Cherry-picked logging upgrades from old pipeline.
This adds a log statement with what is run for each step, date on the log file, and for R scripts, prints out a param string.
To consider:
[] should we move the logs to the associated directory in processed or keep separate?
[] add input checks & logging with nextflow.schema
Cherry-picked logging upgrades from old pipeline. This adds a log statement with what is run for each step, date on the log file, and for R scripts, prints out a param string.
To consider: [] should we move the logs to the associated directory in
processedor keep separate? [] add input checks & logging with nextflow.schema