User: Tom

gravatar for Tom
Tom500
Reputation:
500
Status:
Trusted
Location:
Bielefeld University, CeBiTec, Germany
Last seen:
12 hours ago
Joined:
1 year, 3 months ago
Email:
t*******@googlemail.com

Posts by Tom

<prev • 85 results • page 1 of 9 • next >
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Answer: A: Missing CWL files in a Directory when passed as input
... I'm not able to test this right now, but my guess would be: Everything works as intended CWL-wise, meaning a symlink to the directory is created in the temporary directory where step two is carried out. Calling `ls` with the `-l `flag causes it to not follow symlinks, so nothing is listed. Best reg ...
written 12 days ago by Tom500
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Comment: C: Input specific output filenames
... Hi again! `inputs.seqfile` is an array. While the elements in the array probably have a basename, the array itself does not. Would taking the name of the first file in the array be sufficient for your purposes? inputs.seqfile[0].basename Also note that `basename` includes the file extension, ...
written 12 days ago by Tom500
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Comment: C: Input specific output filenames
... Please post the complete tool, i'm sure we can solve this. ...
written 15 days ago by Tom500
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Answer: A: Input specific output filenames
... See https://www.commonwl.org/user_guide/05-stdout/index.html You can choose any name you want for the file created from `stdout`. Using a javascript expression, you can easily derive the name from other parameters. For your case (using an `inputs` section i made up) this might look like inputs ...
written 16 days ago by Tom500
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Comment: C: Why do researchers prefer to use Oxford Nanopore Technologies' 1D and sequencing
... The 1D² basecaller is guessing which of the reads are pairs (meaning one read is the complement of the other). Reads might get matched erroneously. If you have access to the ONT community forums there is a post explaining this problem in depth. I have heard people say they feel 1D² is just not wort ...
written 5 weeks ago by Tom500
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Comment: C: Change execution directory before running a tool (CWL)
... Alright, good to know! Have you tried passing the script's name as an argument (like in the example above) instead of using `inputBinding`? Because if the directories are created as planned and no job input for script is provided, i would expect cwltool to: - use default values for `script` and `da ...
written 5 weeks ago by Tom500
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Answer: A: Change execution directory before running a tool (CWL)
... Hi Andreas, i am not sure about the `InitialWorkDirRequirement` you are using. According to the CWL specs `entryname` is only supposed to overwrite the `basename` property of the entry, so i'm wondering if the "code" and "script" subdirectories are actually being created. If you know for a fact tha ...
written 5 weeks ago by Tom500
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Comment: C: Add an item from input to an output array in CWL
... I would be very happy to do so. Since i have to submit my master's thesis this month i'm a little stressed out and won't be able to take care of it right now. I have made a calendar entry to make sure i won't forget. I spent a lot of time reading and writing CWL documents in the past months. A more ...
written 6 weeks ago by Tom500
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Comment: C: Add an item from input to an output array in CWL
... This is great! I didn't know about `linkMerge`, wish i would have learned this sooner. ...
written 6 weeks ago by Tom500
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Comment: C: CWL: Array of strings in workflow
... Great, glad i could help! Feel free to ask if there is any problem implementing this. When first using `StepInputExpressionRequirement` i struggled for quite a while. If you were successful, please remember to mark the thread as solved by clicking on the appropriate button next to an answer that so ...
written 7 weeks ago by Tom500

Latest awards to Tom

Scholar 11 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
Teacher 11 days ago, created an answer with at least 3 up-votes. For A: samtools sort: failed to create temporary file "/BOredq/NA12878.sorted.bam.tmp.0
Teacher 5 weeks ago, created an answer with at least 3 up-votes. For A: samtools sort: failed to create temporary file "/BOredq/NA12878.sorted.bam.tmp.0
Scholar 6 weeks ago, created an answer that has been accepted. For A: CWL to write into for writing lines one from one file to new file
Teacher 6 weeks ago, created an answer with at least 3 up-votes. For A: samtools sort: failed to create temporary file "/BOredq/NA12878.sorted.bam.tmp.0
Scholar 7 weeks 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 3 months 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 4 months 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 months 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 7 months 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 7 months 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 7 months ago, voted at least 25 times.
Scholar 7 months 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 7 months ago, created an answer that has been accepted. For A: CWL to write into for writing lines one from one file to new file
Student 15 months ago, asked a question with at least 3 up-votes. For CommandLineTool doesn't finish

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