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Wave v1.44.0

Feature updates and improvements​

Container building​

  • Added support for Pixi lock files with the conda/pixi:v1-lock template by @pditommaso in #1246

General​

  • Added the --soci option to the Wave CLI by @pditommaso in #1226
  • Changed SOCI job IDs to use si- and sp- prefixes by @pditommaso in #1250

Bug fixes​

Container building​

  • Fixed multi-element WAVE_ENTRY_CHAIN values on freeze builds to use a JSON array by @pditommaso in #1247

General​

  • Fixed Kubernetes job launches to adopt an existing job when a launch is redelivered by @Tyagiquamar in #1222

New contributors​

  • @Tyagiquamar made their first contribution in #1222

Full changelog: https://github.com/seqeralabs/wave/compare/v1.43.0...v1.44.0

Nextflow 26.10.5

Feature updates and improvements​

Wave​

  • Added the wave.soci option for SOCI lazy loading by @pditommaso in #7991

Bug fixes​

Language features​

  • Changed channel.interval to use a daemon timer to avoid hanging the JVM by @bentsherman in #7981
  • Fixed formatting of typed publish targets by @bentsherman in #7960
  • Fixed missing source channel edges in the DAG for typed processes by @bentsherman in #7979

Wave​

  • Fixed and simplified the Wave build templates docs by @pditommaso in #7951

General​

  • Fixed cloud integration tests by @pditommaso in #7895

Dependencies​

  • Bumped nf-seqera@0.26.2
  • Bumped nf-wave@1.22.5
  • Bumped sched-client to 0.113.0 in nf-seqera for idempotent task submission by @pditommaso in #7952

Full changelog: https://github.com/nextflow-io/nextflow/releases/tag/v26.10.5

Wave v1.43.0

Feature updates and improvements​

Dependencies​

  • Updated public.cr.seqera.io/seqeralabs/nf-jdk Docker tag to v25.0.5 by @seqeralabs-renovate[bot] in #1231
  • Updated io.micronaut.platform:micronaut-platform dependency to v4.10.22 by @seqeralabs-renovate[bot] in #1228
  • Updated Gradle minor and patch dependencies by @seqeralabs-renovate[bot] in #1230
  • Updated GitHub Actions by @seqeralabs-renovate[bot] in #1229

General​

  • Added SOCI v2 indexes for ephemeral, freeze, and mirror containers by @pditommaso in #1227
  • Changed the Claude PR review to run only on @claude mentions by @pditommaso in #1210
  • Moved the ECR tests to a dedicated test account with an OIDC role by @ShahzebMahmood in #1218
  • Moved builds and tests to scheduled GitHub Actions runners by @pditommaso in #1224

Bug fixes​

General​

  • Fixed blob location routing for repositories with more than two path segments by @pditommaso in #1240

Full changelog: https://github.com/seqeralabs/wave/compare/v1.42.2...v1.43.0

Fusion v2.6.13

Fusion v2.6.13 fixes NFS service mode regressions introduced in v2.6.12 and adds support for custom Azure Blob Storage endpoints.

How to pin this version​

fusion {
enabled = true
containerConfigUrl = 'https://fusionfs.seqera.io/releases/v2.6.13-amd64.json'
}
info

For ARM64 CPU architecture, use containerConfigUrl = 'https://fusionfs.seqera.io/releases/v2.6.13-arm64.json'.

Feature updates and improvements​

Azure​

  • Added AZURE_STORAGE_ENDPOINT to set a custom Azure Blob Storage endpoint, such as an Azurite emulator.

Bug fixes​

NFS service mode​

  • Fixed deleting a large directory failing with Directory not empty.
  • Fixed empty output files failing the task with Missing output file(s).
  • Fixed clean relaunches after a Spot reclamation seeing files from the previous attempt.
  • Fixed a large end-of-task upload blocking file operations of other tasks on the same host.

Fusion Snapshots​

  • Fixed snapshot restores failing with bad mode 0100744 on files written by an upstream task.

Upgrade notes​

  • Drop-in replacement for v2.6.12. No configuration changes required.
  • An invalid AZURE_STORAGE_ENDPOINT fails the mount.

Seqera Enterprise v26.2.3

Feature updates and improvements​

Pipelines​

  • Added a Quick launch button to the empty state of the Runs page. Next to it, Launch pipeline appears when the workspace has pipelines, and Add pipeline when it has none.

