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NEWS
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11.08.2021 Version 1.3.35
Notification added for old container users.
09.08.2021 Version 1.3.34
Minor bug fixed initialrun.nf file.
02.08.2021 Version 1.3.33
s3cmd replaced with aws cli.
02.08.2021 Version 1.3.32
Homepage pipeline number increased to 60 for scrolling.
Email Recipients option added to run page.
EMAIL_BODY_ADMIN parameter added to .sec file.
01.08.2021 Version 1.3.31
The Run Notes section is optionally created on the run status page.
Download button added for uploaded files.
27.07.2021 Version 1.3.30
Write permission to group feature added to process and pipelines.
22.07.2021 Version 1.3.29
Minor admin dashboard bug fixed.
Major bug fixed in cronjob submission.
19.07.2021 Version 1.3.28
Major bug fixed in defparams feature.
SQL query of active users improved for admin dashboard.
Minor bug fixed in pipeline import function.
18.07.2021 Version 1.3.27
Minor bug fixed in the label creation of the run page.
Processed Samples by Pipeline and Active Users data added to Admin Dashboard.
17.07.2021 Version 1.3.26
{{DNEXT_RUN_URL}} global variable added for scripts.
Nextflow script creation improved for advanced node connections.
11.07.2021 Version 1.3.25
Minor bug fixed in Run Status filter resets.
CUSTOM_FILE_LOCATION_MESSAGE and CUSTOM_HELP_MESSAGE parameters added to .sec file under [UICONFIG] section.
Github link delete icon added to pipeline page.
11.07.2021 Version 1.3.24
AWS s3 rm command updated to effectively use the beforerun script.
Beforeschedule script added for cron jobs.
09.07.2021 Version 1.3.23
Collection duplication support added for run duplication.
08.07.2021 Version 1.3.22
Minor bug fixed in process modal.
Data dropdown added for Admin Dashboard to differentiate run and run attempts.
Minor bug fixed for Admin Dashboard.
Left sidebar removed if feature_metadata.tsv is not published in UCSC Genome Browser report.
02.07.2021 Version 1.3.21
Warning added for automated execution.
Automated execution is allowed for single run submission when frequency is not set.
Run word replaced with Attempt in run page dropdown.
UCSC Genome Browser links added to count table.
Lab filter added to Total Runs by Pipeline graph.
Error vs success run counts added to Admin Dashboard.
Average Run Time plot added to Admin Dashboard.
01.07.2021 Version 1.3.20
Size of the add/edit process modal increased. Height control handles were added to the editor.
30.06.2021 Version 1.3.19
Admin Dashboard added.
29.06.2021 Version 1.3.18
Pipeline permission update module updated for admin.
Run status page filtering improved.
28.06.2021 Version 1.3.17
UCSC Genome Browser module added to reports.
21.06.2021 Version 1.3.16
First Submission Date option added to scheduled run settings.
Regex support added to s3 file searches.
13.06.2021 Version 1.3.15
Minor bug fixed in the e-mail notification.
Minor bug fixed in the scheduled run checking function.
File upload bug fixed in the run report page.
03.06.2021 Version 1.3.14
Google login method upgraded. GOOGLE_CLIENT_ID (https://developers.google.com/identity/gsi/web/guides/get-google-api-clientid) is required for ALLOW_SIGNUPGOOGLE in .sec file.
02.06.2021 Version 1.3.13
EMAIL_TYPE feature added to .sec file. Available options: DEFAULT (for sendMail), SMTP or HTTP
Email notification feature added.
File addition error fixed for high amounts.
02.06.2021 Version 1.3.12
Run status page filtering improved.
Automatic run execution feature added to run page.
20.05.2021 Version 1.3.11
Label feature added for pipeline inputs and @label flag added for process settings.
NXF_DEFAULT_DSL value set to 1 by default.
{{DNEXT_WEB_RUN_DIR}} {{DNEXT_WEB_REPORT_DIR}} global variables added.
19.05.2021 Version 1.3.10
Minor bug fixed in autofilling executor settings.
Auto-merging feature added while creating collections.
04.05.2021 Version 1.3.09
Minor bug fixed in Executor Settings configuration in nextflow.config file.
04.05.2021 Version 1.3.08
Minor update for Spreadsheet view.
