Feature/watch path#754
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gongyixiao merged 16 commits intodevelopfrom Mar 17, 2020
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setting --aggregate with no tsv file as input during watch leads to no aggregation of samples, even as pairing and mapping files are populating and complete. Approving pull request for now, but we need to address the use case in the future.
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Add
--watchmode to support watching for changes in--mapping/--bamMapping <tsv>and--pairing <tsv>usingwatchPath()See:
https://www.nextflow.io/docs/latest/channel.html?highlight=watchpath#watchpath
https://docs.oracle.com/javase/tutorial/essential/io/notification.html#overview
https://docs.oracle.com/javase/tutorial/essential/io/examples/WatchDir.java
Notes:
This only works when you make changes to the file you are watching on the same node that your nextflow main process is running due. Meaning if you are running
nextflow run pipeline.nfon node-01, you need to login to node-01 to make changes to the file you are watching.Please ensure all of your inputs in the file you are watching is absolutely correct, because
--watchmode is built to last forever, so if invalid entries appear in the input file, the pipeline will simply ignore it (maybe even without a warning), or the pipeline will stop execution.