broadinstitute/horsefish issues and pull requests

#165 - remove hardcoding of sample_id

Pull Request - State: open - Opened by jpramosbarroso 12 months ago

#164 - fixing grouping_col bug

Pull Request - State: closed - Opened by jpramosbarroso about 1 year ago

#163 - pgs visualization script

Pull Request - State: closed - Opened by jpramosbarroso about 1 year ago

#162 - Merge CreatSampleManifest task to StartDragen workflow

Pull Request - State: open - Opened by schaluva about 1 year ago

#161 - Vds compression

Pull Request - State: open - Opened by schaluva about 1 year ago

#160 - start dragen wdl + dockstore updates

Pull Request - State: closed - Opened by mfisher29 about 1 year ago

#159 - Initial commit for reheader_cram script

Pull Request - State: closed - Opened by jpramosbarroso about 1 year ago - 1 comment

#158 - Bump jinja2 from 3.1.2 to 3.1.3 in /scripts/pgs

Pull Request - State: open - Opened by dependabot[bot] about 1 year ago
Labels: dependencies

#157 - DI-308 migration tool update

Pull Request - State: closed - Opened by ncalvanese1 about 1 year ago

#156 - generalized version of enterics/pgs visualization python script

Pull Request - State: closed - Opened by schaluva about 1 year ago

#155 - Bump pip from 22.1.1 to 23.3 in /scripts/pgs

Pull Request - State: open - Opened by dependabot[bot] about 1 year ago
Labels: dependencies

#154 - Visuzalization Script for PGS Generated Data - associated WDL Lives in viral-pipelines

Pull Request - State: closed - Opened by schaluva about 1 year ago

#153 - Bump pip from 21.1 to 23.3 in /scripts/wfl/twisttcap

Pull Request - State: open - Opened by dependabot[bot] over 1 year ago
Labels: dependencies

#152 - Bump pip from 21.1 to 23.3 in /scripts/tdr/create_snapshot_from_submission_failures

Pull Request - State: open - Opened by dependabot[bot] over 1 year ago
Labels: dependencies

#151 - Bump pip from 21.1 to 23.3

Pull Request - State: open - Opened by dependabot[bot] over 1 year ago
Labels: dependencies

#150 - Bump pip from 21.1 to 23.3 in /scripts/emerge

Pull Request - State: open - Opened by dependabot[bot] over 1 year ago
Labels: dependencies

#149 - Bump pip from 21.1 to 23.3 in /scripts/tdr/export_pipeline_outputs_to_tdr

Pull Request - State: open - Opened by dependabot[bot] over 1 year ago
Labels: dependencies

#148 - [FE-62] Create bulk-set-requester-pays script

Pull Request - State: closed - Opened by samanthahv over 1 year ago

#147 - RARE-X: ignore ingest json files with 0 data to ingest into dataset

Pull Request - State: closed - Opened by schaluva over 1 year ago

#146 - scratch for export snapshot

Pull Request - State: open - Opened by schaluva over 1 year ago

#145 - Adding TDR migration tool scripts (DI-265)

Pull Request - State: closed - Opened by ncalvanese1 over 1 year ago - 2 comments

#144 - Samtools Split for Reprocessing CRAMs

Pull Request - State: open - Opened by schaluva over 1 year ago

#143 - Create object md5

Pull Request - State: closed - Opened by schaluva over 1 year ago

#142 - [GRO]: write script to get list of all outputs of successful workflows in a workspace

Pull Request - State: open - Opened by schaluva over 1 year ago

#141 - [FE-59] Update set_requester_pays.sh script to pass a project to bill in the request when disabling RP

Pull Request - State: closed - Opened by samanthahv over 1 year ago

#140 - eMerge: Retry Failed PRS Workflows

Pull Request - State: closed - Opened by schaluva over 1 year ago

#139 - [AT-412] Multi-bucket rsync script

Pull Request - State: closed - Opened by KutnerBroadie over 1 year ago - 2 comments

#138 - Update create_md5_object WDL to create backup copy, tmp copy, and compare file sizes before overwriting

Pull Request - State: closed - Opened by schaluva over 1 year ago

#137 - Generic WDL Shell Script Runner

Pull Request - State: closed - Opened by schaluva almost 2 years ago

#136 - [AT-384] WDLs for AnVIL File Validation, WDL for Running Shell Script, Dockerfile for AWS + Gcloud

Pull Request - State: closed - Opened by schaluva almost 2 years ago

#135 - [FE-25] Create script to GET requester pays status of a workspace bucket

Pull Request - State: closed - Opened by samanthahv almost 2 years ago - 4 comments

