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Viash: A meta-framework for building reusable workflow modules

Authors: Cannoodt, Robrecht; Cannoodt, Hendrik; Schaumont, Dries; Waldrant, Kai; Van de Kerckhove, Eric; Boschmans, Andy; De Maeyer, Dries; +1 Authors

Viash: A meta-framework for building reusable workflow modules

Abstract

Viash 0.8.6 (2024-04-26): Bug fixes and improvements for CI Fix some issues in some edge cases. Add options for testing in a CI environment. Given that these options are not meant for general use, they are hidden from the help message. Some improvements are made to run in Nextflow Fusion. DOCUMENTATION docker setup strategy: Fix inconsistencies in the documentation (PR #657). repositories: Fix uri -> repo in the repositories documentation (PR #682). NEW FUNCTIONALITY viash test and viash ns test: Add a hidden --dry_run option to build the tests without executing them (PR #676). viash test and viash ns test: Add a hidden --deterministic_working directory argument to use a fixed directory path (PR #683). component names: Verify that component namespace and name combinations are unique (PR #685). BUG FIXES NextflowPlatform: Fix publishing state for output arguments with multiple: true (#638, PR #639). Executable: Check whether a multiple output file argument contains a wildcard (PR #639). NextflowPlatform: Fix a possible cause of concurrency issues (PR #669). Resources: Fix an issue where if the first resource is not a script, the resource is silently dropped (PR #670). Docker automount: Prevent adding a trailing slash to an automounted folder (PR #673). NextflowPlatform: Change the at-runtime generated nextflow process from an in-memory to an on-disk temporary file, which should cause less issues with Nextflow Fusion (PR #681).

If you use this software, please cite our article in the Journal of Open Source Software.

Related Organizations
Keywords

FOS: Computer and information sciences, Nextflow, Docker, Bioinformatics, Cloud computing, Software development, Reproducibility, Workflows

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selected citations
These citations are derived from selected sources.
This is an alternative to the "Influence" indicator, which also reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically).
BIP!Citations provided by BIP!
popularity
This indicator reflects the "current" impact/attention (the "hype") of an article in the research community at large, based on the underlying citation network.
BIP!Popularity provided by BIP!
influence
This indicator reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically).
BIP!Influence provided by BIP!
impulse
This indicator reflects the initial momentum of an article directly after its publication, based on the underlying citation network.
BIP!Impulse provided by BIP!
0
Average
Average
Average