modules/velocyto
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_${bam.baseName}" }
ext.args = '-t CB -O BAM'
}
Optional mask must be passed with ext.args
and option --mask
This is why I need to stage in the work dir 2 bam files (cellsorted and original).
See also velocyto turorial
Description
Velocyto is a library for the analysis of RNA velocity. velocyto.py CLI use
Path(resolve_path=True)
and breaks the nextflow logic of symbolic links.
If in the work dir velocyto find a file named EXACTLY cellsorted_[ORIGINAL_BAM_NAME]
it will skip the samtools sort step.
Cellsorted bam file should be cell sorted with:
samtools sort -t CB -O BAM -o cellsorted_input.bam input.bam
See module test for an example with the SAMTOOLS_SORT nf-core module. Config example to cellsort input bam using SAMTOOLS_SORT:
withName: SAMTOOLS_SORT {
ext.prefix = { "cellsorted_${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 turorial