Better Call Variants

• Switched to bbtools/callvariants wrapper (to replace crashing lofreq call).
• Workflow has now less steps and is more nimble.
• Tested on B.1.1.7 and B.1.351 variants sequenced with Illumina NextSeq.

Strict Max

• Added strictmaxindel flag to bbmap.sh (maxindel=200) to avoid inclusion of weird alignments that can cause lofreq call crash.

• Don't use strictmaxindel flag! as it affects badly indel calling. Either remove the flag from refgenome rule params (in the hope that there are no reads in the library that cause lofreq call to crash) or use previous (lofreq-based) or next versions (v3) using bbtools/callvariants.

Qc Zip

• Updated fastqc.zip file name so that multiqc would pick it up for the report

Pep Talk

• Using PEP configuration.
• Per batch MultiQC.

Simple Consensus

• Simplified workflow by removing consensus sequence collaping rule and merging consensus fasta creation with renaming.

Consensus Fix

• Updated consensus sequence generating wrapper

Consensus Wrap

• Updated consensus sequence wrapper.

No Meta

• Removed possibility to update FASTA names with sample metadata, now only sample id will be used

Sniff Effects

• Updated snpeff version from v4.3 to v5.0
• Downloaded new sars-cov-2 v5.0 database from snpeff
• Updated snpeff and snpsift outputs, e.g. snpsift now reports also aa changes.

Quality Street

• Removed sneaked-in print statement