Allow for multiple pairwise comparisons, within one run

[slsevilla]

Description of feature

Currently the pipeline allows for a single pairwise comparison (control vs treatment). Feature addition will allow for multiple comparisons to be made.

Current workflow

• input sample_manifest (sample | fastq_1 | fastq_2 | treat_or_ctrl)
• run pipeline N=1 with single control group, single contrast group

Proposed workflow

• input project_manifest (sample | fastq_1 | fastq_2 | treat_or_ctrl | libraryID | groupID)
• split project_manifest into N sample_manifests (sample | fastq_1 | fastq_2 | treat_or_ctrl), by groupID col
• create nextflow.config files with updated information (IE libraryID from project_manifest)
• run pipeline N=unique(groupID) with single control group, single contrast group
• all results will go to the same dir structure

Needed features

• add new project_manifest check
• add module to create sample_manifests
• add functionality in cruise wrapper to submit multiple runs

[kelly-sovacool]

This proposal looks good! Only thing I would change is instead of having this logic handled by the wrapper, we can do it all in nextflow and not have to submit multiple pipeline runs.

[slsevilla]

Agreed - better plan!