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LieberInstitute / BiocMAP

Our typical analysis steps for WGBS data, starting from FASTQ reads and ending with the construction of bsseq objects. Created using nextflow
http://research.libd.org/BiocMAP/
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Bismark genome preparation should be performed conditionally #18

Closed Nick-Eagles closed 3 years ago

Nick-Eagles commented 3 years ago

Currently, in the second module, bismark_genome_preparation is run here as a required step upon first execution of the module (or whenever new annotation files are used). While this is not terribly problematic, it is a waste of time for many use cases, especially when MethylDackel is the preferred default tool to use for methylation extraction. Ideally, bismark_genome_preparation should only be run when new annotation is used AND the --use_bismark option is specified, very similarly to how lambda-pseudoalignment-related workflow steps are run conditionally based on specification of the --with_lambda option. This may require creation of a new process.

Nick-Eagles commented 3 years ago

bismark_genome_preparation is only required for alignment with bismark, which isn't even performed by this pipeline. I've removed its usage entirely in this commit, making this issue obsolete.