Merge branch 'master' into 24.2.0-cycle-27-changelog

.gitignore

@@ -31,3 +31,7 @@ internal/tmp
 
 # Local Netlify folder
 .netlify
+
+# OSS repo clones
+multiqc_docs/multiqc_repo
+wave_docs/wave_repo

.gitmodules

@@ -1,6 +0,0 @@
-[submodule "wave_docs/wave_repo"]
-	path = wave_docs/wave_repo
-	url = https://github.com/seqeralabs/wave
-[submodule "multiqc_docs/multiqc_repo"]
-	path = multiqc_docs/multiqc_repo
-	url = https://github.com/MultiQC/MultiQC

changelog/multiqc/v1.25.2.mdx

@@ -0,0 +1,55 @@
+---
+title: MultiQC v1.25.2
+date: 2024-11-20
+tags: [multiqc]
+---
+
+Multiple bug fixes and minor updates.
+
+{/* truncate */}
+
+### Feature updates and improvements
+
+- Add natural sort for sample sorting ([#2959](https://github.com/MultiQC/MultiQC/pull/2959))
+- Custom content: for `plot_type: image`, support `custom_data` config with section name and description. Fix misleading logging ([#2939](https://github.com/MultiQC/MultiQC/pull/2939))
+- Config validation improvements (group messages, cast types, validate column headers) ([#2899](https://github.com/MultiQC/MultiQC/pull/2899))
+
+### Fixes
+
+- Workaround for displaying sample grouping in Safari because of missing `visibility: collapse` ([#2941](https://github.com/MultiQC/MultiQC/pull/2941))
+- Fix table CSV export where a title contains a comma ([#2911](https://github.com/MultiQC/MultiQC/pull/2911))
+- Showing table in notebooks: respect `col1_header` ([#2914](https://github.com/MultiQC/MultiQC/pull/2914))
+- Customizing `custom_table_header_config`: fix docs, support both the old and the new ways ([#2955](https://github.com/MultiQC/MultiQC/pull/2955))
+- Table scatter mini-plots: fix rounding and range ([#2956](https://github.com/MultiQC/MultiQC/pull/2956))
+- File line block iterator: fix reading long lines that do not fit one block ([#2935](https://github.com/MultiQC/MultiQC/pull/2935))
+- Fix `cond_formatting_rules` type hint to avoid validation error ([#2922](https://github.com/MultiQC/MultiQC/pull/2922))
+- Fix `config.prepend_dirs` or `-d -dd 1` ([#2913](https://github.com/MultiQC/MultiQC/pull/2913))
+- Sample grouping fixes ([#2920](https://github.com/MultiQC/MultiQC/pull/2920)):
+  - Keep sample name column fix width to avoid jumping
+  - Fix hiding columns through the modal
+- Custom content fixes:
+  - Avoid showing `section_comment` both for module and section when they have the same ID ([#2954](https://github.com/MultiQC/MultiQC/pull/2954))
+  - Address issue of sections without search patterns and headers in files ([#2921](https://github.com/MultiQC/MultiQC/pull/2921))
+  - Fix duplicated custom content sections in the report ([#2921](https://github.com/MultiQC/MultiQC/pull/2921))
+  - Fix support for `plot_type: violin` ([#2957](https://github.com/MultiQC/MultiQC/pull/2957))
+
+### Module updates
+
+- ngsbits: add submodule samplegender ([#2854](https://github.com/MultiQC/MultiQC/pull/2854))
+- nanoq: change lineplots for barplots ([#2934](https://github.com/MultiQC/MultiQC/pull/2934))
+- Qualimap: clarify the direction of the transcript in coverage plot ([#2946](https://github.com/MultiQC/MultiQC/pull/2946))
+- picard: add table with all metrics to VariantCallingMetrics section ([#2885](https://github.com/MultiQC/MultiQC/pull/2885))
+- Nanostat: add general stats columns ([#2961](https://github.com/MultiQC/MultiQC/pull/2961))
+- Samtools: add insert size to general stats table ([#2905](https://github.com/MultiQC/MultiQC/pull/2905))
+
+### Module fixes
+
+- bcl2fastq: fix missing `R1_*`/`R2_*` metrics ([#2965](https://github.com/MultiQC/MultiQC/pull/2965))
+- Cutadapt: fix for null values from r2 data ([#2936](https://github.com/MultiQC/MultiQC/pull/2936))
+- Qualimap: fix parsing ∞ value ([#2937](https://github.com/MultiQC/MultiQC/pull/2937))
+- bclconvert: fix undetermined barcodes plot ([#2976](https://github.com/MultiQC/MultiQC/pull/2976))
+- featurecounts: fix missing section name and anchor ([#2967](https://github.com/MultiQC/MultiQC/pull/2967))
+
+### Infrastructure
+
+- Pin kaleido to 0.2.1 (new 0.4.1 does not embed a browser and thus not portable) ([#2963](https://github.com/MultiQC/MultiQC/pull/2963))

changelog/seqera-cloud/v24.1.0_cycle17.mdx

@@ -6,8 +6,8 @@ tags: [seqera cloud]
 
