Merge branch 'master' into justinegeffen-patch-4

changelog/fusion/v2.3.6.mdx

@@ -0,0 +1,9 @@
+---
+title: Fusion v2.3.6
+date: 2024-10-21
+tags: [fusion]
+---
+
+### Bug fixes
+
+- Fix S3 compactions between different regions

changelog/fusion/v2.3.7.mdx

@@ -0,0 +1,9 @@
+---
+title: Fusion v2.3.7
+date: 2024-10-29
+tags: [fusion]
+---
+
+### New features and improvements
+
+- Backport: Timeout on FUSE mount retry failure

changelog/fusion/v2.3.8.mdx

@@ -0,0 +1,9 @@
+---
+title: Fusion v2.3.8
+date: 2024-11-04
+tags: [fusion]
+---
+
+### Bug fixes
+
+- Fix security vulnerabilities

changelog/fusion/v2.4.4.mdx

@@ -6,16 +6,17 @@ tags: [fusion]
 
 Bugfix release to improve stability.
 
-{/* truncate */}
-
 ### Feature updates and improvements
 
-- Fix: move a folder with inner folders and big files
-- Fix: propagate truncating to zero to the remote store
-- Fix: move that overwrites a file scheduled to upload
 - Azure: Prefer Nextflow-provided SAS token for authentication
 - Define a default exit code 174 on Fusion IO error
 
+### Bug fixes
+
+- Move folders that contain subfolders and big files
+- Propagate truncating to zero to remote storage
+- File moves overwriting files scheduled for upload
+
 ### How to pin this version
 
 ```groovy
@@ -25,4 +26,6 @@ fusion {
 }
 ```
 
-_NOTE: For ARM64 use https://fusionfs.seqera.io/releases/v2.4.4-arm64.json_
+:::info 
+For ARM64 CPU architecture, use `containerConfigUrl = 'https://fusionfs.seqera.io/releases/v2.4.4-arm64.json'`.
+:::

changelog/fusion/v2.4.5.mdx

@@ -0,0 +1,13 @@
+---
+title: Fusion v2.4.5
+date: 2024-10-29
+tags: [fusion]
+---
+
+### Bug fixes
+
+- Timeout on FUSE mount retry failure
+- Error when overwriting a symbolic link
+- Correct spot instance termination detection
+- Force unmount and upload dirty data on failed unmount
+- Cancel scheduled upload that is overwritten by an empty file

changelog/fusion/v2.4.6.mdx

@@ -0,0 +1,9 @@
+---
+title: Fusion v2.4.6
+date: 2024-11-04
+tags: [fusion]
+---
+
+### Bug fixes
+
+- Fix security vulnerabilities

changelog/fusion/v2.4.7.mdx

@@ -0,0 +1,21 @@
+---
+title: Fusion v2.4.7
+date: 2024-12-11
+tags: [fusion]
+---
+
+### Feature updates and improvements
+
+- Add license validation
+- Integrate Fusion snapshots
+- Make `stopFusion` timeout configurable (via `FUSION_STOP_SHUTDOWN_TIMEOUT`)
+
+### Bug fixes
+
+- Fusion shutdown only once
+- File moves overwriting files scheduled for upload
+- Force unmount and upload dirty manager on failed unmount
+- Correct spot instance termination metadata path
+- Error when overwriting a symbolic link
+- Add a timeout to Fusion stop function
+- Upload symbolic links in parallel 

changelog/fusion/v2.4.8.mdx

@@ -0,0 +1,14 @@
+---
+title: Fusion v2.4.8
+date: 2024-12-20
+tags: [fusion]
+---
+
+Bugfix release to improve stability.
+
+### Bug fixes
+
+- Do not delete the logs file during spot reclaim
+- Upload logs file in parts to support files larger than 5 GB 
+- Remove leftover `.bak` file when using BAM and Tabix index 
+- Security: Bump golang.org/x/crypto from 0.25.0 to 0.31.0

changelog/fusion/v2.5.0.mdx

@@ -0,0 +1,37 @@
+---
+title: Fusion v2.5.0
+date: 2025-01-14
+tags: [fusion]
+---
+
+Fusion 2.5.0 significantly enhances performance and efficiency in file operations. 
+
+Fusion now handles small files more effectively and intelligently manages Nextflow task files by minimizing intermediate file uploads. A key improvement is the selective retention of only essential task output files upon completion, reducing storage overhead. Network optimization has been implemented to decrease bandwidth usage by consolidating upload operations. Additionally, the underlying architecture has undergone substantial refactoring to support the future integration of diverse remote storage solutions, setting the foundation for expanded storage capabilities.
+
+### Feature updates and improvements
+
+- Chunked async content management
+- Nextflow-compatible pattern classifier
+- Define a default exit code on Fusion-IO errors
+- Object API refactoring
+- Bump golang.org/x/crypto to 0.31.0
+- Bump golang.org/x/net to 0.33.0
+
+### Bug fixes 
+
+- AsyncStore move issues
+- Log file deletion during spot instance reclamation 
+- Transient object persistence
+
+### How to pin this version
+
+```bash
+fusion {
+  enabled = true
+  containerConfigUrl = 'https://fusionfs.seqera.io/releases/v2.5.0-amd64.json'
+}
+```
+
+:::info 
+For ARM64 CPU architecture, use `containerConfigUrl = 'https://fusionfs.seqera.io/releases/v2.5.0-arm64.json'`.
+:::

