v2.1.1

• Add option to specify custom barcode file with --barcode and log in *WasteFlow_log.json

• Fix read-after-write race condition in samtools mpileup causing missing ref alleles in depth and vcf files (see #8)

• Add option to include additional freyja demix parameters (ex. --lineageyml and --meta) with --demix_params

v2.1.0

• Update from freyja v1.4.9 to freyja v1.5.1

• Option to skip primer trimming step with iVar by specifying --skip_trim (ex. for probe enriched samples)

v2.0.4

• Upgrade Freyja v1.4.7 to v1.4.9

v2.0.3

• Fix bug causing trim galore and bwa processes not to work

• Correct name of mutation table directory to match conifg

• Make tag in combine_reps more informative by specifying sample ID

• Update README to specify naming format of technical replicates in order to combine sequencing reads

v2.0.1

• Change errorStrategy to 'ignore' all failures on Freyja demix (lineage_freyja) process, not only negative control samples

• Change errorStrategy to 'retry' twice on SnpEff (annotate_snpeff) process in case it is the first time pipeline is being run. SnpEff database needs to be downloaded and the first time will download but fail, then because it is now present rerunning will work.

• Adjust QC align commands to be more informative (samtools coverage and depth).

• Add trace file to track samples (that fail lineage_freyja process).

• Reuse ref_ch defined in treatment workflow for effluent

v2.0.0

• Resolve cvxpy.error.SolverError with update to Freyja v1.4.7 that groups sublineages if insufficient read depth covering lineage differentiating mutations. This adds the Freyja --depthcutoff option which is not present in older versions and would cause an error.
  4c09101

• Handle negative control samples (only samples with "neg" substring - still fails otherwise) that are empty and would previously cause the pipeline to terminate after the Freyja demix command is unable to make lineage calls.

• Renaming options and reformatting outputs

v1.4.0

• Truncate VCF files that are without calls to 0 bytes for filtering before Freyja demix command

• Ability to rerun back across depth and vcf files generated by Freyja (iVar) or Freebayes, inclusive of current data directory. Useful for re-classifying lineages across historical dataset after updating Freyja barcode.

v1.3.2

• Logic to check for snp annotation as part of mutation csv adjusted

• Priming trimming (iVar) adjusted for Nextera-generated data. Over trimming occurred prior to this change.

v1.3.0

• Option to run pipeline on individual samples (default: 1 x for fq, 1 x rev fq) or on the combined result of multiple replicates (ex. 3 x for, 3 x rev)

• Mutation table functionality - cleaned and formatted output of Freebayes-called, SnpEff-annotated mutations per sample in input directory when --annotate_snps active plus option to combine this output across multiple directories specified by --table_search_string

• Optional bootstrapping functionality - Freyja bootstrapped estimates of lineage & WHO VOC/VOI

• Freyja kept at v1.4.2 for validation purposes

v1.0.0

• Restructure pipeline into 3 workflows - backward incompatible with v0.1.6

• Freebayes-based lineage calls by Freyja activated with --freebayes switch

• Update to Freyja v1.4.2 for barcode versioning functionality

• Rename output directory to include pipeline version currently run & output log file with Freyja barcode used on date pipeline was run