sn_immediateStatus.pl
Emails an immediate report on whether a run has warnings
This plugin is meant to be run as one of the first plugins in a workflow.
It reads samples.tsv and the fastq files in the directory and determines:
- Does every sample have fastq file(s)?
- Is every fastq file associated with a sample?
Table of the immediate reaction, with columns
- ErrType
- fastq - A fastq file was found, but no sample "owns" it.
- sample - A sample was listed in
samples.tsvbut no fastq files were found.
- Sample - either the sample or the fastq file in question
- ErrKeyword - A shorthand way of writing out the Error column
- Error - A specific error message. It might offer help such as suggesting the correct fastq files or the correct sample.
An email with the table is sent to those listed in snok.txt and emails.conf.