v4.2.1 - Githubissues

B-UMMI / INNUca

INNUENDO quality control of reads, de novo assembly and contigs quality assessment, and possible contamination search

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v4.2.1 #28

Closed miguelpmachado closed 4 years ago

miguelpmachado commented 5 years ago

Change MLST QA/QC:

Samples with known MLST scheme but for which it was not possible to find a scheme will now raise a warning instead of fail

Update mlst version

Change base image of INNUca's Docker image (to perl:5.30, a Debian 9 image) for Perl and old Kernel version compatibilities
Install and update mlst dependencies
Install Java JDK headless but provide extra font loading capabilities (mainly for FastQC, but also Trimmomatic and Pilon)

Minor changes:

Check if the mlst novel alleles file exists before trying to cleaning it
Catches subprocess error when the program to run is not installed

miguelpmachado commented 4 years ago

Now saves the total number of reads and bp sequenced