changelog/fusion/v2.5.1.mdx

@@ -0,0 +1,26 @@
+---
+title: Fusion v2.5.1
+date: 2025-01-27
+tags: [fusion]
+---
+
+Bugfix release to improve stability.
+
+### Bug fixes
+
+- Logs removed when `removeLogs` is false
+- Unique IDs in file fragments
+- Remove exit code on `serveFusion`
+
+### How to pin this version
+
+```bash
+fusion {
+  enabled = true
+  containerConfigUrl = 'https://fusionfs.seqera.io/releases/v2.5.1-amd64.json'
+}
+```
+
+:::info 
+For ARM64 CPU architecture, use `containerConfigUrl = 'https://fusionfs.seqera.io/releases/v2.5.1-arm64.json'`.
+:::

changelog/multiqc/v1.27.1.mdx

@@ -0,0 +1,46 @@
+---
+title: MultiQC v1.27.1
+date: 2025-02-07
+tags: [multiqc]
+---
+
+### Fixes and improvements in AI summaries:
+
+- AI summaries should now work with `bioconda install multiqc` without additional dependencies
+- Supporting other LLM providers with a custom endpoint passed through the command line ([docs](https://docs.seqera.io/multiqc/ai#choosing-a-provider))
+- Option to anonymize sample names
+
+{/* truncate */}
+
+### Feature updates and improvements
+
+- AI summaries:
+
+  - Add **Chat with Seqera AI** buttons to all summaries ([#3067](https://github.com/MultiQC/MultiQC/pull/3067))
+  - Add options to configure custom OpenAI endpoint ([#3083](https://github.com/MultiQC/MultiQC/pull/3083))
+  - Support anonymizing sample names ([#3074](https://github.com/MultiQC/MultiQC/pull/3074))
+  - Use `tiktoken` to estimate token counts for all providers ([#3064](https://github.com/MultiQC/MultiQC/pull/3064))
+  - Remove the dependency on `langchain`, `openai`, and `anthropic` packages ([#3066](https://github.com/MultiQC/MultiQC/pull/3066))
+  - Always save prompt to file ([#3078](https://github.com/MultiQC/MultiQC/pull/3078))
+  - Box plot: use statistics instead of raw values ([#3077](https://github.com/MultiQC/MultiQC/pull/3077))
+  - Fix for in-browser summaries: when **Clear summary** clicked on global, clear also the generated extended summary ([#3068](https://github.com/MultiQC/MultiQC/pull/3068))
+  - Make token count warning a debug ([#3071](https://github.com/MultiQC/MultiQC/pull/3071))
+
+- Improving table small scatter plots:
+
+  - Support hide, rename, highlight ([#3082](https://github.com/MultiQC/MultiQC/pull/3082))
+  - Remove legend to make more space ([#3081](https://github.com/MultiQC/MultiQC/pull/3081))
+
+- Configuring from `env`: resolve empty to `None` ([#3072](https://github.com/MultiQC/MultiQC/pull/3072))
+- Do not print stack trace on `KeyboardInterrupt` unless verbose ([#3063](https://github.com/MultiQC/MultiQC/pull/3063))
+- Custom content:
+  - Allow leading empty columns when parsing `.TSV` ([#3059](https://github.com/MultiQC/MultiQC/pull/3059))
+  - Handle empty input files ([#3086](https://github.com/MultiQC/MultiQC/pull/3086))
+
+### Module updates
+
+- Sequali: change DOI to article link ([#3084](https://github.com/MultiQC/MultiQC/pull/3084))
+
+### Module fixes
+
+- FastQC: fix **Per Base Sequence Content** heatmap ([#3075](https://github.com/MultiQC/MultiQC/pull/3075))