03.05.2021 Version 1.3.07
When condition bug fixed for Val qualifiers.
Spreadsheet support was added to process options on the run page.
29.04.2021 Version 1.3.06
When condition upgraded for val qualifiers.
Session refresh calls replaced with web workers.
29.04.2021 Version 1.3.05
Process test upgraded for test parameters.
27.04.2021 Version 1.3.04
Run settings modal upgraded to support multiple nested modules.
@hidden tag added for process settings.
26.04.2021 Version 1.3.03
ProjectID and description support added for DMeta submissions.
21.04.2021 Version 1.3.02
Dmeta input support upgraded for larger datasets.
20.04.2021 Version 1.3.01
Input declarations belonging to headers/configs of modules will not be parsed.
New DNEXT variables (DNEXT_PUBLISH_DIR, DNEXT_LAB, DNEXT_USERNAME, DNEXT_EMAIL) added for replacement.
New pipeline files (beforerun.sh and afterrun.sh) are supported.
29.03.2021 Version 1.3.00
Single file upload error fixed for filenames that have spaces.
Duplicate channel error fixed in nextflow.nf file.
29.03.2021 Version 1.2.99
Process test button removed if user not the owner of the process.
Process saving removed from process test button.
Process test improved for qualifier set. Multiple values are supported within an array.
28.03.2021 Version 1.2.98
Minor bug fixed for nextflow.config file creation in the process test.
28.03.2021 Version 1.2.97
Channel creation method fixed for multiple optional inputs.
Rmarkdown module updated to prevent writing on original pipeline file.
Process test bug fixed for initial execution.
Process test run triggers saving process.
Paired channel creation error fixed for process tests.
23.03.2021 Version 1.2.96
Bug fixed in the shared projects table.
21.03.2021 Version 1.2.95
Pipeline defaults feature added (defparams) to overwrite default values of the processes.
17.03.2021 Version 1.2.94
Minor fix for debrowser report loading.
App support improved for startup scripts.
16.03.2021 Version 1.2.93
Report page rendering improved for various file types.
DEBrowser metadata support upgraded.
Channel creation method upgraded for optional inputs.
23.02.2021 Version 1.2.92
Profile Variables removed from nf file and added to initial run config.
Rmarkdown rendering bug fixed.
23.02.2021 Version 1.2.91
project_pipeline and run_log tables updated to store bigger data.
18.02.2021 Version 1.2.90
Executor settings for nextflow options fixed for LSF.
09.02.2021 Version 1.2.89
Minor bug fixed in fillFormByName function.
08.02.2021 Version 1.2.88
Save button added to test window.
Secure flag added to wget command for initial run: --secure-protocol=TLSv1.
Bug fixed for SSO login.
03.02.2021 Version 1.2.87
Trailing and leading spaces trimmed from pipeline, run and profile pages.
01.02.2021 Version 1.2.86
Test process bug fixed for $HOSTNAME variable.
INITIAL_RUN_DOCKER, INITIAL_RUN_SINGULARITY parameters added to .sec file under CONFIG section.
31.01.2021 Version 1.2.85
Collection creation table updated to prevent pagination change.
30.01.2021 Version 1.2.84
Ajax warning added for ended user session.
Markdown headerID's removed for container error.
28.01.2021 Version 1.2.83
Single file modal added to run page.
25.01.2021 Version 1.2.82
Run status loading bug fixed in process testing tab.
17.01.2021 Version 1.2.81
chooseDefaultRunEnv feature disabled.
17.01.2021 Version 1.2.80
Special character control added to upload file section.
Reset of upload added on hide of upload modal.
14.01.2021 Version 1.2.79
Minor bug fixed in channel creation function.
11.01.2021 Version 1.2.78
Test script feature added to process window.
Default Run Environment feauture added.
03.01.2021 Version 1.2.77
Fix for pipeline editing for admin.
29.12.2021 Version 1.2.76
The regex section in the process window is deprecated.
Process/pipeline update improved by using existing g-nums in the workflow.
Optional outputs upgraded to support multiple process outputs that share the same location.
Duplicate output channel error fixed.
22.12.2021 Version 1.2.75
Fix for space containing lines in search of files in run page.
20.12.2021 Version 1.2.74
Bug fix in nf file creation.
20.12.2021 Version 1.2.73
@optional tag added to process input settings.
