User: ngsbioinformatics

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Posts by ngsbioinformatics

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Comment: A: Parse CWL to graph data structure or database?
... I too am looking for something like what you described. I want to create a workflow from a python script (or any language for the matter), convert to a digraph and store. The digraph can then be converted to CWL or WDL or anything else. We would also need to import the digraph from CWL to conve ...
written 11 weeks ago by ngsbioinformatics30
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Comment: C: CWL Workflow renaming outputs
... I believe in your outputs, you actually need to specify: outputs: outA: type: File outputSource: untarA/example_out outB: type: File outputSource: untarB/example_out However, I'm also not clear on how you would rename example_out so they don't conflict. ...
written 10 months ago by ngsbioinformatics30
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How to plot workflow as image
... I see cwltool has an option '--print-dot', but it doesn't seem to print anything. I'm trying to use this with my workflow that works: cwltool --print-dot bwa-mapping-workflow.cwl bwa-mapping-workflow-input.yml and cwltool --print-dot bwa-mapping-workflow.cwl Is there a way to get a plot o ...
cwl written 3.9 years ago by ngsbioinformatics30 • updated 3.4 years ago by Michael R. Crusoe1.8k
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Answer: A: Genomic Bam To Transcriptome Bam
... I believe you want this tool sam-xlate from UBU: https://github.com/mozack/ubu/wiki It doesn't take a GTF, but rather a BED file in refFlat (I believe) format. ...
written 4.6 years ago by ngsbioinformatics30
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Answer: A: Which Bioinformatic Friendly Pipeline Building Framework?
... Of all these pipeline infrastructures, which allow you to distribute parts of the pipeline to compute nodes and other parts on a single node, such as the GATK Exome Pipeline. You can map the samples on different nodes, but when doing indel realigning or recalibration, its best to have all the sample ...
written 4.8 years ago by ngsbioinformatics30 • updated 7 months ago by RamRS27k
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Comment: C: Which Bioinformatic Friendly Pipeline Building Framework?
... Make is good but not scalable in any way. Cluster support for shared and distributed filesystems (such as Amazon) are pretty much not possible with make. ...
written 4.8 years ago by ngsbioinformatics30 • updated 7 months ago by RamRS27k
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Answer: A: Plink: Quick Way To Combine Two Datasets Using Only Common Markers
... I would do this in R (as you can do this for an infinite number of sets by doing an intersection of the intersection...) common.snps = intersect(map1$V2,map2$V2) write.table(common.snps, file="common_snps.txt", sep="\t", col.names=F, row.names=F, quote=F )   ...
written 6.0 years ago by ngsbioinformatics30

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Popular Question 2.2 years ago, created a question with more than 1,000 views. For How to plot workflow as image

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