Nextflow Registry | nf-core/velocyto@0.0.0-0c7146d

nf-core/velocyto @ 0.0.0-0c7146d

Velocyto is a library for the analysis of RNA velocity. velocyto.py CLI use Path(resolve_path=True) and breaks the nextflow logic of symbolic links. If in the work dir velocyto find a file named EXACTLY cellsorted_[ORIGINAL_BAM_NAME] it will skip the samtools sort step. Cellsorted bam file should be cell sorted with:

    samtools sort -t CB -O BAM -o cellsorted_input.bam input.bam

See module test for an example with the SAMTOOLS_SORT nf-core module. Config example to cellsort input bam using SAMTOOLS_SORT:

    withName: SAMTOOLS_SORT {
        ext.prefix = { "cellsorted_${bam.baseName}" }
        ext.args = '-t CB -O BAM'
    }

Optional mask must be passed with ext.args and option --mask This is why I need to stage in the work dir 2 bam files (cellsorted and original). See also velocyto tutorial

count rnaseq rna velocity bam

Latest version: 0.0.0-0c7146d

Total downloads: 1

Source: nf-core/modules

Authors: @tucano

Maintainers: @tucano

Summary

    samtools sort -t CB -O BAM -o cellsorted_input.bam input.bam

See module test for an example with the SAMTOOLS_SORT nf-core module. Config example to cellsort input bam using SAMTOOLS_SORT:

    withName: SAMTOOLS_SORT {
        ext.prefix = { "cellsorted_${bam.baseName}" }
        ext.args = '-t CB -O BAM'
    }

Optional mask must be passed with ext.args and option --mask This is why I need to stage in the work dir 2 bam files (cellsorted and original). See also velocyto tutorial

Get started

Add the following snippet to your workflow script to include this module.

include { VELOCYTO } from 'nf-core/velocyto'

License

MIT License

Process

`Name`	`VELOCYTO`

Input 2 channels

#1 tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'sample1' ]`
`barcodes` file	Valid barcodes file, to filter the bam `*.tsv.gz`
`bam` file	Sorted BAM/CRAM/SAM file `*.{bam,cram,sam}`
`sorted_bam` file	Cell sorted BAM/CRAM/SAM file generated with `samtools sort -t CB -O BAM -o cellsorted_possorted_genome_bam.bam possorted_genome_bam.bam` `*.bam`

`gtf` file	genome annotation file `*.gtf`

Output 2 channels

#1 loom tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'sample1' ]`
`*.loom` file	Loom file with counts divided in spliced/unspliced/ambiguous. `*.loom`
`*.velocyto.log` file	Loom file with counts divided in spliced/unspliced/ambiguous. `*.loom`

#2 versions

`versions.yml` file	File containing software versions `versions.yml`

Tool	Description	Homepage
velocyto	A library for the analysis of RNA velocity.	https://github.com/velocyto-team/velocyto.py

Version	0.0.0-0c7146d
Commit ID	135d883a43b1a2324b4112cd270cf22e20835533
Release Date	08 Apr 2026 19:22:20 (UTC)
Download URL	https://registry-stage.nextflow.io/api/v1/modules/nf-core%2Fvelocyto/0.0.0-0c7146d/download
OCI Store URL	https://public.cr.stage-seqera.io/v2/nextflow/plugin-stage/modules/nf-core/velocyto/blobs/sha256:66aba820996cfa3a6c58516d23444dd457a412bd4bdd993cf154197bcc008fb5
Size	3.3 KB
Checksum	sha256:66aba820996cfa3a6c58516d23444dd457a412bd4bdd993cf154197bcc008fb5
Downloads	1

Version	Date	Status	Downloads	Size	Diff
0.0.0-0c7146d	08 Apr 2026 19:22:20 (UTC)		1	3.3 KB	-