User: ionox0

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ionox0160
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Posts by ionox0

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Comment: C: toil stats under-reporting memory usage?
... It's actually the full sized hg19 reference, would you happen to be able to confirm the units for this command perchance? ...
written 1 day ago by ionox0160
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toil stats under-reporting memory usage?
... The output from `toil stats ` seems to be reporting values ~5000K (5Mb), but I believe it should be more like 5G file:///home/johnsoni/pipeline_0.0.39/ACCESS-Pipeline/cwl_tools/bwa-mem/bwa-mem.cwl Memory min med ave max total 5659K 59 ...
toil cwl written 1 day ago by ionox0160
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best practice for renaming file in CWL workflow
... I've been using this method to rename files at the end of a step: processed_fastq_1: type: File outputBinding: glob: ${ return '**/' + inputs.fastq1.basename } outputEval: | ${ self[0].basename = inputs.add_rg_SM + '_R1.fastq.gz'; ...
cwl written 1 day ago by ionox0160
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Comment: C: possible to show job names in toil stats command using cwl workflow
... I believe that this is a limitation specific to using CWL with toil I have a PR here to address this: https://github.com/DataBiosphere/toil/pull/2397 ...
written 11 days ago by ionox0160
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possible to show job names in toil stats command using cwl workflow
... I'm using toil 3.15.0 with a cwl workflow, and I was wondering if there was a way to have the `toil stats` command list the names of the jobs in the workflow, when my jobs are defined in CWL. Right now the output shows job names as one of "ResolveIndirect", "CWLGather" ,"CWLWorkflow", "CWLScatter", ...
toil cwl written 12 days ago by ionox0160 • updated 6 days ago by Michael R. Crusoe1.1k
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Comment: C: scatter over optional argument
... I assume that to apply the default value to all of the inputs we would need to specify this `adapters: [null, null, null...]`? ...
written 23 days ago by ionox0160
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Bottleneck for scattered subworkflows
... Hi I have a question regarding when steps are able to run in parallel. We noticed that sometimes all of the jobs from a scatter must complete before moving to the next I was wondering whether a scattered subworkflow can start before all the inputs to that step are available, or does a subworkflow ...
toil cwl written 26 days ago by ionox0160 • updated 25 days ago by Carlos Borroto1.8k
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Possible to combine inputs using valueFrom for scatter
... Is it possible to combine multiple inputs from another step using `valueFrom` so that they can be scattered over? For example something like: inputs: input_one: Directory input_two: Directory steps: a_step: run: ../../cwl_tools/noise/calculate_noise.c ...
cwl written 6 weeks ago by ionox0160 • updated 5 weeks ago by Michael R. Crusoe1.1k
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Comment: C: Purpose of secondaryFiles in InputParameter and CommandInputParameter
... a CommandLineTool with secondaryFiles in one of the CommandInputParameters cannot be used in a workflow I don't believe this should be a problem in CWL, this should be supported: inputs: input_bams: type: type: array items: File inputBinding: ...
written 6 weeks ago by ionox0160
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Comment: C: scatter over optional argument
... Thank you @bogdan! Would it also work with multiple elements in the list? As in would the `--illumina` value get applied to multiple jobs if `adapters: [null]`? Or will it only process the first pair of fastqs? ...
written 9 weeks ago by ionox0160

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Supporter 23 days ago, voted at least 25 times.
Popular Question 5 weeks ago, created a question with more than 1,000 views. For What is the recommended way to debug JavaScript in CWL?
Scholar 3 months ago, created an answer that has been accepted. For A: CWL: array of files as an input
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: InitialWorkDirRequirement error with array of Directories
Scholar 6 months ago, created an answer that has been accepted. For A: Taking directory path for reading as well as writing files
Scholar 6 months ago, created an answer that has been accepted. For A: What is the recommended way to debug JavaScript in CWL?
Scholar 8 months ago, created an answer that has been accepted. For A: Taking directory path for reading as well as writing files

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