@file tag added to show file modal by using process settings.
Show_settings option now supports "params.inputs" and shows them in the process settings.
Optional inputs are supported, no need to enter NA for optional inputs.
16.12.2021 Version 1.2.72
Uploaded single file could be used in the run page.
Default initial run code could be overwritten by the "initialrun.nf" file in the base directory.
14.12.2021 Version 1.2.71
Merge selected files button added.
Optional input feature upgraded to support AWS batch environment.
13.12.2021 Version 1.2.70
Delete run option added into run status page
Remove run warning fixed in projects page.
13.12.2021 Version 1.2.69
DEFAULT_RUN_ENVIRONMENT option added to .sec file.
12.12.2021 Version 1.2.68
DEFAULT_GROUP_ID option added to .sec file.
08.12.2021 Version 1.2.67
The pipeline page is updated to pipeline and process editing for admin.
PDF loading in datatables prevented.
Debrowser metadata file support added.
Minor bug fixed in the profile page autoload.
05.12.2021 Version 1.2.66
Run page loading improved.
Environment Variables in Public Run Environment Templates fixed.
Run environment and work directory fields swapped in the run page.
Editing details of the files feature added to run page.
22.11.2021 Version 1.2.65
Overwrite:true option removed from PublishDir to prevent copy operations on resumed runs.
Run Status page loading improved.
18.11.2021 Version 1.2.64
PublishDir Regex improved for multiple file types.
Fix will allow the use of @ symbol in description of inputs.
10.11.2021 Version 1.2.63
Bug fixed for Dmeta run parameter submission.
04.11.2021 Version 1.2.62
DolphinNext Debrowser_URL parameter updated. Full link needs to be provided in .sec file.
04.11.2021 Version 1.2.61
Initial run config updated to support high number of inputs.
Please select Amazon Keys warning removed from run page.
31.10.2021 Version 1.2.60
Publishdir pattern ({{publishdir:outputPattern}}) added to use output folder in a script.
30.10.2021 Version 1.2.59
Logout location set as basepath.
User table for admin fixed.
28.10.2021 Version 1.2.58
Secret line (@DNEXT_SECRET_LINE) feature added.
26.10.2021 Version 1.2.57
Environment variables field added to run environments.
22.10.2021 Version 1.2.56
Multiple directory support added for Dmeta.
13.10.2021 Version 1.2.55
Dmeta process options support added.
29.09.2021 Version 1.2.54
OKTA SAML 2.0 login support added.
22.09.2021 Version 1.2.53
Mysql8 support added.
07.09.2021 Version 1.2.52
Delete intermediate files for awsbatch feature added.
31.08.2021 Version 1.2.51
Okta fix for entry of the first user.
Documentation updated for AWS Batch.
30.08.2021 Version 1.2.50
Minor fix for Dmeta run submission.
28.08.2021 Version 1.2.49
Database table names converted to lowercase.
PDF loading bug fixed in report page.
27.08.2021 Version 1.2.48
Composer php version requirement removed.
23.08.2021 Version 1.2.47
SSO login support for OKTA added. sec file configuration:
[OKTACONFIG]
SSO_LOGIN=true
CLIENT_ID=id
CLIENT_SECRET=secret
ISSUER=https://youroktadomain.com/oauth2/default
OKTA_API_TOKEN=token
13.08.2021 Version 1.2.46
Initial run improved for special characters.
27.07.2021 Version 1.2.45
Local execution of initial run allowed.
GHPCC path mount upgraded.
24.07.2021 Version 1.2.44
Minor upgrade for Dmeta run submission.
19.07.2021 Version 1.2.43
Dmeta Target Collection dropdown updated for custom collection names.
16.07.2021 Version 1.2.42
Initial run update for gzip handling.
getLsDir API call added.
28.06.2021 Version 1.2.41
Error handling fixed for "ignore".
02.06.2021 Version 1.2.40
Into/set warning fixed.
26.05.2021 Version 1.2.39
Optional val qualifier support added.
24.05.2021 Version 1.2.38
Process settings button upgraded in run page.
19.05.2021 Version 1.2.37
Download pipeline button error fixed.
18.05.2021 Version 1.2.36
AWS Batch support added.
25.04.2021 Version 1.2.35
Minor update to support single quotes in autofill feature of run forms.
