User: Tom

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Tom520
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Bielefeld University, CeBiTec, Germany
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1 day, 9 hours ago
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Posts by Tom

<prev • 86 results • page 2 of 9 • next >
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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 11 weeks ago by Tom520
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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 11 weeks ago by Tom520
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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 11 weeks ago by Tom520
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Answer: A: CWL: Array of strings in workflow
... You can tackle this at tool-level, by adding this as an argument to your `CommandLineTool` (see field `arguments` [here][1]) arguments: - valueFrom: ["CollectAlignmentSummaryMetrics"] prefix: PROGRAM= separate: false position: 10 Alternatively, use `StepInputExpre ...
written 11 weeks ago by Tom520
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Answer: A: Add an item from input to an output array in CWL
... In the `valueFrom: $(self.concat(inputs.input_added_in_step2))` expression, `inputs` will reference the inputs of the workflow step, not the input section at the beginning of the workflow document. Looking at the `valueFrom` section in [this segment of the specifications][1] leads me to believe ther ...
written 11 weeks ago by Tom520
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Comment: C: Processing Raw Nanopore Data
... Can you tell us about the GPU you have in your system? If it doesn't have an adequate GPU and you are forced to do CPU basecalling then i would recommend using guppys "fast" config. CPU basecalling with the default config takes days to weeks on a single machine. ...
written 3 months ago by Tom520
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Answer: A: samtools sort: failed to create temporary file "/BOredq/NA12878.sorted.bam.tmp.0
... Your cwl-runner is writing everything to a temporary directory before collecting the final output and placing it in /Bigdata. The solution depends on which cwl-runner you are using. For cwltool, you could use the command line parameters `--tmpdir-prefix` and `--tmp-outdir-prefix` and specify a devi ...
written 3 months ago by Tom520
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Comment: C: cwl: Source 'outputtbi' of type ["null", "File"] may be incompatible
... Hi! I am sure there is an easy fix for this. Please post your workflow and tool (olympus.cwl). I see that you have already posted the workflow below, but i'm not willing to try and decipher it as long as it doesn't have any line breaks. General Answer: The `type` of the item your workflow is tryin ...
written 3 months ago by Tom520
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Comment: C: How can I Write the workflow including too much inputs params
... I'm not sure i understand correctly. If you mark input parameters as optional like this inputs: reads: type: File? inputBinding: prefix: -r Then the workflow won't have to provide these inputs to the tool. ...
written 3 months ago by Tom520
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Comment: C: cwl: Multiple matches for output item that is a single file
... This is definitely a correct way of catching multiple .fq.gz files. I'm not familiar with the style of notation you used in the first version, i can't figure out why it failed. Sorry! Maybe somebody else can help. ...
written 3 months ago by Tom520

Latest awards to Tom

Scholar 5 weeks 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 5 weeks 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 9 weeks 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 10 weeks 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 10 weeks 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 11 weeks 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 4 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 5 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 7 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 8 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 8 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 8 months ago, voted at least 25 times.
Scholar 8 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 8 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 16 months ago, asked a question with at least 3 up-votes. For CommandLineTool doesn't finish

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