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Make BCO the default format #14

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Make BCO the default format #14

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66d9cc2
Make BCO the default format
bentsherman Sep 29, 2023
eec8ec3
Merge branch 'master' into bco-default
bentsherman Sep 29, 2023
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4 changes: 2 additions & 2 deletions README.md
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Expand Up @@ -16,7 +16,7 @@ plugins {
prov {
enabled = true
overwrite = true
file = "${params.outdir}/manifest.json"
file = "${params.outdir}/bco.json"
}
```

Expand All @@ -36,7 +36,7 @@ The path of the provenance manifest (default: `manifest.json`).

`prov.format`

The manifest format. Can be `legacy` or `bco` (default: `legacy`).
The manifest format. Can be `legacy` or `bco` (default: `bco`).

*Note: The BCO format is experimental and may change in future releases. Visit the [BCO User Guide](https://docs.biocomputeobject.org/user_guide/) to learn more about this format and how to extend it with information that isn't available to Nextflow.*

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1 change: 0 additions & 1 deletion nextflow.config
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Expand Up @@ -9,5 +9,4 @@ params {
prov {
overwrite = true
file = "${params.outdir}/bco.json"
format = 'bco'
}
2 changes: 1 addition & 1 deletion plugins/nf-prov/src/main/nextflow/prov/ProvObserverFactory.groovy
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Expand Up @@ -43,7 +43,7 @@ class ProvObserverFactory implements TraceObserverFactory {

final file = config.navigate('prov.file', ProvObserver.DEF_FILE_NAME)
final path = (file as Path).complete()
final format = config.navigate('prov.format', 'legacy') as String
final format = config.navigate('prov.format', 'bco') as String
final overwrite = config.navigate('prov.overwrite') as Boolean
final patterns = config.navigate('prov.patterns', []) as List
new ProvObserver(path, format, overwrite, patterns)
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