cromwell local execution takes up too much disk space
People want to run WDLs locally with Cromwell (v0.17 and/or other versions). When run it can use BIG BAMs and they are COPIED on the local file system. During the copy, people can run out of disk...
View Articleday one firecloud newbiequestion ... can't pull docker image
I type in linux command line: docker pull broadinstitute/cromwell I see ... Using default tag: latest Pulling repository docker.io/broadinstitute/cromwell Tag latest not found in repository...
View ArticleNo Create Workspace button
Hi The "Creating a New Workspace" in the FireCloud Basics section says that there will be a "Create New Workspace" button on the Firecloud Workspaces window, but there is no such button on the...
View ArticleFirecloud API - Request for set annotation function
While not documented, I noticed there is a https://portal.firecloud.org/service/api/workspaces/namespace/workspace/importEntities option, but it seems to require a text file as an input. I don't mind...
View ArticleCloning a workspace?
\ At https://portal.firecloud.org/#workspaces I click on the first workspace, I come to https://portal.firecloud.org/#workspaces . I click on "+ Clone", I get the message "No Google Projects...
View ArticleGoogle Bucket Directories as task input
I suspect the answer is "no" or "not yet" but, is there a way to pass an entire directory as a single input to a WDL task? In Firehose, you could pass a directory as a string input and because the jobs...
View ArticleError Viewing Inputs for a Task
When clicking on the Inputs hyperlink for a job, I'm unable to view them and get the following error: Uncaught TypeError: re-find must match against a string. I don't have any Array inputs or outputs...
View ArticleHide Default Workspaces
Hi Firecloud Team, It would be nice if I could hide all default/tutorial workspaces at once, instead of having to search for a specific workspace. Right now I cannot list just the workspaces I created...
View ArticleJob Status - "Unknown"
Hi Firecloud team, I'm getting the Unknown job status again. Previously I thought it was a mistake on my part, but I seem to always get it now. When I run the task individually, it works fine, and...
View ArticleRunning Jobs Not Showing up in Monitor
I am running analysis on a large cohort of around 900 samples on Firecloud. After starting the analysis, I timed out. I hit go again on the jobs and had another time out. After this, I looked at the...
View ArticleCan't access bucket on workspace I just created
Hi Firecloud Team, I made a workspace "broad-firecloud-testing/BRCA_PanCan" When I click on the bucket link I get "You do not have sufficient permissions to view this page." and gsutil ls also returns...
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Gistic2 Analysis task stuck running/aborting
I've got two tasks that appear to be stuck (see attached image), one I tried to abort but it is only listed as "Aborting", the other is listed as running, but should only have taken 20ish minutes and...
View ArticleFirecloud Installation Issue
Following the installation instructions in the firecloud-cli readme, I have run all the appropriate steps. Python 2.7.10 was already installed on my machine I installed pip by running sudo easy_install...
View ArticleDuplicate Samples in same Sample Set
Hi Firecloud, When importing samples to a sample set which already exist in that sample set, firecloud duplicates the samples without throwing an error or saying anything. So, after importing samples...
View Articleduplicate variable names allowed in WDL?
I recently pushed a WDL that had in the workflow section duplicate variable "pairName". In the method configs section, I kept entering a value for the first of the duplicate and saw that the value...
View ArticleUI hangs in trying to view erroneous submissions?
I created a workspace and imported a method configuration with a root entity type of pair into it. Next, I successfully submitted against a pair, but then deleted the pair from the data model (using...
View Articleduplicate workflow submission?
I am submitting a single workflow on a single pair (not a pair set), but it seems that duplicate workflows are running? Please see the attached PDF. This seems confusing. Is this proper behavior? If it...
View ArticleA workflow with seemingly at least one task running doesn't have an abort button
One of the tasks failed apparently, but it seems the others are running. Billing presumably occurs as long as something is running. As long as there is billing should there be an abort button? I wanted...
View ArticleUI status seems inconsistent with bucket status?
My UI for a job... not only does it NOT have an abort button and mark a job as "Running" BUT inspection of the bucket directory for the submission and workflow shows files de-localized and also shows a...
View ArticleI try to edit a method config, but clicking the save button doesn't seem to...
Please see attached PDF too. I have a method configuration “esalinas/qc” in my workspace “EDDIE_QC_WORKSPACE” I am trying to edit one of its inputs “QC_Workflow.refFasta” and save it to be able to...
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