Stream NextFlow logs in realtime #40
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yashpatel6
approved these changes
Sep 1, 2023
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Description
This uses the
selectorsmodule to poll for the NextFlow process's outputs so that they can be logged in real-time.This has the additional bonus of ensuring that every line in the logfiles is prepended with a logging header; that makes parsing them after-the-fact so much easier (for everything except tracebacks, but this doesn't make parsing those any harder).
Here is an example of the first and last 10 lines of an NFTest log file before these changes - literally all of the NextFlow job output is captured in one log record, which is recorded immediately before NFTest exits:
After these changes, this is the output that appears on stdout (hence why this is an sbatch log file):
The actual NFTest logfile has a few more DEBUG-level records that detail the specifics of the assert statements made for each test:
Checklist
This PR does NOT contain Protected Health Information (PHI). A repo may need to be deleted if such data is uploaded.
Disclosing PHI is a major problem1 - Even a small leak can be costly2.
This PR does NOT contain germline genetic data3, RNA-Seq, DNA methylation, microbiome or other molecular data4.
.png, .jpeg),.pdf,.RData,.xlsx,.doc,.ppt, or other output files.To automatically exclude such files using a .gitignore file, see here for example.
I have read the code review guidelines and the code review best practice on GitHub check-list.
I have set up or verified the
mainbranch protection rule following the github standards before opening this pull request.The name of the branch is meaningful and well formatted following the standards, using [AD_username (or 5 letters of AD if AD is too long)]-[brief_description_of_branch].
I have added the major changes included in this pull request to the
CHANGELOG.mdunder the next release version or unreleased, and updated the date.Footnotes
UCLA Health reaches $7.5m settlement over 2015 breach of 4.5m patient records ↩
The average healthcare data breach costs $2.2 million, despite the majority of breaches releasing fewer than 500 records. ↩
Genetic information is considered PHI.
Forensic assays can identify patients with as few as 21 SNPs ↩
RNA-Seq, DNA methylation, microbiome, or other molecular data can be used to predict genotypes (PHI) and reveal a patient's identity. ↩