User: jeltje.van.baren

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Posts by jeltje.van.baren

<prev • 9 results • page 1 of 1 • next >
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Answer: A: CWL: How to parse output of steps in workflow
... This last solution is perfect for my particular problem, thanks! I fully agree on not untarring whole directories if you need a single file, but this is for a DREAM challenge and I'm only allowed one index.tar.gz for the full workflow. Other steps need other files. Looking forward to the v1.1 rele ...
written 2.6 years ago by jeltje.van.baren80
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CWL: How to parse output of steps in workflow
... I have a workflow that starts with untarring a file into a directory. In the second step, I need one file from that directory as parameter ` --genomeDir` for my tool. Currently this is solved like so: Workflow snippet: star: run: ../tools/STAR.cwl in: index: tar/ou ...
workflow cwl written 2.6 years ago by jeltje.van.baren80
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Comment: C: hard copies instead of symlinks from InitialWorkDirRequirement ? - SOLVED
... I was using an older version of cwl. Once I upgraded, the problem went away. One thing I couldn't figure out for a while is how to call initialWorkDir properly. Here's the relevant piece of cwl: requirements: - class: InlineJavascriptRequirement - class: InitialWorkDirRequirement ...
written 2.7 years ago by jeltje.van.baren80
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In CWL, how to make arrays optional input
... How do I make an array optional input? This works: cwlVersion: v1.0 class: CommandLineTool inputs: insertSize: type: type: array items: int inputBinding: prefix: -s separate: true inputBinding: p ...
cwl written 2.8 years ago by jeltje.van.baren80 • updated 2.8 years ago by karl.nordstrom90
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hard copies instead of symlinks from InitialWorkDirRequirement ? - SOLVED
... NOTE: The below was due to using an older version of cwl-runner. I am trying to debug https://github.com/Sage-Bionetworks/SMC-RNA-Examples/blob/master/workflow/smcFusionQuant-INTEGRATE-workflow.cwl One of the issues is that I can't figure out how to get the input and output of a tool in the same l ...
cwl written 2.9 years ago by jeltje.van.baren80
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Comment: C: Convert A Psl File To A Sam File And Also Write Sequences To The Sam File?
... See https://www.biostars.org/p/4957/#210232 for details ...
written 3.2 years ago by jeltje.van.baren80
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Answer: A: Conversion Of Blat Output To Sam/Bam
... This `psl2sam.pl` solution no longer works very well. I verified this by uploading the input psl and the output sam (converted to bam) to the UCSC genome browser. Since this page comes up as the first hit on Google, here's a better solution using [bedtools][1], which you can `apt-get` on ubuntu ...
written 3.2 years ago by jeltje.van.baren80 • updated 10 weeks ago by RamRS24k
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Comment: A: Tutorial: Analyze exome Copy number variation (CNV) in single patient or in popu
... I use Varscan on exome data, so it seems to me that I should the exome target list as Marker list - maybe by taking the exon mid point (since markerPosition only allows one coordinate). Thoughts? Incidentally, I've found that using the exome target list as whitelist in samtools mpileup greatly redu ...
written 4.1 years ago by jeltje.van.baren80
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Comment: C: Absolute/Hapseg on Exome (WES) Data?
... I second Christian's request. If I get it running, maybe I can answer your question :-) ...
written 5.3 years ago by jeltje.van.baren80

Latest awards to jeltje.van.baren

Appreciated 2.7 years ago, created a post with more than 5 votes. For A: Conversion Of Blat Output To Sam/Bam
Teacher 2.9 years ago, created an answer with at least 3 up-votes. For A: Conversion Of Blat Output To Sam/Bam

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