#134 - Update examine_gcs_contents for md5s

Pull Request - State: closed - Opened by ncalvanese1 almost 2 years ago

#133 - [AnVIL] generate md5 sums for list of anvil files

Pull Request - State: closed - Opened by schaluva almost 2 years ago

#132 - [DFE-805] - Cfos data tables

Pull Request - State: closed - Opened by KutnerBroadie almost 2 years ago

#131 - DFE-805 Rek cfos demo updates

Pull Request - State: closed - Opened by KutnerBroadie almost 2 years ago

#130 - DFE-805 cfos data tables demo updates

Pull Request - State: closed - Opened by KutnerBroadie almost 2 years ago - 1 comment

#129 - Cfos data tables

Pull Request - State: closed - Opened by KutnerBroadie almost 2 years ago

#128 - FE-4 update workspace_cleanup with docker

Pull Request - State: closed - Opened by bahill about 2 years ago

#127 - [DFE-805] Allow processing of multiple pages in Terra tables script for data import

Pull Request - State: closed - Opened by kilonzi about 2 years ago

#126 - Adding script to examine GCS path contents

Pull Request - State: closed - Opened by ncalvanese1 about 2 years ago

#125 - Update Anv ws set-up to add anvil_devs to AD

Pull Request - State: closed - Opened by ncalvanese1 about 2 years ago - 1 comment

#124 - demo request for PR and script

Pull Request - State: closed - Opened by schaluva about 2 years ago

#123 - ingest json files from bucket to respective tdr dataset tables

Pull Request - State: closed - Opened by schaluva about 2 years ago

#122 - [DFE-802] Create script to gather failures from a snapshot-by-reference submission and create new snapshot from them

Pull Request - State: closed - Opened by mmorgantaylor about 2 years ago

#121 - records into ingest body - no control file

Pull Request - State: closed - Opened by schaluva over 2 years ago

#120 - Update WFL setup README for Twist-TCAP

Pull Request - State: closed - Opened by mmorgantaylor over 2 years ago

#119 - Merge the working mop function

Pull Request - State: closed - Opened by mmorgantaylor over 2 years ago - 2 comments

#118 - [DFE-415] Fix on_error error with deletions from list

Pull Request - State: closed - Opened by mmorgantaylor over 2 years ago

#117 - [DFE-790] update mop to support submissions path

Pull Request - State: closed - Opened by mmorgantaylor over 2 years ago - 2 comments

#116 - add in optional value for requester pays project

Pull Request - State: closed - Opened by schaluva over 2 years ago

#115 - add project for requester pays to copy anvil data to delivery workspace

Pull Request - State: closed - Opened by schaluva over 2 years ago

#114 - [SU-202] Add new Terra service banner scripts to add/remove multiple banners

Pull Request - State: closed - Opened by MatthewBemis over 2 years ago

#113 - Add loadtag ingest

Pull Request - State: closed - Opened by schaluva over 2 years ago

#112 - [DFE-784] Script to set up a new WFL module for Twist-TCAP datasets

Pull Request - State: closed - Opened by mmorgantaylor over 2 years ago

#111 - Update utils.py

Pull Request - State: closed - Opened by ncalvanese1 over 2 years ago

#110 - Update clone_anvil_workspace.py

Pull Request - State: closed - Opened by ncalvanese1 over 2 years ago

#109 - add 200 success code for delete workspaces script

Pull Request - State: closed - Opened by mmorgantaylor over 2 years ago

#108 - DI-95 - Findability subset

Pull Request - State: closed - Opened by ncalvanese1 over 2 years ago - 1 comment

#107 - Fixing minor copy-paste bug

Pull Request - State: open - Opened by ncalvanese1 over 2 years ago

#106 - update script with errors and more stdout

Pull Request - State: closed - Opened by schaluva over 2 years ago

#105 - Update path for resources directory

Pull Request - State: closed - Opened by ncalvanese1 over 2 years ago - 1 comment

#104 - DI-78: Validation script and README

Pull Request - State: closed - Opened by ncalvanese1 over 2 years ago - 1 comment