 ### Feature updates and improvements
 
-- Managed identities: Allow organization members and collaborators to list managed identities
-- Data Studios: Data studio user activity auditlog
-- Data Studios: Delete checkpoints
-- Data Studios: Rename checkpoints
-- Data Explorer: Multi-download functionality
+- Managed identities: Allow organization members and collaborators to list managed identities.
+- **Data Studios**: Data studio user activity auditlog.
+- **Data Studios**: Delete checkpoints.
+- **Data Studios**: Rename checkpoints.
+- **Data Explorer**: Multi-download functionality.

changelog/seqera-cloud/v24.2.0_cycle20.mdx

@@ -6,20 +6,20 @@ tags: [seqera cloud]
 
 ### Feature updates and improvements
 
-- Add code blocks syntax highlighting and background color
-- Role selector dropdown detail
-- Update navbar help and support links
+- Add code blocks syntax highlighting and background color.
+- Role selector dropdown detail.
+- Update navbar help and support links.
 
 ### Bug fixes
 
-- Disable launch form submit button during form validation
-- Update team guest welcome email visuals and copy
-- Tag search with underscore
-- Add missing gap between shared badge and labels
-- Data Studios template override
-- View credentials back navigation
-- Data Explorer search bar misalignment
-- Parameters merging in schema form without key in schema
+- Disable launch form submit button during form validation.
+- Update team guest welcome email visuals and copy.
+- Tag search with underscore.
+- Add missing gap between shared badge and labels.
+- Data Studios template override.
+- View credentials back navigation.
+- Data Explorer search bar misalignment.
+- Parameters merging in schema form without key in schema.
 
 ### Version bumps
 

changelog/seqera-cloud/v24.2.0_cycle21.mdx

@@ -6,17 +6,17 @@ tags: [seqera cloud]
 
 ### Feature updates and improvements
 
-- Add global Nextflow configuration support in compute environments
-- Add flexibility for pipeline names in workspaces
-- Add tag propagation to launch templates
-- Add managed identities support for manual Azure Batch compute environments
-- Implement custom launch container logic
+- Add global Nextflow configuration support in compute environments.
+- Add flexibility for pipeline names in workspaces.
+- Add tag propagation to launch templates.
+- Add managed identities support for manual Azure Batch compute environments.
+- Implement custom launch container logic.
 
 ### Bug fixes
 
-- Improve workflow launch screen look and feel
-- Allow pipeline work directory to be changed during pipeline launch
-- Handle special characters in prompt modal confirmation text regex
+- Improve workflow launch screen look and feel.
+- Allow pipeline work directory to be changed during pipeline launch.
+- Handle special characters in prompt modal confirmation text regex.
 
 ### Version bumps
 

changelog/seqera-cloud/v24.2.0_cycle23.mdx

@@ -6,6 +6,6 @@ tags: [seqera cloud]
 
 ### Bug fixes
 
-- Data Explorer: Enable task working directory navigation using Data Explorer in personal workspaces by adding routing
-- Remove -/+ increment buttons from numeric input components in Platform, including compute environment and launch form interfaces
-- Hide compute environment variables section actions when component is disabled (previously indicated that environment variables could be edited in this state)
+- **Data Explorer**: Enable task working directory navigation using Data Explorer in personal workspaces by adding routing.
+- Remove **-/+** increment buttons from numeric input components in Platform, including compute environment and launch form interfaces.
+- Hide compute environment variables section actions when component is disabled (previously indicated that environment variables could be edited in this state).

changelog/seqera-cloud/v24.2.0_cycle24.mdx

@@ -6,27 +6,27 @@ tags: [seqera cloud]
 
 ### Feature updates and improvements
 
-- Updated Azure service principal credentials
-- Data Studios: Add direct Data Explorer browse link to mounted data items
-- Data Studios: Make studio details page tabs routable
-- Define cache configuration once, only override changes
-- Data Explorer: Highlight invalid custom datalinks
-- Disable AWS and Google Batch spot instance auto retry
-- Data Explorer: Remove folder validation
-- Update 204 pipeline schema response description
-- Patch workflow revision
-- Render Parameters UI correctly with new schemas based on 2020-12 draft
-- Upgrade to Angular 16
-- Pipeline launch form: Delegate form creation to a form builder service
+- Updated Azure service principal credentials.
+- **Data Studios**: Add direct Data Explorer browse link to mounted data items.
+- **Data Studios**: Make studio details page tabs routable.
+- **Data Explorer**: Highlight invalid custom datalinks.
+- **Data Explorer**: Remove folder validation.
+- Define cache configuration once, only override changes.
+- Disable AWS and Google Batch spot instance auto retry.
+- Update 204 pipeline schema response description.
+- Patch workflow revision.
+- Render Parameters UI correctly with new schemas based on 2020-12 draft.
+- Upgrade to Angular 16.
+- Pipeline launch form: Delegate form creation to a form builder service.
 
