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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