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CCBR / LOGAN

https://ccbr.github.io/LOGAN/
MIT License
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refactor directory structure #14

Closed kelly-sovacool closed 10 months ago

kelly-sovacool commented 10 months ago

Currently this repo does not follow the standard nextflow structure. Everything in workflow should be moved elsewhere.

workflow
├── modules
│   ├── copynumber.nf
│   ├── germline.nf
│   ├── qc.nf
│   ├── splitbed.nf
│   ├── structural_variant.nf
│   ├── trim_align.nf
│   ├── variant_calling.nf
│   ├── variant_calling_tonly.nf
│   ├── workflows.nf
│   └── workflows_tonly.nf
├── resources
│   ├── fastq_screen.conf
│   ├── hg38_v0_wgs_calling_regions.hg38.bed
│   ├── hg38_v0_wgs_calling_regions.hg38.interval_list
│   └── split_Bed_into_equal_regions.py
└── scripts
    ├── flowcell_lane.py
    └── RScripts
        ├── combineAllSampleCompareResults.R
        ├── predictGender.R
        └── sampleCompareAncestoryPlots.R

These files should instead be laid out like:

.
├── assets
│   ├── hg38_v0_wgs_calling_regions.hg38.bed
│   └── hg38_v0_wgs_calling_regions.hg38.interval_list
├── bin
│   ├── combineAllSampleCompareResults.R
│   ├── flowcell_lane.py
│   ├── predictGender.R
│   ├── sampleCompareAncestoryPlots.R
│   └── split_Bed_into_equal_regions.py
├── conf
│   └── fastq_screen.conf
├── main.nf
├── modules
│   ├── copynumber.nf
│   ├── germline.nf
│   ├── qc.nf
│   ├── splitbed.nf
│   ├── structural_variant.nf
│   ├── trim_align.nf
│   ├── variant_calling.nf
│   ├── variant_calling_tonly.nf
│   ├── workflows.nf
│   └── workflows_tonly.nf
...

You can also add a top level subworkflows/ directory if needed.