Workflow Documentation

[bshifaw]

Requirements for each workflow

• Adding description in meta
• Adding Ref map file location to description (indicate this is for inter-organizational use: private)
• Adding input description in parameter_meta
• Add example workflow configuration (place in the future wdl_test folder)
• Confirm documentation page appears in the repos site

➜  pipelines
.
├── ONT
│   ├── Assembly
│   │   ├── ONTAssembleWithCanu.wdl  [Ryan]
│   │   └── ONTAssembleWithFlye.wdl  [Ryan]
│   ├── Epigenomics
│   │   └── ONTMethylation.wdl  [Steve]
│   ├── MultiAnalysis
│   │   ├── ONTPfHrp2Hrp3Status.wdl. 
│   │   └── ONTPfTypeDrugResistanceMarkers.wdl. 
│   ├── Preprocessing
│   │   ├── ONTBasecall.wdl  [Beri]
│   │   ├── ONTFlowcell.wdl. [Beri]
│   │   ├── ONTFlowcellFromMultipleBasecalls.wdl
│   │   └── ONTProcessBasecall.wdl
│   └── VariantCalling
│       └── ONTWholeGenome.wdl
├── PacBio
│   ├── Alignment
│   │   └── PBFlowcell.wdl  [Fabio]
│   ├── Assembly
│   │   └── PBAssembleWithHifiasm.wdl   [Fabio]
│   ├── Utility
│   │   ├── PBCCSIsoSeq.wdl   [Fabio]
│   │   ├── PBMASIsoSeqDemultiplex.wdl   [Fabio]
│   │   ├── PBMASIsoSeqQuantify.wdl   [Fabio]
│   │   └── TrioBinChildLongReads.wdl.  [Fabio]
│   └── VariantCalling
│       └── PBCCSWholeGenome.wdl. [Fabio]
└── TechAgnostic
    ├── Annotation
    │   └── AnnotateTranscriptomeWithGuide.wdl
    ├── Utility
    │   ├── CleanupIntermediate.wdl
    │   ├── ConvertToHailMT.wdl
    │   ├── DownloadFromFTP.wdl
    │   ├── DownloadFromSRA.wdl
    │   ├── DownloadFromWeb.wdl
    │   ├── FindBamIdentity.wdl
    │   ├── LRConvertBCF.wdl
    │   └── VerifyFingerprint.wdl
    └── VariantCalling
        ├── LRCNVs.wdl  [Steve]
        └── LRJointCallGVCFs.wdl

[SHuang-Broad]

I'll take on two

• ONT/Epigenomics/ONTMethylation.wdl
• TechAgnostic/VariantCalling/LRCNVs.wdl

[rlorigro]

I'll start with these:

• ONTAssembleWithCanu.wdl
• ONTAssembleWithFlye.wdl

[hangsuUNC]

I can work with LRJointCallGVCFs.wdl