User: Tom
Tom • 520
- Reputation:
- 520
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- 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
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... 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
Tom • 520
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... 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
Tom • 520
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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
Tom • 520
1
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1
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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
Tom • 520
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... 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
Tom • 520
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... 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
Tom • 520
0
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1
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... 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
Tom • 520
1
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1
answer
219
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... 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
Tom • 520
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... 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
Tom • 520
1
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2
answers
275
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... This is great! I didn't know about `linkMerge`, wish i would have learned this sooner. ...
written 4 months ago by
Tom • 520
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For A: samtools sort: failed to create temporary file "/BOredq/NA12878.sorted.bam.tmp.0
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