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compare our results with how Janis does WDL→CWL conversions #6

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mr-c opened this issue Apr 21, 2021 · 1 comment

Open

1 task

compare our results with how Janis does WDL→CWL conversions #6

mr-c opened this issue Apr 21, 2021 · 1 comment

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mr-c commented Apr 21, 2021 •

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Limitations: PMCC-BioinformaticsCore/janis-core#69 (comment)

$ pip install janis-pipelines miniwdl
$ WDL=/home/michael/wdl2cwl/wdl2cwl/tests/wdl_files/bowtie_1.wdl \
   python -c 'from janis_core.ingestion.fromwdl import WdlParser; WdlParser.from_doc("$WDL").translate("cwl");'

One may need to add a runtime.disks entry of 1 if that is missing, due to PMCC-BioinformaticsCore/janis-core#93

Document any features we can convert that Janis cannot (and send them a link to our implementation for inspiration)

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mr-c commented Apr 26, 2021

PMCC-BioinformaticsCore/janis-core#69 is their work in progress for WDL import ; see the limitations section for more information

mr-c changed the title ~~explore Janis as a framework for achieving this~~ compare our results with how Janis does WDL→CWL conversions

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