James Gatter

1. Terra on Google Cloud
2. Data
3. Managing data with tables

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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• October 28, 2020 21:31
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1. Terra on Google Cloud
2. Data
3. Managing data with tables

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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• Edited October 28, 2020 20:49
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1. Community
2. General Discussion
3. WDL function read_string() not properly delocalizing paths as files

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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• Edited April 08, 2020 15:59
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1. Community
2. General Discussion
3. WDL function read_string() not properly delocalizing paths as files

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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• Edited April 08, 2020 15:56
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1. Community
2. General Discussion
3. WDL function read_string() not properly delocalizing paths as files

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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• Edited April 08, 2020 13:49
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1. Community
2. General Discussion
3. WDL function read_string() not properly delocalizing paths as files

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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• Edited April 06, 2020 18:07
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WDL function read_string() not properly delocalizing paths as files

Hi,   I’m having an issue with my workflow related to delocalization by Cromwell/Terra.   I have a file named metadata.txt which simply contains a 1-line pathname to the actual file I want to deloc...

• James Gatter
• Edited April 08, 2020 13:33
• 2 followers
• 11 comments
• 1 vote

1. Community
2. General Discussion
3. Jobs say they're running but they do not appear to be

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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• Edited March 09, 2020 20:53
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1. Platform-wide (security, status and updates)
2. Service Notifications
3. Service Incident - December 18, 2019

Thanks Sushma!

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• December 18, 2019 16:47
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