Ben Sherman

Convert to mkdocs

10

This PR converts the docs from asciidoc to markdown / mkdocs material. This conversion is a prerequisite to merging the Nextflow docs, patterns, and Seqera training into a single docs...

Change k8s client to use namespace and service account from nextflow config

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Closes #2266

Fusion support for the azure batch task handler is trickier because much of the task logic (container options, environment vars, submit command) are handled in a separate class `AzBatchService`. So...

Add fusion support to grid executors

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The strategy here is to create a secondary wrapper script that generates the container launch command, and pipes this script into the executor submit command. Just need to confirm that...

Convert docs to Markdown

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Closes #2739 I used the `rst2myst` tool to convert the RST docs to Markdown, which did 99% of the work. There were only two major differences: 1. Same-page links weren't...

Replace rolling filenames with timestamp-based filenames

1

Closes #3186 The only issue currently is that the log file can have a different timestamp than the other report files, because they are evaluated at different points in the...

Closes #2985 This PR adds support for CSI ephemeral volumes, following the same pattern used for configMaps and secrets. The main use case is for [Secrets Store](https://secrets-store-csi-driver.sigs.k8s.io/getting-started/usage.html), which allows you...

Closes #640 This PR takes a simpler approach to global resource limits. It adds a `resourceLimits` directive which is simply a map of limits for each resource directive: ``` process...

Support CSI ephemeral volumes

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Nextflow currently uses PersistentVolumeClaim to use any kind of persistent volume in a generic way, which is good. However, there are also several types of [ephemeral volumes](https://kubernetes.io/docs/concepts/storage/ephemeral-volumes/#types-of-ephemeral-volumes): - emptyDir -...

Document aws sessionToken for temporary credentials

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This commit -- https://github.com/nextflow-io/nextflow/commit/15ac3938542f8995f88f04b9b32ff59ec161c040 -- added support for AWS temporary credentials via the `aws.sessionToken` option. Needs to be documented.