15.04.2021 Version 1.2.34
Amazon RDS MySQL connection and API documentation added.
26.03.2021 Version 1.2.33
Run description edit feature added.
24.03.2021 Version 1.2.32
Dmeta API routes improved by getRunEnv, getRuns and getRun.
17.03.2021 Version 1.2.31
Big file error of tables fixed for reports.
16.03.2021 Version 1.2.30
Special characters removed from collection name.
12.02.2021 Version 1.2.29
Remove new run button added into run management console.
New run detection algorithm upgraded.
29.01.2021 Version 1.2.28
GEO search upgraded.
07.01.2021 Version 1.2.27
JWT cookie support added on login.
JWT_SECRET and JWT_COOKIE_EXPIRES_IN parameters added to Dolphinnext section of .sec file.
[Dolphinnext]
JWT_SECRET=very-strong-jwt-secret-password
JWT_COOKIE_EXPIRES_IN=365
Proxy.php and jquery.ajax-cross-origin removed.
Process nodes updated on change in development mode.
User confirmation added when updating existing system inputs in the run page.
Each executor config preparation moved to server side.
Filled input check bug fixed.
30.11.2020 Version 1.2.26
Project support for dmeta added
19.11.2020 Version 1.2.25
Triple and quadruple file support added to initial run.
11.11.2020 Version 1.2.24
After-sso redirection fixed for Single Sign-on feature.
08.11.2020 Version 1.2.23
Single Sign on feature upgraded.
06.11.2020 Version 1.2.22
initial run .nextflow.log and trace.txt files are added to log tabs in the run page.
Lsf pid checker added to detect killed jobs.
05.11.2020 Version 1.2.21
S3 upload command updated with "aws s3 sync" to support files bigger than 5GB.
02.11.2020 Version 1.2.20
After-SSO login page updated.
Minor bug fixed in import pipeline module.
01.11.2020 Version 1.2.19
$ and ^ characters added into file pattern searches.
29.10.2020 Version 1.2.18
Dmeta api calls simplified.
26.10.2020 Version 1.2.17
Sign in with SSO option added to login page.
Login check feature added to sso login.
Favicon added to page.
23.10.2020 Version 1.2.16
Show homepage parameter added to .sec file.
[UICONFIG]
SHOW_HOMEPAGE=false
23.10.2020 Version 1.2.15
Home page updated.
20.10.2020 Version 1.2.14
Single-Sign On feature added.
Total amount of files are shown in collections list.
Run page loading enhanced by updating sample table.
Dmeta file tab added.
Warning added in case file types or collection types are not the same for the selected files.
Dmeta initiates run using template run.
12.10.2020 Version 1.2.13
Github integration upgraded, password authentication replaced with the access token.
02.10.2020 Version 1.2.12
Rsync command upgraded to minimize rsync command submission.
28.09.2020 Version 1.2.11
GEO download feature fixed.
20.07.2020 Version 1.2.10
Text viewer added to report section.
20.07.2020 Version 1.2.9
Asynchronous loading and warning added for report page.
14.07.2020 Version 1.2.8
CSV file support added to datatables reporting option.
30 sec. timeout added to du command.
10.07.2020 Version 1.2.7
useSoftTabs disabled for script editor to use tab instead of four spaces.
Fastqc added to top of the report list.
22.06.2020 Version 1.2.6
Minor bug fixed in the wizard.
19.06.2020 Version 1.2.5
Loading speed of run status page upgraded.
13.06.2020 Version 1.2.4
Sign-up form upgraded and maximum length limits added to form fields.
Adding samples section improved to remove spaces from file names.
Run status page upgraded to load inputs for admin.
Env and Tuple qualifiers added to parameters.
Known issues section added to documentation.
10.06.2020 Version 1.2.3
Run page loading upgraded.
10.06.2020 Version 1.2.2
Run status page upgraded and separate impersonate button added for admin.
08.06.2020 Version 1.2.1
Minor bug fixed in the updateDN script.
Initial run image updated to fix fastq-dump.
29.05.2020 Version 1.2.0
Minor fix for safari file download in report page.
21.05.2020 Version 1.1.18
Minor upgrade to support single files in a collection.
20.05.2020 Version 1.1.17
* Major Upgrades:
- Sharing pipeline/run with everyone feature is added.