Data Explorer​

  • Added a Create folder action next to Upload in Data Explorer, which creates an empty folder in an AWS S3, Azure Blob Storage, or Google Cloud Storage data repository, including from the data picker in the launch form. Like uploading, it requires write permission on the data repository, so the Launch and View roles cannot create folders, and it is not available for public data repositories.
  • Added a .azure_blob_dir marker file to each folder created in an Azure Blob Storage data repository, the convention Nextflow uses to keep an empty directory. The marker appears in the folder listing, and is not written when the folder already has content.

Bug fixes​

Studios​

  • Fixed long names in the Studios list being truncated at a fixed width even when the column had room to show them.

Credentials​

  • Restricted the Azure Batch and Azure Storage account names in Azure credentials to 3 to 24 letters and digits, matching Azure's account naming rules. A name with other characters, such as URL delimiters, is rejected when the credential is created or updated, before it can be used to build an Azure endpoint URL.

Pipelines​

  • Fixed the Recently updated sort on the Launchpad ignoring pipelines beyond the first 60. Pipelines are now sorted on the server.
  • Fixed the run details page continuing to show the previous run after you opened another run in the same workspace, for example from global search.
  • Fixed adding a pipeline failing when its optional repository avatar could not be fetched. A failed avatar lookup no longer blocks pipeline creation.
  • Fixed a repository request refused by outbound request protection failing with an unexpected error. The error now names the repository and why it could not be accessed.
  • Fixed requests to a Git server configured with an http:// address that redirects to HTTPS losing their credentials. A redirect from HTTP to HTTPS on the same host and default ports now keeps the request headers.
  • Updated the bundled Nextflow version to 25.10.9, which keeps a Bitbucket API token out of the repository clone URL.

Data Explorer​

  • Fixed file lineage in the file preview failing with 503 errors, or missing resumed runs, when it looked up the run that produced a file. The run is now resolved through lineage search, and its link opens the run in its own workspace.
  • Aligned the error for an AWS S3 bucket that the credentials cannot access with the other providers: Data Explorer now reports that the credentials for the bucket are missing or not valid. Other S3 bucket validation failures now return a bad request error instead of the raw S3 error.
  • Fixed a zero-byte name/ folder placeholder blob in an Azure Blob Storage data repository appearing as a blank file inside the folder it represents. It is now omitted from that folder's listing and shown as a folder elsewhere.

General​

  • Extended outbound request protection to every Source Code Management request for pipelines and Studios, adding branch and tag listings, repository validation, and avatar lookups to file reads. Each redirect hop is re-checked, and credentials such as a GitLab PRIVATE-TOKEN header are no longer forwarded to another host on a redirect.
  • Hardened the bucket event endpoint used by pipeline actions. Every SNS message is now signature-verified, and a subscription confirmation must match the stored topic and is completed with the SNS ConfirmSubscription API instead of by fetching a URL from the message.
  • Restricted the Wave pairing proxy to the Seqera Platform API endpoint. A request to any other scheme, host, port, or path is refused with 403.
  • Fixed the pagination of the resource selection dialog in projects being cut off on taller screens.

Upgrade notes​

No database migrations are included in this release.

Outbound request protection covers every Source Code Management request​

TOWER_SSRF_PROTECTION_MODE and TOWER_SSRF_PROTECTION_ALLOWED_HOSTS now govern every Source Code Management request for pipelines and Studios: file reads, branch and tag listings, repository validation, and avatar lookups, each re-checked at every redirect hop. If a Git server resolves to a private address and is not allowed by TOWER_SSRF_PROTECTION_ALLOWED_HOSTS, the default warn mode now logs SSRF protection warnings for these requests too. Search the backend logs again before switching to enforce.

TOWER_HTTP_URL_FETCH_MAX_BODY_BYTES now caps the response of each of these requests, not only file reads, and replaces Nextflow's NXF_GIT_RESPONSE_MAX_LENGTH for all of them. TOWER_HTTP_URL_FETCH_TIMEOUT and TOWER_HTTP_URL_FETCH_CALL_TIMEOUT apply to them as well.

Azure credentials must use valid account names​

Azure credentials are rejected on create or update when the Batch or Storage account name is not 3 to 24 letters and digits. A stored credential with such a name now fails validation, so review existing Azure credentials before you upgrade.

API changes​

The published API contract moves from 1.228.0 to 1.229.0. It adds CreateDataLinkFolder, declares the nullable compute environment fields listed under bug fixes, and declares the account name pattern for the Azure credential batchName and storageName fields. Regenerate any OpenAPI-derived clients against 1.229.0.

