James Gatter
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Recent activity by James Gatter
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Thanks Allie! I found that even if the Arrays aren't marked as Array types in the data table, Cromwell will still accept them so long as they are surrounded by square brackets and delimited by comm...
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Is there any way to automitically parse a .tsv cell that contains a delimiter into an Array? For example turn text ["item1,item2,item3"] into an Array[String] = ["item1", "item2", "item3"]? I real...
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I accidentally removed dev snapshot 10, sorry! If you want to look at the dev version, make sure you are looking at 9, I believe that is the same as alexandria/dropseq_cumulus/1. I think just looki...
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Hi Jason, The methods should be publicly viewable but I've shared the both tools with you just in case. Hope that helps! Oh and the dev snapshot that fails is 9, not 11! James
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Hi Jason, So for delocalization in the log, the wrong files are being delocalized. For example, read_string("metadata.txt") should have looked inside metadata.txt for the path to the desired file, ...
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Hey Jason, I ran it in alexandria/dropseq_cumulus/1. sco.scp.metadata.txt and other files are generated by Cumulus workflow, but they are wrapped in the Array[File] output_scp_files. In dropseq_cum...
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From yesterday and today, we've had 4 or 5 people in our lab encounter this problem when using cumulus/bcl2fastq and cumulus/dropseq_workflow. It seems that some tasks complete delocalization succe...
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Thanks Sushma!
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They seemed to have fixed it!!!https://github.com/DataBiosphere/terra-docker/blob/master/terra-jupyter-bioconductor/CHANGELOG.md
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With a new runtime it still didn't work! `Sys.getenv()` prints only the text below. I think maybe I'm using one of the old custom images (us.gcr.io/broad-dsp-gcr-public/terra-jupyter-bioconductor:0...
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