✅ Refactor each process as module, and fix matched/unmatched mode

[juanesarango]

Following up with #2, in this branch I fix several things:

• refactor each process as module for better organization.
• fix the issue were outputs were not being cached and we relied on a conditional and symlink.
• fix the issues with optional outputs and optional inputs following nextflow patterns.
• each module has an unit test to check with matched and unmatched params.

├── assets
│   └── NO_FILE
├── bin
│   └── bin_cobalt.py
├── modules
│   ├── amber.nf
│   ├── cobalt.nf
│   ├── purple.nf
│   └── sage.nf
├── tests
│   ├── module.binCobalt.nf.test
│   ├── module.runAmber.nf.test
│   ├── module.runAmber.nf.test.snap
│   ├── module.runCobalt.nf.test
│   ├── module.runCobalt.nf.test.snap
│   ├── module.runPurple.nf.test
│   ├── module.runSage.nf.test
│   ├── nextflow.config
│   └── workflow.main.nf.test
├── main.nf
├── nextflow.config
├── nf-test.config
├── Dockerfile
└── README.md

[Copilot]

Copilot reviewed 43 out of 59 changed files in this pull request and generated 1 comment.

Files not reviewed (16)

• main.nf: Language not supported
• modules/amber.nf: Language not supported
• modules/cobalt.nf: Language not supported
• modules/purple.nf: Language not supported
• modules/sage.nf: Language not supported
• nextflow.config: Language not supported
• nf-test.config: Language not supported
• run_matched.sh: Language not supported
• run_sage.sh: Language not supported
• run_unmatched.sh: Language not supported
• tests/data/amber/TEST_TUMOR.amber.baf.pcf: Language not supported
• tests/data/amber/TEST_TUMOR.amber.qc: Language not supported
• tests/data/cobalt/TEST_NORMAL.cobalt.ratio.pcf: Language not supported
• tests/data/cobalt/TEST_TUMOR.cobalt.ratio.pcf: Language not supported
• tests/data/cobalt/binned_100_probes_0.5_LogR/TEST_NORMAL.cobalt.ratio.pcf: Language not supported
• tests/data/cobalt/binned_100_probes_0.5_LogR/TEST_TUMOR.cobalt.ratio.pcf: Language not supported

[ddomenico]

All very necessary changes, nice work! 👍 LGTM, let's try for some tests comparing matched runs to Battenberg.