#103 - add list of directories to copy from resources workspace bucket

Pull Request - State: closed - Opened by schaluva over 2 years ago

#102 - update with emerge_id and poly_id - do not delivery crsp

Pull Request - State: closed - Opened by schaluva over 2 years ago

#101 - [DFE-774] add on/off toggle to requester pays script

Pull Request - State: closed - Opened by mmorgantaylor over 2 years ago

#100 - [DFE-770] Update ingest pipeline outputs to TDR

Pull Request - State: closed - Opened by mmorgantaylor over 2 years ago

#99 - Prs staging wdl and python script

Pull Request - State: closed - Opened by schaluva over 2 years ago

#98 - Update anvil clone 052522

Pull Request - State: closed - Opened by schaluva over 2 years ago

#97 - remove file counts

Pull Request - State: closed - Opened by schaluva over 2 years ago

#96 - Updates to pipeline outputs to TDR, for Twist-TCAP

Pull Request - State: closed - Opened by mmorgantaylor almost 3 years ago

#95 - update anvil clone script

Pull Request - State: closed - Opened by schaluva almost 3 years ago

#94 - add anvil ingest notebooks

Pull Request - State: closed - Opened by schaluva almost 3 years ago

#93 - fix for tsv files with more than single row

Pull Request - State: closed - Opened by schaluva almost 3 years ago

#92 - add bigquery to requirements.txt file

Pull Request - State: closed - Opened by schaluva almost 3 years ago

#91 - Emerge scripts

Pull Request - State: closed - Opened by schaluva almost 3 years ago

#90 - add or remove user from terra group

Pull Request - State: closed - Opened by schaluva almost 3 years ago

#89 - move anvil_tdr_ingest into scripts

Pull Request - State: closed - Opened by schaluva almost 3 years ago

#88 - [DFE-729] Common TDR ingest tools, emphasis on GP-TIM

Pull Request - State: open - Opened by mmorgantaylor almost 3 years ago

#87 - copy projects directory into docker

Pull Request - State: closed - Opened by schaluva almost 3 years ago

#86 - [SUP-633] Use temp file workaround to set cache metadata at object creation

Pull Request - State: closed - Opened by MatthewBemis almost 3 years ago

#85 - Revert "[SUP-633] Use tmp alerts.json file to create object and set caching metadata in one operation"

Pull Request - State: closed - Opened by MatthewBemis almost 3 years ago

#84 - [SUP-633] Use tmp alerts.json file to create object and set caching metadata in one operation

Pull Request - State: closed - Opened by MatthewBemis almost 3 years ago

#83 - Tag push-outputs-to-tdr docker with version

Pull Request - State: closed - Opened by mmorgantaylor almost 3 years ago

#82 - [DFE-736] Fix ingest workflow outputs script to use "replace" functionality

Pull Request - State: closed - Opened by mmorgantaylor almost 3 years ago

#81 - [DFE-730] Quick fix anvil

Pull Request - State: closed - Opened by schaluva almost 3 years ago

#80 - [DFE-730]AnVIL to TDR Ingest: create clone of anvil workspace with auth domains and link to src workspace

Pull Request - State: closed - Opened by schaluva almost 3 years ago

#79 - [DFE-721] update export to support arrays and use TDR update ingest

Pull Request - State: closed - Opened by mmorgantaylor almost 3 years ago

#78 - Updating the DEFAULT_LINK for 2022

Pull Request - State: closed - Opened by jason-cerrato about 3 years ago

#77 - Bump pip from 19.3.1 to 21.1 in /scripts/tdr/twisttcap

Pull Request - State: closed - Opened by dependabot[bot] about 3 years ago
Labels: dependencies

#76 - [DFE-704] add scripts for warp twisttcap wrapper wdl

Pull Request - State: closed - Opened by mmorgantaylor about 3 years ago

#75 - add workspace deletion tools and readme

Pull Request - State: closed - Opened by mmorgantaylor about 3 years ago

#74 - Bump pip from 19.3.1 to 21.1

Pull Request - State: closed - Opened by dependabot[bot] over 3 years ago
Labels: dependencies

#73 - Update terra_service_banner.py to allow for immediate changes

Pull Request - State: closed - Opened by jason-cerrato over 3 years ago

#72 - update default link of service notifications page in service banner

Pull Request - State: closed - Opened by jacmrob over 3 years ago

#71 - [DFE-634] update get_workspace_bucket.py to also get auth domain

Pull Request - State: closed - Opened by schaluva over 3 years ago

#70 - [DFE-631] add script for anvil-tools to get workspace bucket id for workspace with name and project

Pull Request - State: closed - Opened by schaluva over 3 years ago

#69 - fix input file separator to tab from comma

Pull Request - State: closed - Opened by schaluva over 3 years ago

#68 - TDR ingest data and metadata scripts

Pull Request - State: closed - Opened by schaluva over 3 years ago

#67 - edit anvil admins group email from underscore to dash - update readme

Pull Request - State: closed - Opened by schaluva over 3 years ago

#66 - Update README.md

Pull Request - State: closed - Opened by schaluva over 3 years ago - 1 comment

GitHub / broadinstitute/horsefish issues and pull requests