nextflow

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Separate reference docs from manual pages

15

This PR reorganizes the docs in a number of ways: - reorganize manual pages into "Running pipelines" and "Developing pipelines" to be more aligned with the user journey - separate...

bentsherman

Workflow output definitions and schema

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Spun off from https://github.com/nextflow-io/nextflow/issues/4042#issuecomment-1875924234 Currently, the `publishDir` directive is used to define "workflow outputs". It is a "push" model in which individual processes are responsible for deciding which of their...

bentsherman

Improve charliecloud support

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I have tried to address issues with charliecloud. https://github.com/nextflow-io/nextflow/issues/3566 Should be adressed by adding a lockfile to the parent directory of the cache. Adding lockfiles to the cache is prohibited...

nschan

Update Getting Started docs

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Minor edits to the NF GS section, with some new section ideas.

justinegeffen

IT WILL APPLY!

1

https://github.com/nextflow-io/nextflow/blame/a7f233053cc18b17192ede4c869ea252f23bc8d8/docs/config.md#L1310 I recently read the paragraph 'Process selectors' in [Configuration](https://www.nextflow.io/docs/latest/config.html#process-selectors) section. About `withName`, I tried my nextflow (22.04.5.5708), and found that "If it is included under the alias hello, it...

wangshun1121

[proposal] Move some `publishDir` attributes to `process`-level directives

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_Based on a comment originally posted in https://github.com/nextflow-io/nextflow/issues/4205#issuecomment-1704966418_ `publishDir` supports multiple attributes that control file publishing behaviour. The problem with having them structured this way is that if _any_ need...

ewels

Save built-in reports as Tower reports

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Close #3460 This PR saves the built-in reports as Tower reports by inspecting the Nextflow config. If a report is enabled, it will be eagerly sent to the reports file...

bentsherman

Fusion symlink resolution doesn't work with directories

4

We recently added some logic to handle Fusion symlinks, which happen when an input file is included in a published output. We use the `.fusion.symlinks` file to detect and resolve...

bentsherman

## Bug report (Please follow this template replacing the text between parentheses with the requested information) ### Expected behavior and actual behavior Expected: * `nextflow clean -f -before $( nextflow...

rongcuid

When using scratch=true nxf_unstage can fail silently

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## Bug report Issue #1172 persists in version 23.04.3 ### Expected behavior and actual behavior I expect a process task to return a non-zero exit code when task output cannot...

muniheart