- Access of the public pipeline/run could be controlled by setting a release date and getting a sharable link.
- create a temporary link till release date (e.g., for the reviewer) feature added.
- Permission control added for the pipeline and run pages.
- Publicly searchable feature added for admin, which will control the listed pipeline and processes.
* Minor Upgrades:
- Pipeline autosave disabled after clicking cancel on saving.
- New revision button added for process and pipeline.
- Warning added to prevent leaving web page before run submission
- Run termination blocked until run submission.
- Creating a new run page is prevented when only the description or permission of the run edited.
* Bug Fixes:
- Bug fixed by cleaning single quotes in the pipeline name.
08.05.2020 Version 1.1.16
* Fixes:
Minor bug fixed regarding the loading log section.
05.05.2020 Version 1.1.15
Administrator guide added to the documentation.
How to cite added to the documentation.
* Minor updates:
- All changes are saved warning is hidden when the user opens the previous run.
- Readlink command added to work directory size checking function.
26.04.2020 Version 1.1.14
Minor fix for shared runs.
25.04.2020 Version 1.1.13
* Major upgrades:
Each run settings are saved for each run attempts.
Run history dropdown created which allows executing to use previous run attempts.
Run history dropdown shows the amount of space used in DolphinNext servers.
Run history settings added to rename, delete, purge or recover of the run.
Checking work directory space feature added to the run page.
* Minor updates:
Amount of active cloud instances updated without opening the cloud console.
The new run page will be created if the user saves the changes on the last run.
UID of the run is added into the report and log tabs.
Calculate the user's disk usage button added for the admin console.
* Fixes:
Quote usage error fixed for the input parameter of the pipeline.
Bug fixed when collection path entered with spaces.
Validation function added for the paired list of files.
Selective reloading function added to cached browser files.
Minor bug fixed when process and pipeline gid equals to zero.
Checkbox related scrolling animations are fixed for the run page.
24.03.2020 Version 1.1.12
Bug fixed while binding paths to containers.
Default initial run container set to singularity when run container is not enabled.
20.03.2020 Version 1.1.11
The feedback button is replaced with the help sidebar. Messages will be sent to admin by e-mail.
The description field added to run inputs that support HTML syntax.
The warning of the "undefined download directory" is simplified. If a user doesn't enter a path, the Work Directory will be used.
Parameters of the copied run will be refreshed, only if pipeline revision has changed.
19.03.2020 Version 1.1.10
A new option (greaterOrEqual) added to the permission update algorithm for the run page.
16.03.2020 Version 1.1.9
Public pipelines are listed in the pipeline page.
Shared and user projects/runs are separated with separated tables in the pipeline/project/run page.
Users allowed to add run into shared projects.
Additional warnings added when the project is attempted to delete.
shared and user projects/runs are separated in the left sidebar.
permission update algorithm for the shared project is updated.
Pipeline revision is prompted when the user wants to copy a run.
Toast notifications added into the run page to show when the page is saved.
Remove the value of publishing directory when it is not defined in the run environment.
Change the project button added to the run page (move run).
Keep run_description folder from the last attempt of the run when run restarted.
05.03.2020 Version 1.1.8
Run report template updated.
Table support added for markdown.
03.03.2020 Version 1.1.7
CENTRAL_API_URL transferred from .sec file to config.php.
Minor bug fixed in the import function.
02.03.2020 Version 1.1.6
Add file section upgraded to support directory navigation.
Default Readme.md file added into report page.
Word-wrap feature added to markdown editor.
02.03.2020 Version 1.1.5
Add file section upgraded with examples.
Click on error button shows log tab.
Refresh button added to report page.
"Image" option added into "publish to web directory" dropdown and report page.
New visualization type (Run_Description) added to report page which allows to upload/attach files to run logs.
Markdown viewer added into report page.
Editable regions of Run_Description and Rmarkdown are disabled for shared runs.
"source /etc/profile" added to ssh commands.
20.02.2020 Version 1.1.4
Adding public key video added to documentation.
"Assign group to user" option added to admin menu.
"Edit Group Name", "Add member with e-mail" and "Delete member from group" option added to group menu.
Pre-cmd transfered into .dolphinnext.run script.
Shared run status will be loaded into run status page.
