
Beri
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Activity overview
Latest activity by Beri-
Beri commented,
So If there aren't any errors in the stderr and GATK says it was successful chances are it related to Cromwell/WDL. The WDL documentation has some info mentioning possible issues when using read_st...
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Beri commented,
Also, the repo you're pointing to is archived, it's best to use the latest version of the workflow found here.
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Beri commented,
In the WDL script the output block for the M2 task specifies two variables String tumor_sample = read_string("tumor_name.txt")String normal_sample = read_string("normal_name.txt") The read_string()...
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Beri commented,
The workflow log is showing a general message saying the workflow failed, specifically a task called "gtfToCallingIntervals". The you should be able to get more info on what happened in log files s...
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Beri commented,
The associated ticket is currently open. You can try the suggestions mentioned in the thread to help memory usage.
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Beri commented,
There is a cost to storing data in your workspace bucket, the cost is detailed in the workspace Dashboard tab on the right hand column. For more Terra questions please visit the Terra forum
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Beri commented,
Could you elaborate? The main outputs for this workflow are: CRAM, CRAM index, and CRAM MD5 GVCF and its GVCF index BQSR report Summary metrics; to read more about any particular metric, you can s...
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Beri commented,
Let's leave the disk multiplier at 25 for now. For task SamToFastqAndBwaMemAndMba in the WSSCC_alignment workflow increase the memory from 14 to 30 or how ever much you feel comfortable
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Beri commented,
The "https://api.firecloud.org/ga4gh/v1/tools/xegen:WSSCC_bamtocram/versions/1/plain-WDL/descriptor" file doesn't look correct, make sure you copied over the right file. If i'm not mistaken this is...
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Beri commented,
Thanks for sharing your fix!