User: Peter vH

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Peter vH130
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http://www..sanbi.ac.za
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7 years, 9 months ago
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Posts by Peter vH

<prev • 19 results • page 2 of 2 • next >
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From multiple VCF files to multiple sequence alignment?
... Hi there I have multiple VCF files generated from variant calling on sequenced bacteria (*M. tuberculosis*). I would like to create a multiple sequence alignment file (as a step towards computing a phylogeny of the samples) by combining the reference genome with the VCFs. Before I put time and effo ...
vcf alignment bacterial written 4.3 years ago by Peter vH130 • updated 4.2 years ago by Biostar ♦♦ 20
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Comment: C: Using the Directory type in Common Workflow Language
... Some of the CWL folks have directed "support" questions to Biostars recently on the understanding that when they get answered here the answers are easy for people to find in the future. I'll alert the community to this question though. ...
written 4.5 years ago by Peter vH130
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Comment: C: Using the Directory type in Common Workflow Language
... By the way I used this input to the above CWL: testdir: class: Directory location: file:///home/pvh/Documents/code/cwltool/foo ...
written 4.5 years ago by Peter vH130
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Using the Directory type in Common Workflow Language
... In trying to solve a problem posed by Stuti Agrawal, I've been trying to make a working example using the Directory type of CWL v1.0 as an input and not getting very far. I tried writing a tool that pics up the files from a Directory and adds them to a zip file. Note, this doesn't add the directory, ...
cwl written 4.5 years ago by Peter vH130 • updated 4.4 years ago by Michael R. Crusoe1.8k
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Comment: C: Mixing CWL workflow versions (including draft-3 tool in v1.0 workflow)
... Thanks! It works now, here's the final single-step **v1.0** workflow: cwlVersion: v1.0 class: Workflow requirements: - class: StepInputExpressionRequirement inputs: reads1: File reads2: File slidingw: type: string default: "4:30" minl: ...
written 4.5 years ago by Peter vH130
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Comment: C: Mixing CWL workflow versions (including draft-3 tool in v1.0 workflow)
... For interest's sake, here is a single-step **draft-3** workflow that works: cwlVersion: cwl:draft-3 class: Workflow requirements: - class: StepInputExpressionRequirement inputs: - id: reads1 type: File - id: reads2 type: File - id: slidingw ...
written 4.5 years ago by Peter vH130
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Mixing CWL workflow versions (including draft-3 tool in v1.0 workflow)
... I'm working on a CWL v1.0 workflow, using the GGR-cwl trimmomatic tool (https://github.com/Duke-GCB/GGR-cwl/blob/master/trimmomatic/trimmomatic.cwl) as one of the steps. That tool is a draft-3 specification one, which I understand is still parsed by `cwltool`. Here is my current workflow file: ...
cwl written 4.5 years ago by Peter vH130 • updated 4.5 years ago by Michael R. Crusoe1.8k
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Example cwl workflow (for v1.0)?
... I'm trying to write a CWL workflow that will do a simple trim and map procedure on some bacterial short read data that I've got. For the trimming I'm planning on using trimmomatic and I have modified the Duke-GCB trimmomatic tool slightly for this purpose (see https://github.com/pvanheus/GGR-cwl/blo ...
cwl written 4.5 years ago by Peter vH130 • updated 4.5 years ago by Michael R. Crusoe1.8k
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Answer: A: Orthomclpairs Problems -----Orthomcl
... When you do the blast search, do you do all vs all blast (i.e. not just blast of query set vs a different set)? If you don't, you get these three zero length files.  ...
written 6.2 years ago by Peter vH130

Latest awards to Peter vH

Popular Question 2.5 years ago, created a question with more than 1,000 views. For Mixing CWL workflow versions (including draft-3 tool in v1.0 workflow)
Commentator 2.7 years ago, created a comment with at least 3 up-votes. For C: BWA MEM vs BOWTIE2 , which is best?
Commentator 2.7 years ago, created a comment with at least 3 up-votes. For C: BWA MEM vs BOWTIE2 , which is best?
Scholar 2.7 years ago, created an answer that has been accepted. For A: Exclusive parameters in a workflow
Popular Question 2.8 years ago, created a question with more than 1,000 views. For Using the Directory type in Common Workflow Language
Popular Question 3.1 years ago, created a question with more than 1,000 views. For Using the Directory type in Common Workflow Language
Popular Question 3.1 years ago, created a question with more than 1,000 views. For Example cwl workflow (for v1.0)?

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