16.02.2020 Version 1.1.3
Documentaion updated for:
- Quickstart
- Google Cloud
- Wizard
Public run environments added into wizard dropdown in host section.
Download directory parameter added to wizard.
10.02.2020 Version 1.1.2
runUpdate script removed and updateDN.py script updated.
10.02.2020 Version 1.1.1
runUpdate script updated.
Pipeline process and module id's started to save recursively in pipeline data.
Pipeline/process permission/group change algorithm updated.
10.02.2020 Version 1.1.0
Minor bug fixed in updateDN.py script.
31.01.2020 Version 1.0.18
Github feature opened to public.
09.01.2020 Version 1.0.17
Google cloud autoshutdown feature fixed.
Proxy.php validation transfered to BASE_PATH in the .sec file.
ENV_PATH variable added to .sec file to source optional scripts before executing any commands.
UUID validation step added before saving logs.
09.01.2020 Version 1.0.16
Google cloud feature added.
$DEFAULT_IMAGE parameter added to autofill feature and documentation is updated.
Delete intermediate files function updated to delete work directory in the cloud.
Delete report files on rerun added.
23.12.2019 Version 1.0.15
Style of wizard window updated.
Extension of exported DN file fixed.
Minor bug fixed regarding to autofilling.
13.12.2019 Version 1.0.14
Nextflow status update feature upgraded to support uploading file to s3.
Session refresh script added to prevent 30 min. session timeout.
Ace editor selectall bug fix for firefox browser.
Grey background of run and pipeline page icons fixed for firefox/safari browser.
11.12.2019 Version 1.0.13
Minor error on $NXF_SINGULARITY_CACHEDIR path fixed.
Terms and Conditions & Privacy Policy added to wizard.
10.12.2019 Version 1.0.12
Channel factory algorithm and workflow connection approach in D3 updated to support multiple qualifiers with single input parameter.
Process editing allowed after clicking process settings icon.
Edge reconnection feature after changing version of the process/module is added.
10.12.2019 Version 1.0.11
GEO search window improved and bugs are fixed.
Retry button added for GEO search to warn user about failed queries.
07.12.2019 Version 1.0.10
Default GEO download queueSize removed.
Fast-dump retry command added into initial run.
06.12.2019 Version 1.0.9
GEO download queueSize set to 2 by default.
Initial run max retry amount increase to 4.
04.12.2019 Version 1.0.8
GEO download cache clean command added.
03.12.2019 Version 1.0.7
GEO download queueSize set to 4 by default.
GEO query algorithm timeout increased to 2.5 seconds.
02.12.2019 Version 1.0.6
GEO download queueSize set to 10 by default.
24.11.2019 Version 1.0.5
Bug fixed while binding paths to containers.
Bug fixed while choosing empty process and pipeline menu groups.
Menu group editing feature limited for user to avoid duplicate names.
Left sidebar scroll feature added to facilitate drag and drop of processes.
20.11.2019 Version 1.0.4
Memory handing improved in tsv conversion for Debrowser.
18.11.2019 Version 1.0.3
Default parameter set added to dolphinnext.sql.
13.11.2019 Version 1.0.2
Wizard feature upgraded for host option:
- Connection validation
- Java, Nextflow, Docker, Singularity validation added.
13.11.2019 Version 1.0.1
Wizard feature added. Admin might define test server by using .sec file:
SHOW_WIZARD=true
SHOW_TEST_PROFILE=true
TEST_PROFILE_GROUP_ID=18
Please define a run environment and share with group.
Use shared group id to define TEST_PROFILE_GROUP_ID.
Overflow of file tables fixed.
Uppercase s3 path recognition fixed for run page.
Collection search box added in run page.
UpdateDN command updated with absolute path.
12.11.2019 Version 1.0.0
Sign out button bug fixed.
18.10.2019 Version 0.3.75
GEO file download limit added for initial run when local executor is selected.
Autoscale error is fixed for AWS-ignite by increasing tcp.socketTimeout value.
18.10.2019 Version 0.3.74
Pipeline/process search feature upgraded to search within full name.
Tooltip added for long item names in the pipeline and project page.
Filter feature upgraded for admin.
Run status table sql query updated to increase its performance.
Minor bug fixed in bindEveHandler function in runpipeline.js.
