User: bruce.moran

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bruce.moran260
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Posts by bruce.moran

<prev • 79 results • page 1 of 8 • next >
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Comment: C: CWL rerunning completed output
... Thanks Michael, appreciate your input. ...
written 15 days ago by bruce.moran260
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Comment: C: CWL rerunning completed output
... Only have a few months using Make so was assessing the alternatives. I read your paper on this, so appreciate your experience. Do you have anything written on your own preferred solution, especially for production? ...
written 17 days ago by bruce.moran260
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Comment: C: CWL rerunning completed output
... OK, very interesting. Your issue on Github is only a few months old, and caching is described as 'experimental' in the response, so I don't think this is going to be useful for production work I will be doing. Hopefully this will be part of next updates. Many thanks for the input, and the example. ...
written 17 days ago by bruce.moran260
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CWL rerunning completed output
... I like CWL, and would like to use it in a production setting. I am coming from a Make approach, whereby output is not remade unless datestamps of input determine this to be necessary. I cannot find any documentation on this aspect for CWL. I have read the 'Gentle Intro' twice end-to-end thinking thi ...
common workflow language cwl written 19 days ago by bruce.moran260 • updated 18 days ago by well30950
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Comment: C: CWL: print out command lines?
... +1, would like to be able to summarise the full workflow without running samples. Thought perhaps the CWL viewer could be used as a basis for this? ...
written 19 days ago by bruce.moran260
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Comment: C: Ensembl VEP 89 Output Format
... Thanks Emily. Out of curiosity, was that the default previously? I had just updated old scripts which never had that flag. ...
written 28 days ago by bruce.moran260
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Ensembl VEP 89 Output Format
... I have just updated to VEP v89 from v81. Previously the output was an annotated VCF, but now it is a strange, new format. Can someone advise on how to get the former? Thanks, Bruce. command: VCF="input.vcf" OUT=$(echo $VCF | sed 's/vcf/VEP89.vcf/') STATS=$(echo $VCF | sed 's/vcf/VEP8 ...
ensembl vep written 28 days ago by bruce.moran260 • updated 28 days ago by Emily_Ensembl13k
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Comment: C: Pipe BBMap reformat output into SAMtools
... My RTFM is strong (also helps that there is a good FM) ...
written 8 weeks ago by bruce.moran260
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Comment: C: Pipe BBMap reformat output into SAMtools
... Thought about that also, but yes, using kmers. ...
written 8 weeks ago by bruce.moran260
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Comment: C: Pipe BBMap reformat output into SAMtools
... Cool, I had to use addslash and underscore hence the reformat.sh, but good to know. ...
written 8 weeks ago by bruce.moran260

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