nf-core/atlas/pmd @ 0.0.0-6c4ed3a
Summary
Estimate the post-mortem damage patterns of DNA
Get started
Add the following snippet to your workflow script to include this module.
include { ATLAS_PMD } from 'nf-core/atlas/pmd'
License
MIT License
Name
|
ATLAS_PMD |
|---|
meta
map
|
Groovy Map containing sample information e.g. [ id:'test', single_end:false ] |
|---|---|
bam
file
|
Single input BAM file *.bam
|
bai
file
|
The BAI file for the input BAM file *.bai
|
pool_rg_txt
file
|
Optional. Provide the names of read groups that should be merged for PMD estimation. All read groups that should be pooled listed on one line, separated by any white space. Other read groups will be recalibrated separately. *.txt
|
fasta
file
|
The reference genome provided as FASTA file *.fasta
|
|---|
fai
file
|
The FAI file for the reference genome FASTA file *.fai
|
|---|
table
tuple
meta
map
|
Groovy Map containing sample information e.g. [ id:'test', single_end:false ] |
|---|---|
*_PMD_Table.txt
file
|
For all possible transitions the ratio of the transition counts, which are taken from the _counts.txt table, over the total amount of the base that was mutated, for each position and readgroup *_PMD_Table.txt
|
counts
tuple
meta
map
|
Groovy Map containing sample information e.g. [ id:'test', single_end:false ] |
|---|---|
*_PMD_Table_counts.txt
file
|
The counts of all possible transitions for each read position (or up to a certain position, see specific command length) *_PMD_Table_counts.txt
|
empiric
tuple
meta
map
|
Groovy Map containing sample information e.g. [ id:'test', single_end:false ] |
|---|---|
*_PMD_input_Empiric.txt
file
|
A list of pmd patterns estimated with the empirical method for each readgroup *_PMD_input_Empiric.txt
|
exponential
tuple
meta
map
|
Groovy Map containing sample information e.g. [ id:'test', single_end:false ] |
|---|---|
*_PMD_input_Exponential.txt
file
|
A list of pmd patterns estimated with the exponential method for each readgroup *_PMD_input_Exponential.txt
|
versions_atlas
tuple
${task.process}
string
|
The name of the process |
|---|---|
atlas
string
|
The name of the tool |
atlas | sed -e "2!d;s/.*Atlas //"
eval
|
The expression to obtain the version of the tool |
| Tool | Description | Homepage |
|---|---|---|
| atlas | ATLAS, a suite of methods to accurately genotype and estimate genetic diversity | https://bitbucket.org/wegmannlab/atlas/wiki/Home |
| Version | 0.0.0-6c4ed3a |
|---|---|
| Commit ID | 6c4ed3a220310b905a1fc9d04f05be2e0837142b |
| Release Date | 23 Apr 2026 15:02:59 (UTC) |
| Download URL | https://registry.nextflow.io/api/v1/modules/nf-core%2Fatlas%2Fpmd/0.0.0-6c4ed3a/download |
| OCI Store URL | https://public.cr.seqera.io/v2/nextflow/plugin/modules/nf-core/atlas/pmd/blobs/sha256:3b01d068e754d6d03336f8b70151979689d82690f72fdc3561a928032581dbe8 |
| Size | 3.1 KB |
| Checksum | sha256:3b01d068e754d6d03336f8b70151979689d82690f72fdc3561a928032581dbe8 |
| Downloads | 3 |
| Version | Date | Status | Downloads | Size |
|---|