Open bshifaw opened 1 year ago
Requirements for each workflow
➜ 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
I'll take on two
ONT/Epigenomics/ONTMethylation.wdl
TechAgnostic/VariantCalling/LRCNVs.wdl
I'll start with these:
I can work with LRJointCallGVCFs.wdl
Requirements for each workflow