Provided high level descriptions for tasks and workflows without such docs

[SHuang-Broad]

[kvg]

@SHuang-Broad to come up with the task ownership list for documentation responsibilities.

[SHuang-Broad]

15 root level WDLs

WDLs/root level workflows

CanuRunner.wdl
RaconRunner.wdl
QuastRunner.wdl
GuppyRunner.wdl
TestCromwell.wdl
MedakaRunner.wdl
NanopolishRunner.wdl
PB10xSingleFlowcell.wdl
ONT10xSingleFlowcell.wdl
TrioBinChildLongReads.wdl
PBCCSOnlySingleFlowcell.wdl
PB10xSingleProcessedSample.wdl
ONTWholeGenomeSingleFlowcell.wdl
PBCCSWholeGenomeSingleFlowcell.wdl
PBCLRWholeGenomeSingleFlowcell.wdl

subworkflows

WDL FILE	LINE NUMBER	SUB-WORKFLOW
AlignedMetrics.wdl	6	workflow AlignedMetrics
AssembleMT.wdl	6	workflow AssembleMT
AssignChildLongReads.wdl	5	workflow AssignChildLongReadsGivenParentalKmerStats
C3POa.wdl	6	workflow C3POa
CallSVs.wdl	5	workflow CallSVs
CallSmallVariants.wdl	6	workflow CallSmallVariants
Canu.wdl	5	workflow CorrectTrimAssemble
CollectParentsKmerStats.wdl	6	workflow CollectParentsKmerStats
DeepVariantLR.wdl	84	workflow TestCallDeepVariant
DownloadFromSRA.wdl	21	workflow DownloadFromSRA
Figures.wdl	7	workflow Figures
GATKBestPractice.wdl	15	workflow GATKBestPraciceForLR
Guppy.wdl	5	workflow Guppy
Nanopolish.wdl	5	workflow PolishAssembly
Peregrine.wdl	5	workflow Peregrine
PhaseReads.wdl	5	workflow PhaseReads
UnalignedMetrics.wdl	6	workflow UnalignedMetrics

28 WDLs in "./tasks/"

Canu.wdl
Utils.wdl
C3POa.wdl
Guppy.wdl
Quast.wdl
Racon.wdl
Medaka.wdl
PBUtils.wdl
CallSVs.wdl
Figures.wdl
ONTUtils.wdl
NanoPlot.wdl
Finalize.wdl
Peregrine.wdl
Nanopolish.wdl
AlignReads.wdl
PhaseReads.wdl
AssembleMT.wdl
DeepVariantLR.wdl
AlignedMetrics.wdl
AssembleTarget.wdl
DownloadFromSRA.wdl
GATKBestPractice.wdl
UnalignedMetrics.wdl
AnnotateAdapters.wdl
CallSmallVariants.wdl
AssignChildLongReads.wdl
CollectParentsKmerStats.wdl

[SHuang-Broad]

Assignment

Everyone, please pick the workflows that you authored and generate a check list on which

• root level workflows
• sub-workflows

and since all except utility WDLs are self-contained at this stage,

• all tasks in the picked WDL files.

And while we are addressing this issue, please also do the following in your PRs:

• remove commented out code blocks
• provide parameter_meta for all tasks. Note that while doing this, I came to the compromise that not all tasks need these, but all workflows and all tasks that are referenced out of its defining files must do.

Based on history, I've generated the following assignment. Feel free to pick more or unassign yourself if I made a mistake.

[SHuang-Broad]

@ericsong

Root level

• [x] CanuRunner.wdl
• [x] RaconRunner.wdl
• [x] QuastRunner.wdl
• [x] GuppyRunner.wdl
• [x] MedakaRunner.wdl
• [x] NanopolishRunner.wdl

Task level

• [x] Canu.wdl
• [x] Guppy.wdl
• [x] Quast.wdl
• [x] Racon.wdl
• [x] Medaka.wdl
• [x] Nanopolish.wdl

[SHuang-Broad]

@SHuang-Broad

Root level

• [x] TrioBinChildLongReads.wdl
• [x] PBCCSOnlySingleFlowcell.wdl

Task level

• [x] CallSVs.wdl
• [x] Peregrine.wdl
• [x] AlignReads.wdl
• [x] DeepVariantLR.wdl
• [x] DownloadFromSRA.wdl
• [x] GATKBestPractice.wdl
• [x] CallSmallVariants.wdl
• [x] AssignChildLongReads.wdl
• [x] CollectParentsKmerStats.wdl

[SHuang-Broad]

@kvg

Root level

• [ ] TestCromwell.wdl
• [ ] PB10xSingleFlowcell.wdl
• [ ] ONT10xSingleFlowcell.wdl
• [ ] PB10xSingleProcessedSample.wdl
• [x] PBCCSWholeGenomeSingleFlowcell.wdl
• [x] PBCLRWholeGenomeSingleFlowcell.wdl
• [ ] ONTWholeGenomeSingleFlowcell.wdl

1-off tasks?

The following tasks exist in root level workflows. Consider if they should be moved to "tasks/".

WORKFLOW	LINE NUMBER	TASK
TestCromwell.wdl	13	task TestCromwellOnGCS
ONT10xSingleFlowcell.wdl	251	task AnnotateAdapters
PB10xSingleProcessedSample.wdl	200	task RevertBam
PB10xSingleProcessedSample.wdl	243	task SplitBam
PB10xSingleProcessedSample.wdl	284	task GetRunInfo

Task level

• [ ] Utils.wdl
• [ ] C3POa.wdl
• [ ] PBUtils.wdl
• [ ] Figures.wdl
• [ ] ONTUtils.wdl
• [ ] NanoPlot.wdl
• [ ] Finalize.wdl
• [ ] PhaseReads.wdl
• [ ] AssembleMT.wdl
• [ ] AssembleTarget.wdl
• [ ] AlignedMetrics.wdl
• [ ] UnalignedMetrics.wdl
• [ ] AnnotateAdapters.wdl

[SHuang-Broad]

closed by #424