User: Tom

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Tom530
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Posts by Tom

<prev • 93 results • page 3 of 10 • next >
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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 14 months ago by Tom530
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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 14 months ago by Tom530
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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 14 months ago by Tom530
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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 14 months ago by Tom530
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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 14 months ago by Tom530
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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 14 months ago by Tom530
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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 14 months ago by Tom530
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Comment: C: cwl: Multiple matches for output item that is a single file
... Please provide the related .cwl document. Use the 'Code Sample' button to format it. Please put more effort into your posts. You expect people to take the time to provide solutions to your questions, but you never provide even the most basic information. ...
written 14 months ago by Tom530
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Comment: C: CWL : output file refer to inputs param
... This will work for string inputs. I'm adding this in case somebody reading has to handle files. Let's say our input file is named "aspergillus.fastq". The `inputs` section is: inputs: reads: type: File inputBinding: prefix: -r Referencing the input: `$(inp ...
written 14 months ago by Tom530
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Comment: C: CWL :Append the ref input used in toolkit
... The answer regarding `InitialWorkDirRequirement` has already been given. But for anybody reading this in the future: The directory in which a CommandLineTool runs will only be determined after starting the job. You can, however, reference the directory in your cwl documents using `$(runtime.outdir)` ...
written 14 months ago by Tom530

Latest awards to Tom

Voter 12 weeks ago, voted more than 100 times.
Popular Question 7 months ago, created a question with more than 1,000 views. For CommandLineTool doesn't finish
Scholar 12 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
Teacher 12 months 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 13 months 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 13 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
Teacher 13 months 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 13 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 15 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 16 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 19 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 19 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 19 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 19 months ago, voted at least 25 times.
Scholar 19 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 19 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 2.3 years ago, asked a question with at least 3 up-votes. For CommandLineTool doesn't finish

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