 ### Bug fixes
 
-- Connection to Redis SSL server
-- `pairingId` declaration in API schema
-- Copying empty list for cloud data links
-- Visual glitches in launch form
-- Datalink status always null
-- Update last used field in compute environment when creating a data studio job
-- `Terminated by Tower` error
+- Connection to Redis SSL server.
+- `pairingId` declaration in API schema.
+- Copying empty list for cloud data links.
+- Visual glitches in launch form.
+- Datalink status always null.
+- Update last used field in compute environment when creating a data studio job.
+- `Terminated by Tower` error.
 
 

changelog/seqera-cloud/v24.2.0_cycle25.mdx

@@ -6,10 +6,10 @@ tags: [seqera cloud]
 
 ### Feature updates and improvements
 
-- Quick launch now accepts pipelines that do not have a branch named `master`.
+- Quick Launch now accepts pipelines that do not have a branch named `master`.
 - Improved query times on some clean up job queries.
 - NF Launcher image is now by default pulled from `cr.seqera.io` public registry instead of quay.
-- Data studio sessions can now share mounted data across the same workspace.
+- **Data Studios**: Data Studio sessions can now share mounted data across the same workspace.
 - The new Launch Form is now available in Quick Launch and personal workspaces.
 - Improved fetching of the cloud cost estimation for Google Cloud Platform's (GCP) spot instances.
 - ECS container timeout configuration is now defaulted to 10 minutes (`ECS_CONTAINER_CREATE_TIMEOUT=10m,ECS_CONTAINER_STOP_TIMEOUT=10m,ECS_MANIFEST_PULL_TIMEOUT=10m`).

changelog/seqera-cloud/v24.2.0_cycle26.mdx

@@ -22,26 +22,26 @@ If you choose not to merge accounts, you will not be prompted again. If you wish
 
 ### Feature updates and improvements
 
-- Data Studios now support GPUs
-- The pipeline parameters input form now supports JSON schema draft 2020-12
-- Augment Data Studios images with custom Conda environment
-- Data studio creation now includes YAML validation
-- Data Studios build stats are now included in the Dashboard
-- New data studios now include "Add only" and "Add and start" actions
+- Data Studios now support GPUs.
+- The pipeline parameters input form now supports JSON schema draft 2020-12.
+- Augment Data Studios images with custom Conda environment.
+- Data studio creation now includes YAML validation.
+- Data Studios build stats are now included in the Dashboard.
+- New data studios now include "Add only" and "Add and start" actions.
 
 ### Bug fixes 
 
-- Add back to login button in authentication error screen
-- Add custom token cookie login handler for Nextflow requests to receive authentication cookies
-- Data Studios UI fixes
-- Jedis connection pool config which caused potential instabilities
-- Improve Data Studios error messaging 
-- Delete data studio checkpoint on build failure
-- Update default Data Studios tool versions
-- Failed data studios can now be deleted 
-- Set launch form to parameters step view by default when a pipeline schema is present, regardless of specification
-- Dashboard persisted filters exclude workspace IDs the user no longer has access to
-- Do not fetch info for "INVALID" status pipelines, fetch for all other statuses including "DISABLED"
-- Fixed a problem with Azure Entra credential creation
-- Return an empty list of data studios when receiving an invalid status
-- Fallback to primary compute environment when launching a shared pipeline without an associated compute environment from a private workspace
+- Add back to login button in authentication error screen.
+- Add custom token cookie login handler for Nextflow requests to receive authentication cookies.
+- Data Studios UI fixes.
+- Jedis connection pool config which caused potential instabilities.
+- Improve Data Studios error messaging.
+- Delete Data Studio checkpoint on build failure.
+- Update default Data Studios tool versions.
+- Failed Data Studios can now be deleted.
+- Set launch form to parameters step view by default when a pipeline schema is present, regardless of specification.
+- Dashboard persisted filters exclude workspace IDs the user no longer has access to.
+- Do not fetch info for **INVALID** status pipelines, fetch for all other statuses including **DISABLED**.
+- Fixed a problem with Azure Entra credential creation.
+- Return an empty list of data studios when receiving an invalid status.
+- Fallback to primary compute environment when launching a shared pipeline without an associated compute environment from a private workspace.