User: Michael R. Crusoe

Reputation:
1,810
Status:
Trusted
Location:
Common Workflow Language project
Website:
https://orcid.org/0000...
Twitter:
biocrusoe
Scholar ID:
Google Scholar Page
Last seen:
1 month, 1 week ago
Joined:
7 years, 11 months ago
Email:
m*************@gmail.com

Posts by Michael R. Crusoe

<prev • 216 results • page 1 of 22 • next >
0
votes
1
answer
103
views
1
answers
Answer: A: CWL: Min and max for tool input values (float,int)
... Constrains on input values has been proposed, but not yet implemented nor added to the CWL standards yet: https://github.com/common-workflow-language/common-workflow-language/issues/764 ...
written 5 weeks ago by Michael R. Crusoe1.8k
6
votes
0
answers
288
views
0
answers
News: CWL user support moving to https://cwl.discourse.group/; many thanks to Biostars for over 4 years of support!
... Dear Biostars, Thank you for over 4 years of supporting the Common Workflow Language project and its users. As CWL has grown beyond bioinformatics, we have moved to another forum site. Anyone with any question related to CWL, bio* related or not, is welcome to ask and answer questions (along with ...
thanks news cwl written 8 months ago by Michael R. Crusoe1.8k • updated 3 months ago by ATpoint36k
2
votes
2
answers
432
views
2
answers
Comment: C: CWL: Using the "EnvVarRequirement" to pass an environment variable to a script
... `/scripts/runfolder-check.sh: line 31: /scripts/runfolder-check.sh.dev.log: Read-only file system` The script is trying to write a log file in its directory. It should either use `$TMPDIR`, or write the log to a user specified path. ...
written 9 months ago by Michael R. Crusoe1.8k
2
votes
1
answer
307
views
1
answers
Answer: A: CWL: Does cwltool support to download both input file and its secondaryFiles rem
... Hello Linda, and thank you for your posting, Yes, this should work, but use `location` instead of `path` when specifying using URLs ref_file: location: http://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/GRCh38_reference_genome/GRCh38_full_analysis_set_plus_decoy_hla.fa ...
written 9 months ago by Michael R. Crusoe1.8k
2
votes
1
answer
324
views
1
answers
Answer: A: secondaryFiles where nameroot differs
... Hello Peter vH, I think there are two separate challenges here: 1) describing a File with secondaryFiles that don't share anything in common name-wise and 2) staging a File and its secondaries inside a named directory For (1), on can provide the plain name for each of the desired secondaryFiles ...
written 9 months ago by Michael R. Crusoe1.8k
2
votes
1
answer
385
views
1
answers
Comment: C: Input specific output filenames
... A simpler variation of the `stdout`: stdout: $(inputs.reads.nameroot)_console_log.txt ...
written 9 months ago by Michael R. Crusoe1.8k
1
vote
2
answers
372
views
2
answers
Answer: A: how do I default to /dev/null in CommandLineTool
... Another solution, using an empty file: cwlVersion: v1.0 class: CommandLineTool inputs: optional_file: type: File default: class: File size: 0 basename: empty contents: "" inputBinding: {} baseCommand: [ ...
written 10 months ago by Michael R. Crusoe1.8k
2
votes
2
answers
372
views
2
answers
Answer: A: how do I default to /dev/null in CommandLineTool
... Hello Azat Badretdin, You'll need to use a [CWL Javascript Expression](https://www.commonwl.org/user_guide/13-expressions/index.html) Here is an example: cwlVersion: v1.0 class: CommandLineTool requirements: InlineJavascriptRequirement: {} inputs: optional_fi ...
written 10 months ago by Michael R. Crusoe1.8k
1
vote
3
answers
1.1k
views
3
answers
Comment: C: Is there a schema for CWL inputs/job files?
... Hey Karl. Yep, you are very close to a valid schema salad representation for the `1st_tool.cwl`'s input section. You'll need to add `- $import: "schema_salad/metaschema/metaschema_base.yml"` to the beginning of the document and leave out the `Inputs` section, then the following will work: $ sc ...
written 10 months ago by Michael R. Crusoe1.8k
1
vote
0
answers
323
views
0
answers
Comment: C: cwltool "invalid field" error messages
... FYI, this sounds like an error in `cwltool`, I am investigating ...
written 11 months ago by Michael R. Crusoe1.8k

Latest awards to Michael R. Crusoe

Teacher 5 months ago, created an answer with at least 3 up-votes. For A: CWL: how to set default values
Appreciated 5 months ago, created a post with more than 5 votes. For A: Output going to stdout?
Scholar 7 months ago, created an answer that has been accepted. For A: Example cwl workflow (for v1.0)?
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: CWL: how to set default values
Scholar 12 months ago, created an answer that has been accepted. For A: Example cwl workflow (for v1.0)?
Voter 12 months ago, voted more than 100 times.
Scholar 12 months ago, created an answer that has been accepted. For A: Example cwl workflow (for v1.0)?
Teacher 13 months ago, created an answer with at least 3 up-votes. For A: CWL: how to set default values
Teacher 14 months ago, created an answer with at least 3 up-votes. For A: CWL: how to set default values
Appreciated 14 months ago, created a post with more than 5 votes. For A: Output going to stdout?
Scholar 14 months ago, created an answer that has been accepted. For A: Example cwl workflow (for v1.0)?
Scholar 15 months ago, created an answer that has been accepted. For A: Example cwl workflow (for v1.0)?
Commentator 15 months ago, created a comment with at least 3 up-votes. For C: CommandLineTool doesn't finish
Commentator 15 months ago, created a comment with at least 3 up-votes. For C: CommandLineTool doesn't finish
Teacher 15 months ago, created an answer with at least 3 up-votes. For A: CWL: how to set default values
Scholar 16 months ago, created an answer that has been accepted. For A: Example cwl workflow (for v1.0)?
Teacher 17 months ago, created an answer with at least 3 up-votes. For A: CWL: how to set default values
Scholar 17 months ago, created an answer that has been accepted. For A: Example cwl workflow (for v1.0)?
Scholar 19 months ago, created an answer that has been accepted. For A: Mixing CWL workflow versions (including draft-3 tool in v1.0 workflow)
Scholar 19 months ago, created an answer that has been accepted. For A: Example cwl workflow (for v1.0)?
Teacher 19 months ago, created an answer with at least 3 up-votes. For A: CWL: how to set default values
Scholar 20 months ago, created an answer that has been accepted. For A: Example cwl workflow (for v1.0)?
Scholar 21 months ago, created an answer that has been accepted. For A: Example cwl workflow (for v1.0)?
Teacher 23 months ago, created an answer with at least 3 up-votes. For A: CWL: how to set default values
Commentator 23 months ago, created a comment with at least 3 up-votes. For C: 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: 562 users visited in the last hour