changelog/seqera-cloud/v24.3.0-cycle3_27f712a.mdx

@@ -0,0 +1,24 @@
+---
+title: Seqera Cloud v24.3.0-cycle3_27f712a
+date: 2025-02-10
+tags: [seqera cloud]
+---
+
+### Feature updates and improvements
+
+- Studios:
+    - Display the applied date filter on the Dashboard page.
+    - Add support for custom templates for input control options such as workspace visibility and session lifespan.
+- Fusion:
+    - Default to Amazon Linux 2023 AMI when Fusion v2 is enabled.
+    - Add support for Fusion licensing.
+- (Enterprise only) Add a job to save usage metrics to files so usage data can be accessed and shared by users even when they’re not connected to License Manager.
+- Implement `FaviconService` that changes the favicon based on pipeline run or Studio status.
+- Increase `accessTokenExpirationTime` by 10% to always trigger a token refresh when Platform is open in a browser tab that isn't hibernated.
+- Allow Nextflow configuration parameters with embedded references to other parameters to be shown verbatim.
+- Extend zombie jobs detection on all workflows reaching one of the terminal states (`SUCCEEDED`, `FAILED`, `CANCELLED`).
+
+### Bug fixes 
+
+- Fixed an additional reference to the `mainScript` parameter in the `pipeline-info` API response.
+- Improved security of passthrough redirection on Platform authentication.

changelog/seqera-cloud/v24.2.0_cycle28.mdx → changelog/seqera-cloud/v24.3.0_024e9bb.mdx

@@ -1,10 +1,10 @@
 ---
-title: Seqera Cloud v24.2.0_cycle28
-date: 2025-01-22
+title: Seqera Cloud v24.3.0_024e9bb
+date: 2025-01-24
 tags: [seqera cloud]
 ---
 
-### Breaking change
+### Breaking changes
 
 - Restore `errorStrategy` and `maxRetries` default Nextflow config for AWS and GCP launches. Platform will not overwrite existing error strategy coded in the pipeline repository.
 - If you want to automatically retry on task failures (e.g., from spot reclamations), you will now need to explicitly set `errorStrategy` and `maxRetries`.

changelog/wave/v1.12.4.mdx

@@ -4,7 +4,7 @@ date: 2024-09-26
 tags: [wave]
 ---
 
-- Fix build succeded & status response [8a760b39](https://github.com/seqeralabs/wave/commit/8a760b39283800d3331ea7cfac2648a748c15571)
+* Fix build succeded & status response [8a760b39](https://github.com/seqeralabs/wave/commit/8a760b39283800d3331ea7cfac2648a748c15571)
 
 {/* truncate */}
 

changelog/wave/v1.13.10.mdx

@@ -0,0 +1,12 @@
+---
+title: Wave v1.13.10
+date: 2024-10-29
+tags: [wave]
+---
+
+## Feature updates and improvements
+
+* Log slow processing stream messages by @pditommaso in [e8a6b7ee](https://github.com/seqeralabs/wave/commit/e8a6b7eeabe52cc1fa6079a15bdc268552dca7b0)
+* Prevent scan when mode is not defined by @pditommaso in [d42bcae1](https://github.com/seqeralabs/wave/commit/d42bcae17dd40c90dfa8f4d67f06b890f9c402d8)
+
+**Full changelog**: https://github.com/seqeralabs/wave/compare/v1.13.9...v1.13.10

changelog/wave/v1.13.11.mdx

@@ -0,0 +1,13 @@
+---
+title: Wave v1.13.11
+date: 2024-11-02
+tags: [wave]
+---
+
+## Feature updates and improvements
+
+* Bump org.apache.commons:commons-compress:1.27.1 by @munishchouhan in https://github.com/seqeralabs/wave/pull/722
+* Cap number of scan vulnerabilities reported by @munishchouhan in https://github.com/seqeralabs/wave/pull/728
+* Save scan record async by @pditommaso in https://github.com/seqeralabs/wave/pull/730
+
+**Full changelog**: https://github.com/seqeralabs/wave/compare/v1.13.10...v1.13.11

changelog/wave/v1.13.9.mdx

@@ -0,0 +1,12 @@
+---
+title: Wave v1.13.9
+date: 2024-10-29
+tags: [wave]
+---
+
+## Feature updates and improvements
+
+- Fix inspect view by @munishchouhan in https://github.com/seqeralabs/wave/pull/724
+- Fix inspect view by @munishchouhan in https://github.com/seqeralabs/wave/pull/725
+
+**Full changelog**: https://github.com/seqeralabs/wave/compare/v1.13.8...v1.13.9

