User: bogdan.gavrilovic
bogdan.gavrilovic • 210
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Posts by bogdan.gavrilovic
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... Did you consider using StepInputExpressionRequirement (https://www.commonwl.org/v1.0/Workflow.html#StepInputExpressionRequirement)?
You can set a `valueFrom` using JS expression and transform a step input with $(self[0]) from, e.g. [ [ 1, 2 ] ] to [ 1, 2 ]. ...
written 9 weeks ago by
bogdan.gavrilovic • 210
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Answer:
A: Load/parse cwl in python
... You can use `pyyaml`.
Install with `pip install pyyaml`
Load a CWL (which can be in JSON or YAML format) using
with open(cwl_file_path, 'r') as cwl_file:
cwl_dict = yaml.safe_load(cwl_file)
This will return a python dict with all the fields. ...
written 8 months ago by
bogdan.gavrilovic • 210
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... I would suggest adding a simple `mv` command to the end of the command line, via arguments, e.g.
```
arguments:
- position: 1000
shellQuote: false
valueFrom: ' && mv $(inputs.fastq1.basename) $(inputs.add_rg_SM)_R1.fastq.gz'
```
then you could just glob `$(inputs.add ...
written 9 months ago by
bogdan.gavrilovic • 210
1
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1
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454
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Comment:
C: scatter over optional argument
... Yes, that is correct. ...
written 9 months ago by
bogdan.gavrilovic • 210
2
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1
answer
373
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1
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... This depends on where you run the workflow. Some executors have a feature to delete unnecessary intermediate files to save up on disk space during execution. Setting the secondary file on output of the first step would signal that the `^.bai` file is needed and should not be deleted. ...
written 11 months ago by
bogdan.gavrilovic • 210
0
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1
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... Hi,
There's two issues here.
1) Looks like the input for the step (workflow input) was not a list, but null(not defined). The scatter method must work with a list on input. At least an empty list should be provided `[ ]`.
2) If you scatter over an empty list, 0 commands will be execute ...
written 11 months ago by
bogdan.gavrilovic • 210
1
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1
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328
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... I suppose that you want to add this parameter to the command line somewhere. You can use `arguments` to add the desired default value if the original value is not set.
inputs:
- id: window
type:
type: record
fields:
- name: windowSize
...
written 12 months ago by
bogdan.gavrilovic • 210
1
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... Hi,
I think you have no reason for concern.
When an input/output type is defined as any list of types, e.g. `[string, File]` - it means that the item that appears on that input/output in execution is one of these possible types (unless input is a defined as `[wave, particle]`, in that case it ca ...
written 13 months ago by
bogdan.gavrilovic • 210
2
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1
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... Hi, seems to me like you are doing everything right regarding CWL.
Possible problem could be that when you scatter `fastqc_check.cwl`, two jobs are created and each job outputs the file with the same name `$(inputs.sample)_fastqc.summary`.
Try to change the `fastqc_check.cwl` tool to output some ...
written 13 months ago by
bogdan.gavrilovic • 210
1
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1
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430
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... The modified expression tool would look like this.
```
cwlVersion: v1.0
class: ExpressionTool
requirements: { InlineJavascriptRequirement: {} }
inputs:
a_File:
type: File
inputBinding:
loadContents: true
expression: |
${ return { "array_string": JSON.parse(inputs.a_File.content ...
written 13 months ago by
bogdan.gavrilovic • 210
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For A: Use filename found in an input Directory in a CommandLineTool
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For A: Use filename found in an input Directory in a CommandLineTool
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For A: Use filename found in an input Directory in a CommandLineTool
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15 months ago,
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For A: Use filename found in an input Directory in a CommandLineTool
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For A: Use filename found in an input Directory in a CommandLineTool
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For A: Use filename found in an input Directory in a CommandLineTool
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15 months ago,
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For A: Use filename found in an input Directory in a CommandLineTool
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