nf-core/sequenzautils/bam2seqz @ 0.0.0-0c7146d
Summary
Sequenza-utils bam2seqz process BAM and Wiggle files to produce a seqz file
Get started
Add the following snippet to your workflow script to include this module.
include { SEQUENZAUTILS_BAM2SEQZ } from 'nf-core/sequenzautils/bam2seqz'
License
MIT License
Process
Name
|
SEQUENZAUTILS_BAM2SEQZ |
|---|
Input
3 channels
#1
tuple
meta
map
|
Groovy Map containing sample information e.g. [ id:'test', single_end:false ] |
|---|---|
normalbam
file
|
BAM file from the reference/normal sample *.{bam}
|
tumourbam
file
|
BAM file from the tumour sample *.{bam}
|
fasta
file
|
Reference FASTA file *.{fasta}
|
|---|
wigfile
file
|
GC content wiggle file *.{wig.gz}
|
|---|
Output
2 channels
#1
seqz
tuple
meta
map
|
Groovy Map containing sample information e.g. [ id:'test', single_end:false ] |
|---|---|
*.gz
file
|
Seqz file *.{seqz.gz}
|
#2
versions
versions.yml
file
|
File containing software versions versions.yml
|
|---|
| Tool | Description | Homepage |
|---|---|---|
| sequenzautils | Sequenza-utils provides 3 main command line programs to transform common NGS file format - such as FASTA, BAM - to input files for the Sequenza R package. The program - bam2seqz - process a paired set of BAM/pileup files (tumour and matching normal), and GC-content genome-wide information, to extract the common positions with A and B alleles frequencies. | https://sequenza-utils.readthedocs.io/en/latest/index.html |
| Version | 0.0.0-0c7146d |
|---|---|
| Commit ID | 135d883a43b1a2324b4112cd270cf22e20835533 |
| Release Date | 08 Apr 2026 19:13:26 (UTC) |
| Download URL | https://registry-stage.nextflow.io/api/v1/modules/nf-core%2Fsequenzautils%2Fbam2seqz/0.0.0-0c7146d/download |
| OCI Store URL | https://public.cr.stage-seqera.io/v2/nextflow/plugin-stage/modules/nf-core/sequenzautils/bam2seqz/blobs/sha256:f15e3e76b9053e03b75ed406d6591e407912cfb3baeeafa0165f48556bd28d63 |
| Size | 2.5 KB |
| Checksum | sha256:f15e3e76b9053e03b75ed406d6591e407912cfb3baeeafa0165f48556bd28d63 |
| Downloads | 1 |
| Version | Date | Status | Downloads | Size | Diff |
|---|---|---|---|---|---|
| 0.0.0-0c7146d | 08 Apr 2026 19:13:26 (UTC) | 1 | 2.5 KB | - |