Security updates​

  • CVE-2026-91403, CVE-2026-113470: Updated the Java base image for the backend and database migration containers to Amazon Corretto 25.0.5, which blocks the compromised eMudhra intermediate certificates and removes the affected emSign roots.
  • CVE-2023-54404 (GHSA-mrhx-c7xc-m3w5): Updated the zod dependency of the web frontend to 4.6.7. Versions before 4.6.6 could exhaust memory validating an oversized array, even when the schema set a maximum length.

Fusion v2.6.12

Fusion v2.6.12 improves Spot reclamation handling in NFS service mode, adds Fusion errors to .command.log, and fixes S3 work directories whose role cannot tag objects.

How to pin this version​

fusion {
enabled = true
containerConfigUrl = 'https://fusionfs.seqera.io/releases/v2.6.12-amd64.json'
}
info

For ARM64 CPU architecture, use containerConfigUrl = 'https://fusionfs.seqera.io/releases/v2.6.12-arm64.json'.

Feature updates and improvements​

NFS service mode​

  • Added early upload of task work directories when a Spot reclamation notice arrives. The fusion-nfs image turns it on with FUSION_NFS_RECLAIM_EARLY_FLUSH=true.
  • Changed the fusion-nfs image to run a new implementation of Fusion's file metadata layer.

General​

  • Added Fusion errors to the task's .command.log, so they appear in the Seqera Platform execution log.

Metrics​

  • Added the fusion_cache_refaults_total, fusion_cache_refaults_bytes_total, fusion_chunk_prefetch_wasted_total, and fusion_chunk_prefetch_wasted_bytes_total counters for cache thrashing. See The cache is thrashing.

AWS​

  • Changed the S3 anonymous-access warning to include why credentials could not be retrieved.

Bug fixes​

NFS service mode​

  • Fixed a failed NFS mount falling back to a regular mount. Fusion now exits with 173, or 172 for a malformed FUSION_NFS_SOURCE. See Exit codes 172 and 173.
  • Fixed tasks relaunched on the same host failing with exit code 174.
  • Fixed cleanup of a large previous attempt timing out and failing the task with exit code 173.

Fusion Snapshots​

  • Fixed snapshot restores in NFS service mode failing with exit code 175 or 177. Checkpoints are now uploaded while the task runs.
  • Fixed tasks that finished during a Spot reclamation notice being relaunched and failing with exit code 175. Requires fusion-snapshot 1.10.0.

AWS​

  • Fixed S3 work directories failing to mount with exit code 174 when the role lacks s3:PutObjectTagging.
  • Fixed Nextflow command files (.command.run, .command.sh, .command.stage, and .command.in) losing their FUSION_TAGS tags.

Dependencies​

  • Updated CI, build pipeline, and dependencies.

Upgrade notes​

  • Drop-in replacement for v2.6.11. No configuration changes required.
  • FUSION_NFS_RECLAIM_EARLY_FLUSH has no effect outside the fusion-nfs image.
  • S3 lifecycle rules filtered on nextflow.io/metadata=true match .command.run and .command.sh again.

Seqera Enterprise v25.3.8

This is a maintenance release. It contains no feature changes and no bug fixes.

Upgrade notes​

No breaking changes. Standard upgrade procedure applies. No database migrations are included in this release.

Security updates​

  • CVE-2026-113470: Updated the Java base image for the backend and database migration containers to Amazon Corretto 17.0.21, which removes the affected emSign roots. The compromised eMudhra intermediate certificate authorities covered by CVE-2026-91403 were already blocked in v25.3.7; Corretto 17.0.21 carries the same block.

Seqera Enterprise v26.1.6

Bug fixes​

Platform API​

  • Fixed generated API clients and schema validators rejecting valid 2xx responses. Optional credential, pipeline, workflow, task, team, participant, user, and organization response properties are now declared nullable in the OpenAPI specification. Runtime serialization is unchanged.
  • Fixed compute environment responses failing schema validation. Nullable AWS Batch, Forge, and common compute configuration fields are now declared, forged and deleted Forge resources are modelled as string-valued maps, and ForgeConfig.arm64Enabled, ForgeConfig.fargateHeadEnabled, and secretsKmsKeyId are nullable when a persisted configuration omits them.
  • Fixed credential responses emitting null AWS and GitHub secret values. Null secrets are now omitted from the JSON response while write-only OpenAPI semantics are retained, and the conditional workspaceId requirement for workspace-owned versus user-owned credentials is documented.
  • Fixed the workflow, task, load, statistics, launch, and job response contracts to match the values actually returned, and corrected LogPage.entries to an array of strings.
  • Fixed the pipeline version creator metadata, repository list values, and the dataset, participant, data-link, label, and Studios response contracts to match the values actually returned.
  • Fixed dataset downloads losing the stored media type, and declared CSV, TSV, and octet-stream response media types for dataset version downloads.
  • Fixed the GA4GH WES endpoints returning 500 instead of 404 for a run ID that does not exist. Run describe, status, and cancel now return and document 404, and member lookup documents 404.

