avoid space in identifier

EBI-Metagenomics / workflow-is-cwl

This repository contains CWL descriptions of the various tools which will allow you to build workflows for the annotation of transcripts

https://www.elixir-europe.org/

Apache License 2.0

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avoid space in identifier #25

Closed stain closed 5 years ago

stain commented 5 years ago

CWL Viewer falls over with spaces in id:

file:///tmp/1542275784560-0/workflows/TranscriptomeAssembly-wf.cwl#run_assembly/single reads does not look like a valid URI, trying to serialize this will break.
file:///tmp/1542275784560-0/tools/Trinity/Trinity-V2.6.5.cwl#single reads does not look like a valid URI, trying to serialize this will break.
I'm sorry, I couldn't load this CWL file, try again with --debug for more information.
The error was: "file:///tmp/1542275784560-0/tools/Trinity/Trinity-V2.6.5.cwl#single reads" does not look like a valid URI, I cannot serialize this as N3/Turtle. Perhaps you wanted to urlencode it?

This fix renames single reads in Trinity tool.

stain commented 5 years ago

CWL Visualization after fix: https://view.commonwl.org/workflows/github.com/stain/workflow-is-cwl/tree/avoid-spaces/workflows/TranscriptomeAssembly-wf.cwl

TranscriptomeAssembly-wf.cwl

stain commented 5 years ago

Related to common-workflow-language/schema_salad#132 although this was not in an enum

hmenager commented 5 years ago

thanks a lot @stain!

arnaudmeng commented 5 years ago

Thank you very much @stain !!

mr-c commented 5 years ago

Huh,

Resolved 'workflows/FastQC-multifiles-wf.cwl' to 'file:///home/travis/build/mscheremetjew/workflow-is-cwl/workflows/FastQC-multifiles-wf.cwl'
Tool definition failed validation:
workflows/FastQC-multifiles-wf.cwl:18:1: checking field `steps`
workflows/FastQC-multifiles-wf.cwl:19:5:   checking object `workflows/FastQC-multifiles-wf.cwl#fastqc`
workflows/FastQC-multifiles-wf.cwl:26:5:     Field `run` contains undefined reference to `file:///home/travis/build/mscheremetjew/workflow-is-cwl/tools/FastQC/FastQC-v0.11.5.cwl`
The command "bash travis/workflow-cwl-validation-tests.sh" exited with 1.

But neither workflows/FastQC-multifiles-wf.cwl nor tools/FastQC/FastQC-v0.11.5.cwl is part of this PR..

mscheremetjew commented 5 years ago

@mr-c no worries. You are working on the assembly branch and for that branch the integration test was already failing even before you apply your changes. https://travis-ci.org/mscheremetjew/workflow-is-cwl/builds/435897848

hmenager commented 5 years ago

agree with @mscheremetjew. the fail isn't related to the PR from @stain, it is just an outdated tool link. we just need to replace FastQC-v0.11.5.cwl, FastQC-v0.11.7.cwl, don't we @mscheremetjew ?

hmenager commented 5 years ago

(therefore I think it should be merged, and the tool reference could be fixed but independently, right?)

mscheremetjew commented 5 years ago

@hmenager Merged it. Also I fixed the reference to the right version of FastQC. we'll find out what the integration test will say now.

hmenager commented 5 years ago

awesome, thanks!