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`workflow-tool.nf` and `tool.nf` are different. `tool.nf` has all the processes. `workflow-tool.nf` has a workflow that calls all the process. See examples here: https://github.com/uclahs-cds/pipeline-call-gSNP/tree/main/module
Generally, that's true though we don't necessarily have a formal guideline about this. We try to modularize processes and then create separate workflows (ex. call-gSNP has some core processes that are then used by the various workflows like single-sample mode, multi-sample mode, etc.).
For this case, we'll probably eventually want to have something like: bcftools.nf (for BCFtools processes), manta.nf (for Manta processes), delly.nf (for DELLY processes), workflow-manta.nf (defines just the workflow for Manta using processes from manta.nf, bcftools.nf, etc. as needed), workflow-delly.nf (workflow for DELLY using processes from delly.nf, bcftools.nf, etc. as needed). No need to change it in this PR though, it can be done with the separation of the tools in future development
Originally posted by @maotian06 in #76 (comment)
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