This Nextflow DSL2 pipeline calls variants on long read alignment. It is run after sanger-tol/readmapping in the Sanger ToL production suite but with options to run on unaligned reads.
This subworkflow takes the aligned CRAM file location and estimates the location of all the other required files. If not ToL file structure, then the input file is needed.
For the first milestone, it requires the genome and CRAM aligned files, which can be provided as params, or in samplesheet, or using ToL ID.
Some engineering required. Logical workflow which decides the different ways input is accepted.
Description of feature
This subworkflow takes the aligned CRAM file location and estimates the location of all the other required files. If not ToL file structure, then the input file is needed.
For the first milestone, it requires the genome and CRAM aligned files, which can be provided as params, or in samplesheet, or using ToL ID.
Some engineering required. Logical workflow which decides the different ways input is accepted.