17.10.2019 Version 0.3.73
Run status table updated:
- sorting feature fixed
- pipeline revision added
- Not submitted runs added.
17.10.2019 Version 0.3.72
Autofill feature will be executed in case "use new revision" is clicked when copying run. It will update executor settings, container options and system inputs.
Bug fixed in autofill function.
16.10.2019 Version 0.3.71
Executor settings first filled with profile defaults on change.
15.10.2019 Version 0.3.70
GEO search bug fixed.
14.10.2019 Version 0.3.69
GEO search improved with web queries and progress information.
11.10.2019 Version 0.3.68
Manual run execution feature added which allows to execute run without defining SSH keys.
10.10.2019 Version 0.3.67
Minor bug fixed regarding to process executors in the run page.
09.10.2019 Version 0.3.66
Job submission code updated.
Minor bugs fixed in the initial run.
Minor bug fix in the add collection modal.
Initial run image updated and fasterq-dump replaced with fastq-dump.
clientFailureDetectionTimeout and FailureDetectionTimeout limits are increased for apache ignite.
02.10.2019 Version 0.3.65
Version logs will be shown when the "version button" clicked.
Warning will be shown when new release of DolphinNext is available.
30.09.2019 Version 0.3.64
Documentation is updated:
- Short Overview, About, Support, Developer Tutorial sections added.
- Quick Start Guide updated.
26.09.2019 Version 0.3.63
Autofill feature for singularity and docker image added to auto-mount paths based on the selected inputs.
Initial run paths auto-mounted based on selected inputs.
Run update command to apply db patches updated.
Run update feature added to admin console (experimental feature and hidden for this revision).
11.09.2019 Version 0.3.62
Warnings added into run page, to show undefined variables in the system inputs.
addProfileVar function in runpipeline.js updated to support multiple profile variables.
10.09.2019 Version 0.3.61
Documentation updated for:
- Executor Settings
- Developer Tutorial
- Reports (new images and DEbrowser section)
- Pipeline examples
10.09.2019 Version 0.3.60
Bug in createMultiConfig function is fixed.
10.09.2019 Version 0.3.59
Minor fix for Pipeline files section.
09.09.2019 Version 0.3.58
Pipeline files section added into pipeline tab.
Bug fixed while copying option process button.
06.09.2019 Version 0.3.57
NXF_SINGULARITY_CACHEDIR is supported by dolphinnext.
03.09.2019 Version 0.3.56
Typo fixed in documentation.
Github password is masked in the logs.
03.09.2019 Version 0.3.55
Login page updated to support login with username.
03.09.2019 Version 0.3.54
Minor fix for config parser.
28.08.2019 Version 0.3.53
Minor fix for workflow width.
27.08.2019 Version 0.3.52
Pipeline page updated with tabs.
Duplicate pipeline button updated.
Autofill json updated for default conditions.
27.08.2019 Version 0.3.51
Pipeline labels updated in the main page.
Sign-up updated to assign admin for the first user.
22.08.2019 Version 0.3.50
Pipeline labels added to main page.
Quote usage fixed in the default value section of the pipeline inputs modal.
14.08.2019 Version 0.3.49
$HOSTNAME="default" variable added to top of the nextflow.config for consistency.
14.08.2019 Version 0.3.48
Minor bug fixed in initial parameters config file.
Autofill feature updated by case sensitive insert for pipeline inputs.
13.08.2019 Version 0.3.47
Github integration completed to publish pipelines into Github.
Pipeline description section supports markdown format to publish it as github readme file.
Nextflow config section added in pipeline page.
Input paramters moved to nextflow.config
Config tag feature added to create mutiple files in Nextflow config file .
Process output as val format supported for modular structure.
Minor bug fixed in createProcessPanelAutoFill function.
24.07.2019 Version 0.3.46
Url download feature added to createCollection and urlDownload step.
Initialcheck step added to initialrun to detect missing files and urls.
Missing files and urls created by separate processes.
Multiple collections support added (individual directories will be used in inputs folder).
Initial run singularity image updated to support awscli.
S3 upload check improved by awscli and --content-md5 header (https://aws.amazon.com/premiumsupport/knowledge-center/data-integrity-s3/)
19.07.2019 Version 0.3.45
Ghpcc mounting upgraded to check path inside of the form fields.
