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WDL Graph enhancements #3369
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Implemented by 8116851
Implemented by 8cab106
Fixed by 8cab106 |
@rodichenko |
WDL Graph enhancements:
Tasks from imported WDL files should be shown in the list of existing tasks in the Properties > Document Tasks list and Actions > Add Call.
It would be useful to show Task's inputs default values in Call (maybe as a hint) if the default value isn't changed in Call.
It would be useful to show Workflow's inputs as a white circle in case of input doesn't have value.
Input/output should be shown as a blue circle if it has any value independent of its connection to other input/output.
Construction
.*
isn't parsed for the call's output. Replacing call output names with a * should act as a match-all wildcard. (From draft-2 SPEC: The following syntax is deprecated but is still supported to maintain backward compatibility)For example: cram2filtered.wdl
output { FilterVariantTranches.* }
gives the errorError parsing wdl script: Line 158, column 29: mismatched input '.' expecting Identifier
.[Version 1.0] Compound types created by user using struct should be shown in the Type dropdown for Parameters.
Relative import should be supported.
[Version draft -2] Parameters specified inside Scatter should be handled as Declarations.
Bugs:
Unknown dependency issue
(?) :mitochondria-pipeline.wdl
For example: gatk4-rna-best-practices.wdl
Inputs for call MergeVCFs
input_vcfs
andinput_vcfs_indexes
have errorsunknown dependency HaplotypeCallerOutputVcf. Did you mean "HaplotypeCallerOutputVcf" (string value)?
andunknown dependency HaplotypeCallerOutputVcfIndex. Did you mean "HaplotypeCallerOutputVcfIndex" (string value)?
correspondingly.For example: PairedEndSingleSampleWf-fc-b37.wdl
Scatter's Item
mapped_bam_size
has errorunknown dependency SamToFastqAndBwaMemAndMba.output_bam. Did you mean "SamToFastqAndBwaMemAndMba.output_bam" (string value)?
For example: Exome_Workflow.wdl
Revert changes button doesn't work if the graph has issues.
[Version draft-2] Error
declaration "docker" of task "GetBwaVersion": Value required
for Call's, Workflow's input parameters. (for example: PairedEndSingleSampleWf-fc-b37.wdl[Version 1.0]
unknown dependency
issue when a custom structure nested within another custom structure is used in the parameter value.For example: WholeGenomeGermlineSingleSample.wdl
[Version 1.0]
unknown dependency
issue when declaration from if block is used in the parameter value.For example: WholeGenomeGermlineSingleSample.wdl
Workflow output parameters:
File? output_bam = provided_output_bam
File? output_bam_index = provided_output_bam_index
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