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nextflow-io
A DSL for data-driven computational pipelines
Extend latest version of nf-ga4gh plugin - most recently published appears to be from Dec. 19 2020
Hello, I am trying to extend the nf-ga4gh TES Executor code and am running into the problem that the code [here](https://github.com/nextflow-io/nextflow/tree/master/plugins/nf-ga4gh/src/main/nextflow/ga4gh/tes/executor) seems to be the bleeding edge, but it does...
The inspect command reports the container used during a pipeline execution, for example: ``` » nextflow inspect . -profile wave { "processes": [ { "name": "RNASEQ:INDEX", "container": "community.wave.seqera.io/library/salmon:1.10.2--fd38303983e26319" }, {...
This PR draft the mapping of ORAS images names to HTTP ones.
When opening the Console settings dialog the following error is reported ``` Exception in thread "AWT-EventQueue-0" java.util.MissingResourceException: Can't find bundle for base name groovy.console.ui.Console, locale en_ES at java.base/java.util.ResourceBundle.throwMissingResourceException(ResourceBundle.java:2062) at java.base/java.util.ResourceBundle.getBundleImpl(ResourceBundle.java:1700)...
## Bug report When defining the same parameter object structure multiple times in different scope, the values will overwrite (when keys match) or merge (when keys are unique for one...
## Bug report resume option works locally but not with azure batch. I've gone through all the troubleshooting steps and can't find the reason the cache is invalidated ### Expected...
## Bug report ### Expected behavior and actual behavior Expected behavior: When running a workflow with a `-params-file` in `json` format, I expect the `params` property to contain **only** the...
Some libraries found in version 23.10.1 do have vulnerabilities. They need to be updated to the following min version: | Affected library | Severity | Min version needed | -----------------|----------|--------------------|...
The current implementation of custom email templates uses a separate [template file](https://github.com/nextflow-io/nextflow/blob/master/modules/nextflow/src/main/resources/nextflow/mail/notification.txt), like this; https://www.nextflow.io/docs/latest/config.html#scope-notification ```groovy notification { enabled = true template = "assets/mail/notification.txt" } ``` Can we have this...
I have issue pulling from a private gitlab repository, and the error is unclear for me. Maybe clarifying it would be helpful for other users. ### Expected behavior and actual...
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A DSL for data-driven computational pipelines