User: Tom

gravatar for Tom
Tom520
Reputation:
520
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Trusted
Location:
Bielefeld University, CeBiTec, Germany
Last seen:
3 weeks, 2 days ago
Joined:
1 year, 6 months ago
Email:
t*******@googlemail.com

Posts by Tom

<prev • 86 results • page 1 of 9 • next >
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Answer: A: CWL: Using the "EnvVarRequirement" to pass an environment variable to a script
... Hi Sehrish! There seems to be an issue with the `InitialWorkDirRequirement`. You cannot pass a string to the `listings` field. It has to be either files, directories or dirents. We can, however, build a `dirent` for an empty directory named after the `input_folder` string: requirements: ...
written 9 weeks ago by Tom520
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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 3 months ago by Tom520
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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 3 months ago by Tom520
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Comment: C: Input specific output filenames
... Please post the complete tool, i'm sure we can solve this. ...
written 3 months ago by Tom520
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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 3 months ago by Tom520
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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 4 months ago by Tom520
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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 4 months ago by Tom520
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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 4 months ago by Tom520
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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 4 months ago by Tom520
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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 4 months ago by Tom520

Latest awards to Tom

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
Teacher 3 months 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 4 months 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 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
Teacher 4 months 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 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 5 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 9 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 10 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 10 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 10 months ago, voted at least 25 times.
Scholar 10 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 10 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 18 months ago, asked a question with at least 3 up-votes. For CommandLineTool doesn't finish

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