[Failed] Invalid output expression:
Hi, One of my workflow is failed. The message is "Invalid output expression:". I noticed that some of the output optins do not have a value because I do not need them. So, does this mean I should set a...
View Articlegcsfuse on Firecloud
In many cases, an algorithm wants to access just a small portion of a really large file. Scatter jobs operating on a BAM are a major example, but this also occurs when dealing with reference files. The...
View ArticlePermissions to google bucket tied to workspace
I recently joined a team and was granted writer access to a specific workflow. Does this access allow me to view outputs generated prior to my permissions taking effect (eg: if I started this week, can...
View ArticleAccess to Broad_MutationCalling_Filtering_Workflow_BestPractice_OA
Hi, I would like to reproduce Best practice filtering workflow (Broad_MutationCalling_Filtering_Workflow_BestPractice_OA) locally. I do not have access to the Controlled Access version, which has...
View Articlegatk/Somatic_SNV_Indel_Discovery_MC failing in oncotator
Hi I attempted to run M2 based on the configuration in gatk/Somatic_SNV_Indel_Discovery_MC, the workflow runs ok until it hits the Mutect2.oncotate_m2 step with failure messages: Couldn't resolve all...
View ArticleNeed to be able to see the snapshot of the configuration in the monitor tab
Currently looking at a job in the monitor tab one can only see the namespace and the name of the configuration, not the snapshot.
View ArticleWhen redacting a method one can longer view or edit a configuration that...
Instead, one should be able to view the configuration and modify it to point to a new, non-redacted version of the method.
View ArticleProblem with workspaces that were previously published to the data library
After another data release on the GDC website, we found out that the hg38 workspaces that have already been published to he data library now contain the wrong data. To fix that, we needed to delete and...
View ArticleWorkflow doesn't finish although the output was generated in the workspace
Hi, I have a workflow that keep displaying "Running" although the output was already generated in the workspace. I pressed "Abort" button, but the aborting process also seems not working.
View Articlebroken paging links in forum search?
Today in this forum I typed in a search string ("esalinas" to explore my forum activity) and got "110 results". The search results show the first 10 results. Links like << 1 2 3 4 5 6 7 ... 11...
View Article[Failed] ERROR message of "FilterWorkflow.maf_merge_task" in...
Hi, The message is shown as following. Please help me ... message: Task FilterWorkflow.maf_merge_task:NA:1 failed. JES error code 5. Message: 10: Failed to delocalize files: failed to copy the...
View ArticleImport wdl from GCS
Hello- I'm trying to a get a pipeline up and running in FC and can't seem to figure out wdl imports. I'd like to have the main method as a simple wdl that imports various other sub-workflows that are...
View Articlereference to files of items in a pairset with one row empty causes "[]" (an...
Matt Leventhal has a WDL of root entity-type "pair set". For each pair in the pair set. Matt wanted to refer to the files under a specific column. For the WDL input of datatype "Array[File]+" he put in...
View Articleunexpected call-cache miss, and odd timing numbers
I ran a submission on one pair, which had never been run before, and I did not uncheck the 'use call caching' checkbox. It ran and passed. I then ran a new submission on a 5000-ish wide pairset that...
View Articlewhy are forum editor buttons (i.e. attach image) ineffective ?
Hi Did something bad happen to the forum editor buttons? When attempting to embed an image - or format anything - the buttons turn grey with a tooltip but then do nothing when clicked. Both Chrome and...
View ArticleTasks listed as Running/Submitted aren't running
Workspace nci-mnoble-bi-org/dev (already shared with GROUP_support@firecloud.org) lists 4 Running and Submitted workflows in the Summary tab. In the Monitor tab, there are only two Method Configs with...
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hanging/floating link to bucket directory for submission? (minor UI issue?)
In recent submissions in google-chrome, I see a "floating"/"hanging" almost "orphan" external link icon ( see attached image). The link is to the directory in the bucket. I think this used to be...
View ArticlePermission issues transferring data from HPC or another cloud to my workspace...
I tried to copy data to my FC workspace bucket from a HPC cluster using gsutil and got the following error: ResumableUploadAbortException: 401 Anonymous users does not have storage.objects.create...
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Duplicate entry...
I get the error message soon after a submission where it says call-caching is enabled. Is this a call-caching error/issue? Is something from the WDL? The error message seems to be call-caching related...
View ArticleFailure to delocalize files when using my own docker image
Hi- I am having some trouble with file delocalization in firecloud when using my own docker images. So for the setup, I made a dockerfile that contains all of my source code (an autobuild from a github...
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