User: thomas.e

gravatar for thomas.e
thomas.e100
Reputation:
100
Status:
Trusted
Location:
Last seen:
1 year, 8 months ago
Joined:
2 years, 2 months ago
Email:
t*******@wehi.edu.au

Posts by thomas.e

<prev • 17 results • page 1 of 2 • next >
1
vote
1
answer
748
views
1
answers
Comment: C: Output files in the input directory
... Perfect, thanks! (Ensure this value has at least 20 characters (it has 16). ...
written 20 months ago by thomas.e100
0
votes
1
answer
748
views
1
answers
Comment: C: Output files in the input directory
... Thanks - although I did tag it as CWL when I submitted it. ...
written 20 months ago by thomas.e100
2
votes
1
answer
748
views
1
answer
Output files in the input directory
... Hello, I'm using snver which creates its output next to the input files, not in the directory where the program is running. There are no options to control this. I've been racking my brain for 1.5 days to figure out how can I can gather that output. The only thing I've found is a vague post suggest ...
cwl written 20 months ago by thomas.e100 • updated 20 months ago by Michael R. Crusoe1.6k
1
vote
1
answer
574
views
1
answers
Answer: A: tabix and CWL
... I was able to solve the problem by requiring the input file to be in the work directory in my tool requirements: - class: InitialWorkDirRequirement listing: [ $(inputs.inputFile) ] ...
written 2.0 years ago by thomas.e100
1
vote
1
answer
574
views
1
answer
tabix and CWL
... I'm trying to incorporate tabix into a workflow and I'm getting: [job gridss-tabix] /stornext/HPCScratch/home/thomas.e/tmp/tmpdR3yDK$ tabix \ --preset \ vcf \ /stornext/HPCScratch/home/thomas.e/tmp/tmp5etQrA/stg4113c1c5-9ba1-49ff-a6de-d9444c432acc/S1_R1.trimmed.sorted.human.gridss.vcf. ...
cwl written 2.0 years ago by thomas.e100
2
votes
3
answers
1.0k
views
3
answers
Answer: A: How process inputs based on a filename pattern using CWL
... For others looking at this thread, this is how I solved the problem. There may be better ways. Basically, I ran my single file workflow as a sub-workflow in a step that scatters across the input files. I did not attempt to get CWL to scan directories for input files, so I will build the input file ...
written 2.0 years ago by thomas.e100
0
votes
1
answer
1.0k
views
1
answers
Comment: C: How do I pass literals in CWL workflows?
... I think this is only for the CommandLineTool where it is not appropriate to set a default. ...
written 2.0 years ago by thomas.e100
0
votes
1
answer
1.0k
views
1
answers
Comment: C: How do I pass literals in CWL workflows?
... So a case of "broken as designed". Seems to me other literals should be allowed. ...
written 2.0 years ago by thomas.e100
2
votes
1
answer
617
views
1
answer
Does CWL have a search path for commadlinetools?
... I'd like to setup a shared source for command line tools at our site and have people use them in individual workflows. For example: mystep: run: mytool.cwl etc Is it part of the CWL spec that it can search a path, analogous to $PATH, $CLASSPATH or $PYTHONPATH? The documentation seems to imply ...
cwl written 2.0 years ago by thomas.e100 • updated 22 months ago by Michael R. Crusoe1.6k
1
vote
1
answer
1.0k
views
1
answer
How do I pass literals in CWL workflows?
... I want to pass a literal to a tool, for example, the number of threads, in a workflow step. The parameter is defined as an optional int in the tool itself: threads: type: int? inputBinding: prefix: --threads If I do this in the workflow: threads: valueFrom: 4 cwl ...
cwl written 2.0 years ago by thomas.e100 • updated 2.0 years ago by awilke197220

Latest awards to thomas.e

No awards yet. Soon to come :-)

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 514 users visited in the last hour