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This is problematic because the new config parser does not support top-level variable declarations like this.
The quick solution is to copy the timestamp expression into each report filename. But then there is a small chance that some report filenames might differ by one second since the timestamp is computed multiple times.
The deeper problem I think is that there is not a single start timestamp that can be used across all scripts and configs.
It should be possible to define a single timestamp that can be exposed to config files and also used by workflow.start. It would be another implicit config variable such as launchTime.
We could also try to expose the entire workflow variable, but it isn't resolved until later on, so we would have to do some config parser magic to lazy-evaluate expressions that use the workflow variable.
The nf-core pipeline template uses a custom timestamp in the various report file names:
This is problematic because the new config parser does not support top-level variable declarations like this.
The quick solution is to copy the timestamp expression into each report filename. But then there is a small chance that some report filenames might differ by one second since the timestamp is computed multiple times.
The deeper problem I think is that there is not a single start timestamp that can be used across all scripts and configs.
There is
workflow.start
:nextflow/modules/nextflow/src/main/groovy/nextflow/script/WorkflowMetadata.groovy
Line 256 in 12ea4d7
But the default report file names use a different timestamp:
nextflow/modules/nextflow/src/main/groovy/nextflow/trace/ReportObserver.groovy
Line 43 in 12ea4d7
It should be possible to define a single timestamp that can be exposed to config files and also used by
workflow.start
. It would be another implicit config variable such aslaunchTime
.We could also try to expose the entire
workflow
variable, but it isn't resolved until later on, so we would have to do some config parser magic to lazy-evaluate expressions that use theworkflow
variable.cc @ewels @pditommaso for your four cents
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