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View Code? Open in Web Editor NEWThis is the CWL version of the 2GC pipeline.
License: GNU General Public License v3.0
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references have not a valid path in the CWL file
Hi @Athanaseus,
I was looking again at workflux/workflUX#40 and tried to check whether the issue common-workflow-language/cwltool#1241 it's depending on has been resolved.
However, when running:
cwltool --validate "https://raw.githubusercontent.com/Athanaseus/2gc-pipeline/master/selfcal_simulation.cwl"
With the latest version of cwltool, I get:
INFO /usr/local/bin/cwltool 3.0.20200324120055
ERROR Tool definition failed validation:
https://raw.githubusercontent.com/Athanaseus/2gc-pipeline/master/selfcal_simulation.cwl:359:1: checking field
`steps`
https://raw.githubusercontent.com/Athanaseus/2gc-pipeline/master/selfcal_simulation.cwl:423:3: checking object
`https://raw.githubusercontent.com/Athanaseus/2gc-pipeline/master/selfcal_simulation.cwl#bdsf_fits2lsm`
https://raw.githubusercontent.com/Athanaseus/2gc-pipeline/master/selfcal_simulation.cwl:424:5: Field `run`
contains undefined
reference to
`https://raw.githubusercontent.com/home/athanaseus/Documents/gitPackages/Stimela/stimela/cargo/cab/bdsf_fits2lsm.cwl`
https://raw.githubusercontent.com/Athanaseus/2gc-pipeline/master/selfcal_simulation.cwl:556:3: checking object
`https://raw.githubusercontent.com/Athanaseus/2gc-pipeline/master/selfcal_simulation.cwl#crystalball`
https://raw.githubusercontent.com/Athanaseus/2gc-pipeline/master/selfcal_simulation.cwl:557:5: Field `run`
contains undefined
reference to
`https://raw.githubusercontent.com/home/athanaseus/Documents/gitPackages/Stimela/stimela/cargo/cab/crystalball.cwl`
https://raw.githubusercontent.com/Athanaseus/2gc-pipeline/master/selfcal_simulation.cwl:513:3: checking object
`https://raw.githubusercontent.com/Athanaseus/2gc-pipeline/master/selfcal_simulation.cwl#fitstool`
https://raw.githubusercontent.com/Athanaseus/2gc-pipeline/master/selfcal_simulation.cwl:514:5: Field `run`
contains undefined
reference to
`https://raw.githubusercontent.com/home/athanaseus/Documents/gitPackages/Stimela/stimela/cargo/cab/fitstool.cwl`
https://raw.githubusercontent.com/Athanaseus/2gc-pipeline/master/selfcal_simulation.cwl:412:3: checking object
`https://raw.githubusercontent.com/Athanaseus/2gc-pipeline/master/selfcal_simulation.cwl#pybdsf`
https://raw.githubusercontent.com/Athanaseus/2gc-pipeline/master/selfcal_simulation.cwl:413:5: Field `run`
contains undefined
reference to
`https://raw.githubusercontent.com/home/athanaseus/Documents/gitPackages/Stimela/stimela/cargo/cab/pybdsf.cwl`
https://raw.githubusercontent.com/Athanaseus/2gc-pipeline/master/selfcal_simulation.cwl:360:3: checking object
`https://raw.githubusercontent.com/Athanaseus/2gc-pipeline/master/selfcal_simulation.cwl#simms`
https://raw.githubusercontent.com/Athanaseus/2gc-pipeline/master/selfcal_simulation.cwl:361:5: Field `run`
contains undefined
reference to
`https://raw.githubusercontent.com/home/athanaseus/Documents/gitPackages/Stimela/stimela/cargo/cab/simms.cwl`
https://raw.githubusercontent.com/Athanaseus/2gc-pipeline/master/selfcal_simulation.cwl:373:3: checking object
`https://raw.githubusercontent.com/Athanaseus/2gc-pipeline/master/selfcal_simulation.cwl#simulator`
https://raw.githubusercontent.com/Athanaseus/2gc-pipeline/master/selfcal_simulation.cwl:374:5: Field `run`
contains undefined
reference to
`https://raw.githubusercontent.com/home/athanaseus/Documents/gitPackages/Stimela/stimela/cargo/cab/simulator.cwl`
https://raw.githubusercontent.com/Athanaseus/2gc-pipeline/master/selfcal_simulation.cwl:523:3: checking object
`https://raw.githubusercontent.com/Athanaseus/2gc-pipeline/master/selfcal_simulation.cwl#sofia`
https://raw.githubusercontent.com/Athanaseus/2gc-pipeline/master/selfcal_simulation.cwl:524:5: Field `run`
contains undefined
reference to
`https://raw.githubusercontent.com/home/athanaseus/Documents/gitPackages/Stimela/stimela/cargo/cab/sofia.cwl`
https://raw.githubusercontent.com/Athanaseus/2gc-pipeline/master/selfcal_simulation.cwl:432:3: checking object
`https://raw.githubusercontent.com/Athanaseus/2gc-pipeline/master/selfcal_simulation.cwl#tigger_convert`
https://raw.githubusercontent.com/Athanaseus/2gc-pipeline/master/selfcal_simulation.cwl:433:5: Field `run`
contains undefined
reference to
`https://raw.githubusercontent.com/home/athanaseus/Documents/gitPackages/Stimela/stimela/cargo/cab/tigger_convert.cwl`
https://raw.githubusercontent.com/Athanaseus/2gc-pipeline/master/selfcal_simulation.cwl:444:3: checking object
`https://raw.githubusercontent.com/Athanaseus/2gc-pipeline/master/selfcal_simulation.cwl#tmpyh9lrhqj`
https://raw.githubusercontent.com/Athanaseus/2gc-pipeline/master/selfcal_simulation.cwl:445:5: Field `run`
contains undefined
reference to
`https://raw.githubusercontent.com/tmp/tmpyh9lrhqj.cwl`
https://raw.githubusercontent.com/Athanaseus/2gc-pipeline/master/selfcal_simulation.cwl:384:3: checking object
`https://raw.githubusercontent.com/Athanaseus/2gc-pipeline/master/selfcal_simulation.cwl#wsclean`
https://raw.githubusercontent.com/Athanaseus/2gc-pipeline/master/selfcal_simulation.cwl:385:5: Field `run`
contains undefined
reference to
`https://raw.githubusercontent.com/home/athanaseus/Documents/gitPackages/Stimela/stimela/cargo/cab/wsclean.cwl`
https://raw.githubusercontent.com/Athanaseus/2gc-pipeline/master/selfcal_simulation.cwl:485:3: checking object
`https://raw.githubusercontent.com/Athanaseus/2gc-pipeline/master/selfcal_simulation.cwl#wsclean-1`
https://raw.githubusercontent.com/Athanaseus/2gc-pipeline/master/selfcal_simulation.cwl:486:5: Field `run`
contains undefined
reference to
`https://raw.githubusercontent.com/home/athanaseus/Documents/gitPackages/Stimela/stimela/cargo/cab/wsclean.cwl`
This is because the references to the cwl tools in the workflow are not valid anymore. Could you fix that? Then I will hunt again for the fix in cwltool.
Best wishes,
Kersten
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