Release notes

Module

Feature

Description

task submission

Submission template

[Optimized] You can now display 500 or 1,000 records per page. The dialog box height automatically adjusts to the number of records for more efficient browsing. Path: Launch Template > Analysis Entity > Select Data.

Module

Feature

Description

log management

real-time log

[Optimized] The real-time log truncation policy has been adjusted to display more information for running tasks.

Module

Feature

Description

application configuration

runtime attribute

[New] You can now customize the shared memory (shm) size using the shm_mb field in the runtime attributes.

workspace

table

[Optimized] Removed the column limit for tables in a workspace to display all columns.

Module

Feature

Description

application configuration

runtime attribute

[New] Added the oss_cache runtime attribute to customize OSS cache sizes, improving caching efficiency for large files in mount mode.

task submission

Batch termination

[Optimized] Optimized the batch termination logic for faster status updates and higher termination efficiency.

Module

Feature

Description

task management

sub-workflow

[Optimized] Optimized sub-workflow status synchronization to improve reliability for complex task flows.

task management

task details

[Optimized] Clicking a task in the task list now opens its details page in a new tab, preserving the list's state.

Module

Feature

Description

task management

terminate task

[Optimized] Added a confirmation step when terminating a task to warn about potential loss of logs and output.

Module

Feature

Description

task management

task details

[Optimized] Improved WDL syntax error messages to include context, making it easier to locate issues.

Module

Feature

Description

application configuration

runtime attribute

[New] Added support for the timeout parameter in the runtime attributes. You can now set a maximum execution time for a task. Tasks exceeding this time are automatically terminated, and an error is reported in the console.

Module

Feature

Sub-feature

Description

runtime configuration

data loading mode

mount mode

[Optimized] In mount mode, the system now automatically switches to download mode when the mount limit is exceeded, preventing task failures.

runtime configuration

data loading mode

download mode

[Optimized] Improved resumable downloads by enhancing validation and retry mechanisms. This increases the success rate of large file transfers, especially during network interruptions.

Module

Feature

Description

task management

cancel task

[Optimized] Canceled tasks now finish faster by skipping the result upload step.

O&M management

real-time log

[Optimized] Refactored the real-time log architecture to prevent performance issues from frequent or large log outputs.

application management

WDL

[New] Extended WDL to support directories. File paths ending with a forward slash (/) are now automatically recognized as directories.

Module

Feature

Description

application management

WDL

[New] You can now import WDL applications across workspaces.

Module

Feature

Sub-feature

Description

application repository

genomic selection

damo/genomic-selection-dataset

[New] Constructs datasets for genomic selection algorithms.

damo/genomic-selection-train

[New] Trains models for genomic selection algorithms.

damo/genomic-selection-pred-self

[New] Predicts phenotypes for inbred lines using genomic selection algorithms.

damo/genomic-selection-pred-f1

[New] Predicts phenotypes for hybrid F1 using genomic selection algorithms.

Module

Feature

Sub-feature

Description

application configuration

Create Application (WDL)

runtime

[New] You can specify multiple instance types in runtime, such as type=gc6.small,gc5.medium,gc4.medium.

[New] You can declare the disk size directly in runtime. In this case, the nas_cap data disk type is used by default.

[New] The runtime attribute supports four data disk types: cloud_essd, cloud_essd_pl1, nas_per, and nas_cap.

[New] You can mount an OSS bucket by specifying the env field in runtime. This feature supports OSS buckets in the same account or different accounts.

[New] You can use Sentieon by setting the Sentieon license as an environment variable in runtime.

runtime option settings

[New] You can select a data loading mode: mount mode or download mode. The UI defaults to mount mode.

application repository

variant analysis

Sentieon

[Updated] To use Sentieon, you must set the Sentieon license as an environment variable.

sequence alignment

damo/vardict

[New] CPU-parallel-accelerated VarDict.

damo/bwa-mem2

[New] Cloud-optimized bwa-mem2.

damo/bwa-mem2-index

[New] bwa-mem2 index construction.

damo/blastn

[New] Cloud-optimized blastn.

damo/blastn-makedb

[New] blastn database construction.

Module

Feature

Sub-feature

Description

application repository

sequence alignment

damo/align-markdup-bqsr

[New] GPU-accelerated application for sequence alignment, duplicate marking, and Base Quality Score Recalibration (BQSR).

variant calling

damo/haplotype-calling

[New] GPU-accelerated version of HaplotypeCaller.

sequence compression

damo/fqcompress

[New] Application for high-ratio FASTQ file compression.

damo/fqdecompress

[New] Application for decompressing high-ratio compressed FASTQ files.

variant calling index

damo/dna-index

[New] Application for building indexes for GPU-accelerated variant analysis workflows.

Module

Feature

Sub-feature

Description

application repository

population variant calling

damo/dna-variant-calling

[New] GPU-accelerated variant analysis workflow.

damo/joint-calling

[New] CPU+GPU hybrid workflow for population variant analysis.

Release date

Change

Key features

May 28, 2021

Public beta launch of Gene Analysis Service.

• Develop, manage, and analyze bioinformatics workflows using the WDL standard.

• Process sample data of any scale with a serverless genomic compute engine.

• Control CPU and memory compute resources with fine-grained, intelligent scheduling.

• Use common workflows like DNAseq and Joint Calling through integration with the third-party software Sentieon.