changelog/wave/v1.14.0.mdx

@@ -0,0 +1,22 @@
+---
+title: Wave v1.14.0
+date: 2024-11-10
+tags: [wave]
+---
+
+## Feature updates and improvements
+
+* Fix K8s env propagation by @pditommaso in [76f0a456](https://github.com/seqeralabs/wave/commit/76f0a456a792f2a5a9888ce60e1f0075e73337ce)
+* Remove deprecated K8s methods by @pditommaso in https://github.com/seqeralabs/wave/pull/734
+* Bump to Micronaut 4.6 by @pditommaso in https://github.com/seqeralabs/wave/pull/318
+* Bump Java 21 as build requirement by @pditommaso in https://github.com/seqeralabs/wave/pull/519
+* Bump bitbucket.b_c:jose4j:0.9.4 by @pditommaso in [2e10416a](https://github.com/seqeralabs/wave/commit/2e10416a84c1a97716455ccf9b73945466eea28e)
+* Bump bouncycastle:bcpkix-jdk18on:1.78 by @pditommaso in [ede22ce5](https://github.com/seqeralabs/wave/commit/ede22ce5ee65f34f4b832475b0c9d53b2c8e1fb2)
+* Bump jedis 5.1.3 by @pditommaso in https://github.com/seqeralabs/wave/pull/732
+* Bump logback 1.5.12 by @pditommaso in [f5fe3fa4](https://github.com/seqeralabs/wave/commit/f5fe3fa4837e98ea0a9f7c37b7c52b04ea539cd4)
+* Bump make deps runtimeclasspath by @pditommaso in [2a342b18](https://github.com/seqeralabs/wave/commit/2a342b18b0c41ad59ce5674d98863de8fd2d6323)
+* Bump snakeyaml 2.2 by @pditommaso in [6aeb3c33](https://github.com/seqeralabs/wave/commit/6aeb3c330d51ead83e2a4c257d57a299f68645d5)
+* Bump spillway 3.0.0 by @pditommaso in https://github.com/seqeralabs/wave/pull/731
+* Bump explicit dep to websocket module by @pditommaso in [2e413ac2](https://github.com/seqeralabs/wave/commit/2e413ac2ff8ef265168b85b2f9930a0f1c6984e7)
+
+**Full changelog**: https://github.com/seqeralabs/wave/compare/v1.13.11...v1.14.0

changelog/wave/v1.14.1.mdx

@@ -0,0 +1,11 @@
+---
+title: Wave v1.14.1
+date: 2024-11-14
+tags: [wave]
+---
+
+## Feature updates and improvements
+
+* Fix creds validation endpoint by @pditommaso in https://github.com/seqeralabs/wave/pull/740
+
+**Full changelog**: https://github.com/seqeralabs/wave/compare/v1.14.0...v1.14.1

changelog/wave/v1.15.0.mdx

@@ -0,0 +1,18 @@
+---
+title: Wave v1.15.0
+date: 2024-11-18
+tags: [wave]
+---
+
+## Feature updates and improvements
+
+* Migrate to virtual threads - phase 1 by @pditommaso in https://github.com/seqeralabs/wave/pull/746
+* Use runAsync instead supplyAsync by @pditommaso in [ffd0dacd](https://github.com/seqeralabs/wave/commit/ffd0dacd14dc365cabb23a35a9cac4a0f06d37ae)
+* Remove deprecated ThreadPoolBuilder by @pditommaso in [7af3046f](https://github.com/seqeralabs/wave/commit/7af3046fef4ce5880a8cf9454dab7bc5f4d0344b)
+* Replace Guava cache with Caffeine by @pditommaso in https://github.com/seqeralabs/wave/pull/745
+* Update project deps by @pditommaso in [f24b684d](https://github.com/seqeralabs/wave/commit/f24b684d6e1f41e86793e8b998144f99eedd9df5)
+* Bump guava to version 33.3.1-jre by @pditommaso in [328e9ea3](https://github.com/seqeralabs/wave/commit/328e9ea36238af533c316c1868fb8ab7960bca3d)
+* Bump Netty version 4.1.115.Final by @pditommaso in [9ba433ce](https://github.com/seqeralabs/wave/commit/9ba433ce6f9ab68b6c13f6719d9116840217a0fd)
+* Bump Gradle 8.10.2 by @pditommaso in [52272fe1](https://github.com/seqeralabs/wave/commit/52272fe1169c3fc2ea87c895e7f61b3954e996c6)
+
+**Full changelog**: https://github.com/seqeralabs/wave/compare/v1.14.1...v1.15.0

changelog/wave/v1.15.1.mdx

@@ -0,0 +1,13 @@
+---
+title: Wave v1.15.1
+date: 2024-11-20
+tags: [wave]
+---
+
+## Feature updates and improvements
+
+* Check block existence with object operation by @pditommaso in https://github.com/seqeralabs/wave/pull/750
+* Add `/v1alpha2/validate-creds` endpoint by @pditommaso in https://github.com/seqeralabs/wave/pull/752
+* Switch env vars around by @justinegeffen in https://github.com/seqeralabs/wave/pull/748
+
+**Full changelog**: https://github.com/seqeralabs/wave/compare/v1.15.0...v1.15.1