nf-core/mudskipper/bulk @ 0.0.0-3fc6d40
Summary
Convert genomic BAM/SAM files to transcriptomic BAM/RAD files.
Get started
Add the following snippet to your workflow script to include this module.
include { MUDSKIPPER_BULK } from 'nf-core/mudskipper/bulk'
License
MIT License
Process
Name
|
MUDSKIPPER_BULK |
|---|
Input
4 channels
#1
tuple
meta
map
|
Groovy Map containing sample information e.g. |
|---|---|
bam
file
|
Name-Sorted BAM/CRAM/SAM file *.{bam,cram,sam}
|
index
directory
|
Annotation index created by mudskipper/index |
|---|
gtf
file
|
Annotation file *.{gtf,gff,gff3}
|
|---|
rad
string
|
File type |
|---|
Output
3 channels
#1
bam
tuple
meta
map
|
Groovy Map containing sample information e.g. |
|---|---|
${prefix}.bam
file
|
Sorted BAM file *.bam
|
#2
rad
tuple
meta
map
|
Groovy Map containing sample information e.g. |
|---|---|
${prefix}.rad
file
|
RAD file *.rad
|
#3
versions
versions.yml
file
|
File containing software versions versions.yml
|
|---|
| Tool | Description | Homepage |
|---|---|---|
| mudskipper | mudskipper is a tool for converting genomic BAM/SAM files to transcriptomic BAM/RAD files. | https://github.com/OceanGenomics/mudskipper |
| Version | 0.0.0-3fc6d40 |
|---|---|
| Commit ID | 6c4ed3a220310b905a1fc9d04f05be2e0837142b |
| Release Date | 22 Apr 2026 15:23:10 (UTC) |
| Download URL | https://registry.nextflow.io/api/v1/modules/nf-core%2Fmudskipper%2Fbulk/0.0.0-3fc6d40/download |
| OCI Store URL | https://public.cr.seqera.io/v2/nextflow/plugin/modules/nf-core/mudskipper/bulk/blobs/sha256:2bb3f3528a9e96667e52397516687e632c7965d5032c6efd9823c04e5ff9adeb |
| Size | 2.7 KB |
| Checksum | sha256:2bb3f3528a9e96667e52397516687e632c7965d5032c6efd9823c04e5ff9adeb |
| Downloads | 3 |
| Version | Date | Status | Downloads | Size |
|---|---|---|---|---|
| 0.0.0-6c4ed3a | 23 Apr 2026 15:32:27 (UTC) | 3 | 2.7 KB | |
| 0.0.0-3fc6d40 | 22 Apr 2026 15:23:10 (UTC) | 3 | 2.7 KB | |
| 0.0.0-0c7146d | 08 Apr 2026 19:20:18 (UTC) | 3 | 2.7 KB |