User: Tom
Tom • 50
- Reputation:
- 50
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- Trusted
- Location:
- Bielefeld University, CeBiTec, Germany
- Last seen:
- 3 months, 3 weeks ago
- Joined:
- 5 months, 2 weeks ago
- Email:
- t*******@googlemail.com
Posts by Tom
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... What is the context you are working in? There are some possibilities for (university) researchers to get access to government-funded cloud computing. One example would be ELIXIRs cloud services. ...
written 3 months ago by
Tom • 50
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C: CWL Workflow renaming outputs
... In case somebody comes to this thread looking for the second solution i mentioned: Here is a CommandLineTool i use for changing file names during a workflow.
cwlVersion: v1.0
class: CommandLineTool
baseCommand: mv
label: Changes the name of a file and returns the renamed file as out ...
written 4 months ago by
Tom • 50
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Answer:
A: CWL Workflow renaming outputs
... I am fairly new to cwl, so take everything i say with a grain (or even more) of salt.
First of all, the outputSource fields seem faulty. They do not correctly reference the two steps.
outputs:
outA:
type: File
outputSource: untarA/example_out
outB:
type: Fil ...
written 4 months ago by
Tom • 50
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C: CommandLineTool doesn't finish
... I'm having fun as well, but still struggle with lots of basic stuff. Do you have any recommendations regarding resources to learn cwl? I have worked my way through the CWL User Guide ( https://www.commonwl.org/user_guide/ ). I try consulting the cwl specification at https://www.commonwl.org/v1.0/ wh ...
written 5 months ago by
Tom • 50
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C: CommandLineTool doesn't finish
... Neat! I'm sure this will be helpful in making the final workflow more convenient to use. ...
written 5 months ago by
Tom • 50
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C: CommandLineTool doesn't finish
... Thank you so much for all the work you have put into this! Your implementation works for me as well. After some experimentation it seems that --preserve-entire-environment is the crucial part. Even my early attempts with messed up `outputs` finish if i set this flag (i get errors because of the faul ...
written 5 months ago by
Tom • 50
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C: CommandLineTool doesn't finish
... Unfortunately the code you provided seems to yield the same result.
Again, the tool seems stuck at this point:
[job basecallerBioStar.cwl] /tmp/tmpBOQSQ7$ read_fast5_basecaller.py \
--flowcell \
FLO-MIN107 \
--input \
/tmp/tmp6YtzwB/stgab4d9788-6039-49ee-abcb-2e ...
written 5 months ago by
Tom • 50
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C: CommandLineTool doesn't finish
... Thanks for the help! I'm currently working in a virtual machine which is hosted by our faculty. The VM is running a ubuntu image which was specifically built for (manually) doing the steps of a basecalling/assembly/polishing workflow. My goal is to automate this exact workflow using cwl. Only python ...
written 5 months ago by
Tom • 50
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C: CommandLineTool doesn't finish
... Thank you very much for your very elaborate answer!
**Regarding python and the script:**
read_fast5_basecaller.py seems to function only as an entry point for the whole basecalling process. I cannot get it to work using "python" as my base command in the way you described. Even manually invoking i ...
written 5 months ago by
Tom • 50
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... I'm new to cwl and not very experienced in programming in general, so please bear with me.
I have created CommandLineTool which is supposed to use Oxford Nanopore's albacore basecaller to generate .fastq-Files from .fast5 current data.
When using this CommandLineTool, it takes about five minutes t ...
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