Nextflow Modules
Showing module(s) with keyword "rna velocity"
| Module | Keywords | Description |
|---|---|---|
| nf-core/velocyto | count rnaseq rna velocity bam | 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: ```bash 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: ```groovy 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](https://velocyto.org/velocyto.py/tutorial/cli.html#notes-on-first-runtime-and-parallelization) |