Monitoring and observability​

  • Fixed fusion_throughput_bytes telemetry reporting only the first day of the current month for each organization. The current month now counts every day so far. Past months are unchanged.

General​

  • Fixed the Fusion throughput quota never blocking a launch. The launch-time check read the current month's usage as zero because usage is stored as one row per day, so maxFusionThroughputBytes was never enforced. The check now sums the organization's daily rows for the current UTC month, which matches the figure shown on the Fusion usage dashboard.

Upgrade notes​

No breaking changes. Standard upgrade procedure applies. No database migrations are included in this release.

API changes​

The published API contract moves from 1.184.0 to 1.192.0. Most changes correct the specification to describe responses the server already returned, with two exceptions that change responses:

  • Null credential secrets are now omitted. AWS and GitHub secret keys that previously serialized as null are no longer present in credential responses. Clients that read these keys must tolerate an absent key rather than a null value.
  • GA4GH WES returns 404 for unknown runs. Run describe, status, and cancel return 404 instead of 500 when the run ID does not exist.

Regenerate any OpenAPI-derived clients against 1.192.0 to pick up the corrected nullability declarations.

Behavior changes​

  • The Fusion throughput quota is now enforced. Organizations with maxFusionThroughputBytes set have had no effective limit since Fusion usage moved to daily rows. Launches that exceed the configured quota are now blocked. Review configured quotas against current Fusion usage before you upgrade.
  • Fusion telemetry totals increase. The fusion_throughput_bytes value reported for the current month now covers the full month to date rather than its first day.

Security updates​

  • CVE-2026-42198: Updated the PostgreSQL JDBC driver to 42.7.12, which resolves a client-side denial of service during SCRAM-SHA-256 authentication, where a malicious server requests an unbounded PBKDF2 iteration count.
  • CVE-2026-91403, CVE-2026-113470: Updated the Java base image for the backend and database migration containers to Amazon Corretto 17.0.21, which blocks the compromised eMudhra intermediate certificates and removes the affected emSign roots.

Wave v1.42.2

Feature updates and improvements​

Container building​

  • Documented CA certificates in Pixi images by @pditommaso in #1211
  • Documented nested packages build options in the container API by @pditommaso in #1208
  • Added a dedicated Build with Pixi documentation section by @MichaelTansiniSeqera in #1150
  • Added the Pixi build template to the Nextflow configuration reference by @MichaelTansiniSeqera in #1148

Dependencies​

  • Updated node dependency to v24.22.0 by @seqeralabs-renovate[bot] in #1214
  • Updated github.com/moby/buildkit module to v0.34.1 by @seqeralabs-renovate[bot] in #1213
  • Updated public.cr.seqera.io/seqeralabs/nf-jdk:corretto-25.0.4-al2023-jemalloc Docker digest to 15e35e9 by @seqeralabs-renovate[bot] in #1212
  • Updated Gradle minor and patch dependencies by @seqeralabs-renovate[bot] in #1215

General​

  • Removed the Comodo AAA root certificate from the Wave CLI native trust store (CVE-2026-91403) by @pditommaso in #1205
  • Changed the workflow lookup to request the minimal workflow record and stop renewing on any 4xx reply by @pditommaso in #1209
  • Pulled the docs-previewer image from public.cr.seqera.io instead of Harbor by @ShahzebMahmood in #1206
  • Changed the base image to public.cr.seqera.io/seqeralabs/nf-jdk by @pditommaso in #1207
  • Aligned the repository CI with the squad baseline by @cristianrcv in #1204
  • Changed the Homebrew tap release to use the JRELEASER_HOMEBREW_GITHUB_TOKEN secret by @munishchouhan in #1217
  • Stopped copying the release image to the legacy ECR by @ShahzebMahmood in #1216

New contributors​

  • @MichaelTansiniSeqera made their first contribution in #1150

Full changelog: https://github.com/seqeralabs/wave/compare/v1.42.1...v1.42.2

Seqera Cloud v27.1.0_cycle78

Breaking changes​

Private Studios now admit only the users on their allowed users list, the creator included. A creator who is not on the list can still start, stop, edit, and delete the Studio, but cannot connect to it or use its checkpoints. Existing private Studios with no allowed users have their creator added; a Studio already shared with another user keeps its list, and its creator must be added to it to connect.

