
| Tool | Description | Homepage |
|---|---|---|
| ataqv | ataqv is a toolkit for measuring and comparing ATAC-seq results. It was written to help understand how well ATAC-seq assays have worked, and to make it easier to spot differences that might be caused by library prep or sequencing. | https://github.com/ParkerLab/ataqv/blob/master/README.rst |
| Version | 0.0.0-6c4ed3a |
|---|---|
| Commit ID | 6c4ed3a220310b905a1fc9d04f05be2e0837142b |
| Release Date | 23 Apr 2026 15:02:55 (UTC) |
| Download URL | https://registry.nextflow.io/api/v1/modules/nf-core%2Fataqv%2Fataqv/0.0.0-6c4ed3a/download |
| OCI Store URL | https://public.cr.seqera.io/v2/nextflow/plugin/modules/nf-core/ataqv/ataqv/blobs/sha256:835be66a2229be33aebb8f8257f89822f84e65a2ca2b7ff4086c8f5240f9d4ef |
| Size | 3.8 KB |
| Checksum | sha256:835be66a2229be33aebb8f8257f89822f84e65a2ca2b7ff4086c8f5240f9d4ef |
| Downloads | 3 |
| Version | Date | Status | Downloads | Size |
|---|---|---|---|---|
| 0.0.0-6c4ed3a | 23 Apr 2026 15:02:55 (UTC) | 3 | 3.8 KB | |
| 0.0.0-3fc6d40 | 22 Apr 2026 15:02:07 (UTC) |