User: Tom

gravatar for Tom
Tom50
Reputation:
50
Status:
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

<prev • 10 results • page 1 of 1 • next >
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Comment: C: <3000$ in funding for computer equipment. Should I save this for cloud computing
... 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 Tom50
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Comment: 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 Tom50
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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 Tom50
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Comment: 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 Tom50
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Comment: 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 Tom50
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Comment: 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 Tom50
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Comment: 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 Tom50
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Comment: 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 Tom50
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Comment: 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 Tom50
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CommandLineTool doesn't finish
... 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 ...
cwl written 5 months ago by Tom50 • updated 5 months ago by drkennetz360

Latest awards to Tom

Student 5 months ago, asked a question with at least 3 up-votes. For CommandLineTool doesn't finish

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