BfArM-MVH/GRZ_QC_Workflow v1.3.0

on GitHub

What's Changed

• Bump nf-core to v3.5.1
• Derive required thresholds directly from the submission metadata.json / samplesheet.csv #171
  • Use new thresholds API from grz-pydantic-models 2.5.0. This will allow to update required thresholds by bumping grz-pydantic-models from now on.
  • Add check whether provided metrics pass the required thresholds
• Add symbolic link to final report.csv #175
• Fix conda issues: multiqc is updated to 1.32 as conda was broken in the old version #173
• Disable filters in fastp and fastplong, and report both deduplicated and non-deduplicated reads #161
• Add micromamba profile to support micromamba as a single-binary conda replacement #156
• Bump grz-pydantic-models to 2.4.0 #160
  • uses new mean read length threshold
• Add instructions for bumping Docker/Singularity local module environments #162

Full Changelog: v1.2.0...v1.3.0