Preserve order of plugin declarations in config#7227
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Signed-off-by: Jorge Aguilera <[email protected]>
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bentsherman
approved these changes
Jun 12, 2026
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In nf-nomad team we are using 2 plugins, nf-nomad and nf-s5cmd.
nf-s5cmd declares a dependency against nf-nomad and in previous version of nextflow all works fine and plugins are resolved, doesnt matter the order you declare the plugins in the nextflow.config
With last version of pf4j (from 3.12 to 3.14.1) it seems pf4j requires base plugin (nf-nomad) be loaded first
If we specify the plugins via command line ( i.e.
-plugins [email protected],[email protected]) they are loaded in the right order ( as CmdRun parses this asconfig.plugins = cmdRun.plugins.tokenize(',')) and pf4j works finebut if we use the
pluginDSL in,nextflow.confignextflow are using aHashsetand it can't guarantee the order so pipelines fail randomlyThis PR uses
LinkedHashSetto guarantee the order as declared in the closure