BCCDC-PHL/ncov2019-artic-nf

Evaluate changes from upstream repos for inclusion here

dfornika opened this issue · 4 comments

dfornika commented

There have been several changes to the connor-lab/ncov2019-artic-nf and oicr-gsi/ncov2019-artic-nf repositories since this fork was created.

List the changes here, evaluate why they are (or are not) necessary. For those changes that we want to incorporate, make a plan for incorporation into our BCCDC-PHL/ncov2019-artic-nf pipeline.

Our BCCDC-PHL/ncov2019-artic-nf v1.0 corresponds to connor-lab/ncov2019-artic-nf 33b0f4c, which was created on July 24th (2020-07-24).

dfornika commented

On June 25th (2020-06-25), an update to bin/qc.py was merged into connor-lab/ncov2019-artic-nf

The update was also pulled into oicr-gsi/ncov2019-artic-nf on July 14th.

The update changes the QC pass/fail criteria from:

if largest_N_gap >= 10000 or pct_covered_bases >= 85.0:
    if pct_N_bases < 50.0:
         qc_pass = "TRUE"

to:

if largest_N_gap >= 10000 or pct_N_bases < 50.0:
    qc_pass = "TRUE"
dfornika commented

On Nov. 11, the oicr-gsi/ncov2019-artic-nf merged this pull request that updated ivar to v1.3, which includes improvements to primer trimming. This update requires an additional input file primer_pairs.tsv which is a two-column file containing the names of the outermost primers for each amplicon.

dfornika commented

It will probably be better to just create independent issues and evaluate on a case-by-case basis.