Mpileup -B switch addition

Merge pull request #79 from ucsd-ccbb/bugfixes

-B switch for mpileup, left-over test code removal

Pass all consensuses

• three threads will be used for each per-sample processing
• a sample's indel_flagged value will have no effect on its is_accepted value
• ALL samples whose consensus_seq_name value is not NA will pass QC
  • This is regardless of ANY other qc flag or value (including coverage_gte_10_reads)
  • This means they will go on to pangolin and/or tree building
• no samples will be put aside for manual review

Bugfix release

Restores P25 and %>=Q30 columns to summary tables.
Ensures qc+lineages table is successfully produced even when there are NA consensus sequence(s).
Expands unit and regression testing.

Release 1.0.0

New features:

• provide additional output metadata (e.g., sequence run name, ivar software version) for each processed sample
• report a new “indel flag” for any consensus sequence with insertion or deletion counts that are not evenly divisible by 3
• fail acceptance for any sequence with a true indel flag
  *store a cumulative set of indel-failing consensus sequences and their qc results for later manual review by non-CCBB personnel
• parameterize whether to include sequences from all sequencing runs or only from helix sequencing runs in lineage calling and optional subsequent tree building
• unless processing for helix, include static set of historical consensus sequences in lineage calling and optional tree-building
• automatically update pangolin before each lineage calling run
• produce a csv containing qc/acceptance info for both accepted and rejected (cumulative) consensus sequences (see helix limitation above) as well as lineage calls for only accepted sequences
• provide ability to run lineage calling without tree-building
• modify pipeline parameters to better scale for very large sequencing runs
• expand unit test suite
• add continuous integration to github repository to run python unit tests on each check-in
• move pipeline and data onto new return-to-learn governed AWS account

0.4.0 release with helix support (i.e., per-seq-run pangolin)

Merge pull request #16 from ucsd-ccbb/helix_v0

0.4.0 release with helix support (i.e., per-seq-run pangolin)

0.3.6

Adds flexible lane merging, consensus insertion & deletion counts, new folder structure, extended qc spreadsheet

Adds pangolin, multiqc; fixes plot handling of failed samples

0.3.0

Updated w v0.3.0 snapshot id

Includes SE/PE, merged/unmerged handling and directory refactor

0.2.0

Updated for v 0.2.0

Initial release

Shown to produce same variant and consensus results against ARTIC data provided by Moshiri Niema on 2021-02-11 as Niema workflow (whose results were vetted as good by Anderson lab).