Collection Date

• added possibility to include sample collection date info to fasta header

Fix Me Up For The Wintertime

• Fixed broken multi run mapping to refgenome (only one run was saved to resulting bam). Refgenome mapping now outputs sam.
• Updated workflow dag graph

Mark On Violin

• Updated README.md
• Updated samples table import. Added delimiter auto-detection, so that any common delimiter can be used.

Lot Of Wind

• Fixed snpsift input file: use unfiltered (all) snps in snpsift.

Old White

• improve indel calling

New Strain Train

• Removed lofreq viterbi for good.

Great Bias

• alignment preprocessing and variant calling is based on lofreq
• rearranged repo structure

Speed Up

• base quality and indel recalibration
• removed host and rrna mapping
• fastq_screen is optional and takes place only when databases are available

Four Weeks

First release of the workflow.