Sehyun Oh

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3. combine outputs

Ok. I just added the email as a reader of my workspace (TOSC19-CNVWorkflow_master). Below are the submission ids for jobs with or without CreateFoFN. Tool with CreateFoFN >>> submission-id: 4ffed12...

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• June 26, 2019 01:32
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3. combine outputs

Hi Beri, There is no error - everything runs 'successfully'. But the outputs from SelectVariants never be used as a list of input files (= multiple -V arguments) for CombineVariants. So each sample...

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• June 25, 2019 21:02
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3. input type coercion

Thanks Beri! I missed it out but could fixed it providing a proper path. :) But I still have a same problem with recognizing MuTect outputs as SelectVariants inputs. Here is the error. 2019/06/12 0...

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• Edited June 12, 2019 01:13
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3. input type coercion

Thanks Beri! Move SelectVariants call in the scatter bracket fixed the above error. But it seems like SelectVariants can't recognize the output from MuTect1 task. Here is the error. 2019/06/11 20:0...

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• June 11, 2019 20:25
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3. Data entity type for MuTect

Hi Sushma, This is THE answer! ;) I don't recall exactly how I uploaded the data tables before, but apparently, they weren't linked properly. I uploaded them making sure the linking steps, and now ...

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• Edited June 05, 2019 20:22
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3. Localization of reference files

Hi Sushma, I made this tool worked by putting the index file in the same bucket, and actually that was my initial question: the related reference files (.dict, .idx etc.) need to be stored under th...

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• June 05, 2019 14:54
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3. Localization of reference files

I double-checked whether the permission was an issue, but it doesn't seem like. I tested on a tool that worked when I used related files (e.g. index file) stored in a same bucket. I copied the coms...

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• Edited June 05, 2019 06:37
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3. Changing machine type for my tool

Thanks for the kind answer on my silly question, Sushma! I totally forgot the runtime attributes in WDL. :p

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• Edited June 05, 2019 06:26
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3. Data entity type for MuTect

Sorry about posting a wrong output. This is what I got from mutect2_nio tool. Mutect2.tumor_reads_index - Expected single value for workflow input, but evaluated result set was emptyMutect2.tumor...

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• June 05, 2019 06:23
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3. Data entity type for MuTect

Hi Sushma, I tried this.case_sample.WXS_bam_path and this.case_sample.WXS_bai_path for tumor_reads and tumor_read_index attributes, respectively. It failed right away with the error below. M1_only....

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• June 04, 2019 21:42
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