"Profile Variables" field added to profile settings.
13.07.2019 Version 0.3.44
Upload file feature upgraded to support rsync resume/retry.
12.07.2019 Version 0.3.43
Minor bug fix for loading run page.
Documentation update.
08.07.2019 Version 0.3.42
View button added to sample table in run page.
Singularity image url support added.
30.06.2019 Version 0.3.41
Slurm executor supported added.
Admin delete user feature added.
Hide ssh keys from user feature added.
Default parameters will be autofilled for initial opening of the run page.
25.06.2019 Version 0.3.40
Empty folder warning fixed in view directory.
ShowInfoModal freeze fixed.
Bug fixed on autoshutdown feature of amazon instances.
16.06.2019 Version 0.3.39
Upload module added.
07.06.2019 Version 0.3.38
Pipeline examples added to documentation.
06.06.2019 Version 0.3.37
Bug fixed for null server log retrieved.
06.06.2019 Version 0.3.36
Bug fixed when s3 path entered with backslash.
Adding files upgraded to support multiple directories.
Initial run script copied from nf folder and their inputs entered from outside in ssh command.
03.06.2019 Version 0.3.35
Bug fixed regarding to impersonating user and updating their run status.
03.06.2019 Version 0.3.34
Overwrite the published files when resumed.
31.05.2019 Version 0.3.33
Initial run image update.
30.05.2019 Version 0.3.32
Show settings feature added to workflow inputs.
27.05.2019 Version 0.3.31
Minor update related to default load of form fields.
27.05.2019 Version 0.3.30
Array rows upgraded to support default values in form fields. (eg. varname = ["a","b"] //* @input)
Process script upgraded to support form fields.
Each parameter type added to support repetitive processes.
Documentation updated to cover point at above.
24.05.2019 Version 0.3.29
Minor bug fixed to replace empty form options on nextflow file.
Minor bug fixed by changing object key filtering method.
22.05.2019 Version 0.3.28
Pipeline revision are consolidated as dropdown in the project details page.
Confirmation modal added for removing run in the project details page.
20.05.2019 Version 0.3.27
Settings icon of the process in the run page enabled when its shared with others.
Dropdown options upgraded to dynamically show dropdown options.
Copy run feature upgraded to allow choosing project.
Move run feature added.
15.05.2019 Version 0.3.26
Input channels are fixed to support multiple channels in set format.
15.05.2019 Version 0.3.25
Channel.fromPath updated to support both files and directories as input.
Minor bug fixed in profile table.
14.05.2019 Version 0.3.24
SSH port and singularity cache directory fields added to profile.
13.05.2019 Version 0.3.23
Minor bug fixed in pipeline developer page.
Minor bug fixed in add file modal.
10.05.2019 Version 0.3.22
Bug fixed to support old file format in run logs.
Bug fixed on file selection modal.
10.05.2019 Version 0.3.21
Datatable show percent table upgraded to support non-integers in report section.
Saving run feature upgraded to execute only run environment is changed.
Run Status ordering is updated based on the date_modified column of run table.
08.05.2019 Version 0.3.20
DolphinNext version added to top of the main page.
Minor fix in user verification.
Language mode added for R scripts.
"Select File Modal" updated. (host and project dropdowns added)
Dropdowns of "Select File Modal" upgraded to deselect rows that are filtered out.
Delete file button added into Select File Modal.
06.05.2019 Version 0.3.19
Saving pubweb functionality added into auto update run status feature.
Saving pubweb functionality upgraded to support published s3 files.
Executor settings bug fixed by autosaving run page when run environment is changed.
Bug fixed to allow quote usage in project and pipeline name.
02.05.2019 Version 0.3.18
Status update based on the "failed" keyword removed.
21.04.2019 Version 0.3.17
Auto shutdown Amazon EC2 instance feature added.
Auto update run status feature added.
Nextflow cloud commands will be executed according to nextflow version defined in .sec file.
API_URL variable added to .sec file. (API_URL=http://localhost/dolphinnext)
API_PATH variable replaced with CENTRAL_API_URL in .sec file. (CENTRAL_API_URL=https://www.dolphinnext.com)
Logs and cloud list added to amazon management console.
Documentation updated.
18.04.2019 Version 0.3.16
Error reporting updated. (Run directory could not created)