User: Tom

gravatar for Tom
Tom530
Reputation:
530
Status:
Trusted
Location:
Last seen:
3 weeks ago
Joined:
2 years, 2 months ago
Email:
t*******@googlemail.com

Posts by Tom

<prev • 93 results • page 2 of 10 • next >
1
vote
1
answer
403
views
1
answers
Comment: C: Input specific output filenames
... Please post the complete tool, i'm sure we can solve this. ...
written 11 months ago by Tom530
4
votes
1
answer
403
views
1
answers
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 11 months ago by Tom530
0
votes
0
answers
315
views
0
answers
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 12 months ago by Tom530
0
votes
1
answer
348
views
1
answers
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 12 months ago by Tom530
1
vote
1
answer
348
views
1
answers
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 12 months ago by Tom530
2
votes
2
answers
563
views
2
answers
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 12 months ago by Tom530
1
vote
2
answers
563
views
2
answers
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 12 months ago by Tom530
0
votes
2
answers
449
views
2
answers
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 12 months ago by Tom530
0
votes
2
answers
449
views
2
answers
Comment: C: CWL: Array of strings in workflow
... I'm not sure i understand. If the arrays are not inputs to the workflow but different for different steps, then you want to hard-code them into the workflow, right? Shouldn't a `StepInputExpression` be what you are looking for? (I have added an example to my suggestion from yesterday to make it more ...
written 12 months ago by Tom530
0
votes
1
answer
295
views
1
answers
Answer: A: Strict validation for input and inputBinding values with same position?
... The CWL specification has a section on how cwl-runners have to handle this situation: https://www.commonwl.org/v1.1/CommandLineTool.html#Input_binding I'm not sure i understand correctly, but i think the runner can either use the order of the items in the document (message > file in your case) o ...
written 12 months ago by Tom530

Latest awards to Tom

Voter 6 weeks ago, voted more than 100 times.
Popular Question 5 months ago, created a question with more than 1,000 views. For CommandLineTool doesn't finish
Scholar 11 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 11 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 12 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 12 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 12 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 12 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 13 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 14 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 17 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 18 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 18 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 18 months ago, voted at least 25 times.
Scholar 18 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 18 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 2.2 years ago, asked a question with at least 3 up-votes. For CommandLineTool doesn't finish

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 712 users visited in the last hour