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nrashi

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nrashi
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Rashi Naresh

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  • Hi @Tiffany_at_Broad ! Thanks for all the detailed information on Groups API and the linking with the web interface. Will check it out soon!
  • Hi @Geraldine_VdAuwera , was interested in knowing of the feature 'Support for JSON arrays in method configuration expressions' has been explained in the documentation somewhere for the users to see some examples? Thanks, Rashi
  • Thanks @Geraldine_VdAuwera !
  • Hi Jason, Thanks for testing, so was this not working earlier because of the Google updates? Also, since I was trying to make it work when the root entity type was set to sample_set, how is this different from setting it to sample, although in bot…
  • Thanks Jason! :)
  • Hi Jason, I just added you and Eddie on the method config! Thanks! Rashi
  • Hi Jason, I just added you to the project leidos-firecloud-eval/samtoolsindex_upscale5 and perhaps you can help me with choosing the right entity type - I was in an impression that making a sample_set out of two samples might help my purpose as Eddi…
  • Hi Jason, I ran the tool after making the changes to these metadata files and it seems to be running fine - using the sample_set as entity. However, while setting the expressions on the inputs and outputs on the method config edit page, how does a …
  • Hi Jason, Thanks for clarifying the order of files as well. I loaded participant.tsv > sample.tsv > sample_set_membership.tsv > sample_set_entity.tsv. I removed the extra TCGA_LUAD line from my sample_set_entity file as you suggested; I st…
  • Thanks Jason, I will try this out and see if removing one line from that file works.
  • @jneff Hi Jason, I would imagine that two rows were needed since am trying to upload two samples here - like in other tsv files one would need one participant per row. But if it only requires to mention once for the whole sample set, I can make that…
  • Hi Eddie, I already tried that. Those are the errors I get on uploading in the format as in documentation. Attached are the screenshots from the tsv files I'm trying to upload. I know there is an order in which these tsv files are uploaded, in that …
  • Hi Eddie, to run my tool on a bunch of bam files; what I understand from the documentation is that this will need a couple of TSV files, namely - sample_set_membership.txt where columns would be sample_set_id and sample_id. sample_id is where I can …
  • Hi Eddie, Are the technical issues resolved now which were limiting to run tasks on Firecloud? Thanks, Rashi
  • Most of those samples have data in the original workspace (TCGA_LUAD_ControlledAccess_V1-0_DATA) they were copied from in additional columns, so that is why I was expecting it be showing up in the destination workspace too.
  • I did try that, but those columns are also the only ones I see in the list too. Attached is a screenshot. I tried it in a new workspace I created, it works fine elsewhere though.
  • @esalinas Hi Eddie, thanks for answering my questions. The question about seeing all the data, sorry about not being so clear earlier - I created a protected data workspace, imported a sample from TCGA_LUAD_ControlledAccess_V1-0_DATA workspace into…
  • @esalinas While I'm trying to run the samtoolsindex tool on a TCGA file, the task failed and also when I click on the workspace's associated bucket, it fails to load as well. Do I need to add TSV files even if the data is copied from an already exi…
  • Also when I'm trying to import data from another workspace, it is not showing me all the data in the workspace copied for a sample; not all columns are displayed as present in the original TCGA workspace after I copy a sample in my workspace, howeve…
  • @esalinas Hi Eddie, if I'm making changes to a method configuration (something that a user uploaded) after I have imported it into a workspace, does the system also apply those changes in the original method configuration in the method repository as…
  • Thank you @esalinas , yes that makes sense now about how to pick and choose to add only a bunch of files from the data set and what address to give in the TSV files. Also it seems that there would be a need to add an input expression for each file b…
  • @esalinas Hi Eddie, yes there are bai files present already, but this is just testing a user tool using existing TCGA data on FC. Coming back to my previous question, the documentation mentions the membership files and load files and updating a me…
  • @esalinas Hi Eddie, I was hoping to upscale this tool in FC, and wanting to add bam files from the existing TCGA bam files in the workspaces/cohorts already present in the Firecloud. How can I do this? I cloned the workspace from which I'm going to…
  • @esalinas, Thanks Eddie, this helps!
  • Hi @esalinas , you mentioned that when you tried to import the WDL I provided, the delocalization was unsuccessful; by this you mean that it did not get imported into the workspace due to some issue in the WDL or there was a system update that was …
  • Thanks @abaumann and @esalinas - adding quotes worked! :)
  • Hi Eddie, Thanks for the solution; I was able to import this in a workspace this time, however when I'm trying to input a BAM file in the expression box - gs://console.cloud.google.com/storage/browser/fc-d24fc78b-8aa4-43fe-a6fb-0519d6bfed3a/sm2G280…
  • Hi Chet, Attached is the WDL and json file. For some reasons the output is not being generated in the directory defined. In addition when am trying to import this WDL on Firecloud, it got uploaded, but nothing happens when I try to import it in a w…