Feature updates and improvements​

Studios​

  • Removed the limit of one additional allowed user on a private Studio, through the API.
  • Added stopping a private Studio, and extending its lifespan from inside the session, for its allowed users.
  • Added checkpoint access for a private Studio's allowed users, covering reading a checkpoint, renaming it, and creating a Studio from it.
  • Added mounting a data link in a Studio when it is in one of the compute environment's allowed S3 buckets, even if it uses other credentials. Applies to AWS Batch, AWS Cloud, and Seqera Compute compute environments.

Compute environments​

  • Added an Allowed S3 buckets field to the Seqera Compute compute environment form for granting access to S3 buckets in your own AWS account.
  • Added a Bucket policy section to the Seqera Compute compute environment details page with the policy to apply to each allowed bucket.
  • Redesigned the compute environments list as a table with columns for name, ID, region, enabled features, last activity, and status.

Monitoring​

  • Changed the run timeline to sort processes in pipeline order by default.
  • Added a Sort processes menu to the run timeline, with Earliest started and Latest started options.
  • Added an Attempt label to retried task rows in the run timeline, and a retry count to each process row.

Co-Scientist​

  • Changed the label below a conversation title to name the organization instead of the workspace.

Agents​

  • Added agents: named, reusable sets of instructions that Co-Scientist runs on your behalf in a workspace. Anyone in the workspace can run an agent without rewriting its prompt.
  • Added a service account as the identity an agent runs under. An agent's work is attributed to that account rather than to the person who created it.
  • Added binding a workspace GitHub App credential to an agent for clone, commit, and push operations in place of the creator's personal access token. Each installation token the agent mints is recorded in the audit log.
  • Added a read-only view of a workspace-owned agent thread in the Co-Scientist drawer, with a Fork button that copies the thread into a personal chat.
  • Added stopping a running agent session.
  • Added automatic disabling of an agent when its service account leaves the workspace.

Actions​

  • Added three event sources to actions: Bucket event, which fires when a marker file arrives in or is removed from cloud storage, Schedule, which fires on a recurring cadence, and Pipeline run event, which fires when a run of a watched pipeline reaches a terminal state.
  • Added an agent Target to the three new event sources, which hands the event to an agent instead of launching a pipeline.
  • Added Daily, Weekly, and Custom schedule options for a scheduled action. A saved action keeps the timezone it was created in.
  • Added Details and Trigger history tabs to the action details page. Trigger history lists each firing of the action and the event payload behind it.
  • Added a View target control to an agent row in Trigger history that opens the agent's conversation in the Co-Scientist drawer.
  • Added editing a saved action's name, labels, marker file, and schedule.
  • Added a label to the runs an agent action starts.
  • Added an optional pipeline and version to the Target of a pipeline run event action.
  • Changed a chained action to skip the run it caused itself.

Service accounts​

  • Added editing a service account's name, description, and workspace access from a dialog on its details page.
  • Blocked removing or deleting a service account that is bound to an active agent.

Access control​

  • Added single sign-out for applications that sign in with Seqera. Signing out of one now ends your Seqera session too.

General​

  • Improved screen reader output by hiding decorative icons and naming the icons that carry meaning.

Bug fixes​

Compute environments​

  • Fixed a compute environment deletion blocked by running workflows or active Studio sessions reporting a generic error instead of naming them.
  • Fixed Azure Batch Forge autoscaling adding one node per queued task instead of filling each node's task slots. Compute environments created earlier keep the previous formula.

Credentials​

  • Fixed the Azure credentials forms accepting Batch and Blob Storage account names that Azure rejects.
  • Fixed a Git credential with a repository base URL applying to other accounts whose names begin with the same text.
  • Fixed a Git credential with a repository base URL being ignored for a pipeline referenced by a short owner/repo name.

Datasets​

  • Fixed the dataset details page showing no avatar for a creator whose avatar comes from their identity provider.

Monitoring​

  • Fixed the run Parameters Groovy view producing text that is not valid Nextflow configuration. The view is now Nextflow config and downloads as a .config file.
  • Fixed the run Parameters JSON view showing a tree with unquoted keys instead of the JSON that Copy and Download produce.

Pipelines​

  • Fixed the Launchpad Recently updated sort ordering only the pipelines on the current page.
  • Fixed a launch form staying invalid with no explanation when the pipeline schema contained a pattern the browser cannot compile.

Projects​

  • Fixed the resource dialog clipping its pagination controls.

General​

  • Fixed icons in disabled buttons rendering at low contrast instead of following the button's color.