Pass-through source to onFilePublish()
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Signed-off-by: Bruno Grande <bruno.grande@sagebase.org>
BrunoGrandePhD
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modules/nextflow/src/main/groovy/nextflow/trace/TraceObserver.groovy
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October 27, 2022 08:35
Signed-off-by: Bruno Grande <bruno.grande@sagebase.org>
Signed-off-by: Bruno Grande <bruno.grande@sagebase.org>
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@bentsherman: Any chance for this to get a final review and possible merge? Thanks! |
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modules/nextflow/src/main/groovy/nextflow/trace/TraceObserver.groovy
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Signed-off-by: Bruno Grande <bruno.grande@sagebase.org>
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modules/nextflow/src/main/groovy/nextflow/processor/PublishDir.groovy
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modules/nextflow/src/main/groovy/nextflow/processor/PublishDir.groovy
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modules/nextflow/src/main/groovy/nextflow/processor/PublishDir.groovy
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Ok, but the |
Co-authored-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com> Signed-off-by: Bruno Grande <bruno.grande@sagebase.org>
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@pditommaso: It does start off as |
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Awesome, thanks |
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During the nf-core hackathon, I started working on a Nextflow plugin called
nf-prov, whose goal is to generate a file manifest of published files. In this initial PR, I was able to create a simple list of published files. In a follow-up PR, I switched to JSON output. Going forward, I would like to include the information about the task doing the publishing as well as input sample provenance.However, the
onFilePublish()observer interface doesn't allow published files to be linked with the task that did the publishing. There are several ways to address this, but the least obtrusive one that I identified is to pass-through thesourcepath, which will enable the plugin to cross-reference with the task output files.I've included a question below.