User: Tom
Tom • 130
- Reputation:
- 130
- Status:
- Trusted
- Location:
- Bielefeld University, CeBiTec, Germany
- Last seen:
- 2 days, 2 hours ago
- Joined:
- 8 months, 3 weeks ago
- Email:
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Posts by Tom
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... I have no idea either! I'm not great at cwl yet. Just facing my own cwl-reated issues almost daily atm, and your threads often come up when i'm looking for solutions. Thank you for providing so many answers! ...
written 5 days ago by
Tom • 130
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... The solution is running cwltool with the `--enable-ext` flag. ...
written 6 days ago by
Tom • 130
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... I just wanted to drop by to say i love that you always take the time to come back and explain, even after solving the issue for yourself. ...
written 6 days ago by
Tom • 130
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... You're welcome!
Please use the checkmark-button on the left to "accept" the answer, so the thread will be marked as solved. ...
written 6 days ago by
Tom • 130
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... You reference `$(inputs.sequences)` in your `InitialWorkDirRequirement` as well as your `outputBinding`. "seqences" does not show up in your `inputs` field though. Hence the error occurs.
If i understand the workflow correctly, then it should be `$(inputs.reference)` / `$(inputs.reference.basename) ...
written 7 days ago by
Tom • 130
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... I have never used amazons workflow service, so i can't directly answer your question. There is, however, a number of pipeline frameworks which can run CWL-Workflows and support amazon web services. [Toil][1] comes to mind, which should be able to automatically mange your aws-resources and distribute ...
written 12 days ago by
Tom • 130
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... Using `InitialWorkDirRequirement` with a `writable:` field set to `true` solves the problem. CWLtool seems to copy all files into a temporary directory and deepbinner is then able to move them out of there.
requirements:
InlineJavascriptRequirement: {}
InitialWorkDirRequirement:
...
written 12 days ago by
Tom • 130
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Comment:
C: CWL Workflow removing input files
... In case it is of interest: When running the tool in Docker it fails because it cannot move the input files out of their directories.
Using `InitialWorkDirRequirement` with `writable: true` solves the problem. ...
written 12 days ago by
Tom • 130
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... The place were you invoke is most likely not referenced in the $PATH environment variable. This means if you call `sh writer.sh` then `writer.sh` has to be in the directory you are calling `sh` from.
However, CWL creates a temporary directory (in your example it was `/tmp/tmpmht4svls` ) where it cop ...
written 15 days ago by
Tom • 130
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... Hi fellow pipeline enthusiast,
Is the script named "writer.sh" or "search.sh"?
In the error you posted, the shell seems to throw the error `search.sh: No such file or directory`. I guess it can't find the script, does nothing except throw the error message and CWL complains because no output file i ...
written 15 days ago by
Tom • 130
Latest awards to Tom
Scholar
6 days ago,
created an answer that has been accepted.
For A: CWL to write into for writing lines one from one file to new file
Scholar
6 days ago,
created an answer that has been accepted.
For A: CWL to write into for writing lines one from one file to new file
Supporter
12 days ago,
voted at least 25 times.
Scholar
12 days ago,
created an answer that has been accepted.
For A: CWL to write into for writing lines one from one file to new file
Scholar
15 days ago,
created an answer that has been accepted.
For A: CWL to write into for writing lines one from one file to new file
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