Nextflow wrapper for ncov-tools

This is a wrapper that helps to submit ncov-tools jobs to our compute cluster.

Usage

This pipeline is intended to be run on the output of the BCCDC-PHL/ncov2019-artic-nf pipeline. The ncov2019-artic-nf output directory is passed as input to this pipeline using the --artic_analysis_dir flag.

The default primer scheme is the Freed et al. 1200bp scheme (aka. V1200). Other primer schemes can be selected using the --primer_scheme_name flag. Valid primer scheme names correspond to directory names in our primer scheme repository.

A metadata.tsv file may be optionally provided. If it is provided, it should follow the format as described in the ncov-tools documentation

The completeness_threshold can optionally be modified. Its default value is the same as that of ncov-tools, 0.75.

The --update_pangolin flag allows control over whether or not pangolin will be updated prior to running ncov-tools.

In the command below, [square brackets] indicate optional parameters. <angled brackets> indicate a placeholder to be replaced by the user in a real pipeline invocation.

nextflow run BCCDC-PHL/ncov-tools-nf \
  -profile conda \
  --cache ~/.conda/envs \
  [--primer_scheme_name <primer_scheme_name> ] \
  [--primer_scheme_version <primer_scheme_version> ] \
  [--update_pangolin] \
  [--completeness_threshold <completeness_threshold>] \
  [--metadata <metadata.tsv>] \
  [--pre_downsampled] \
  [--no_split_by_plate] \
  [--ivar_consensus] \
  [--ivar_variants] \
  --run_name <run_name> \
  --artic_analysis_dir <output/from/ncov2019-artic-nf> \
  --outdir <ncov-tools-output> \

Caveats

• We currently assume that the negative control sample is named starting with the letters NEG, and that no other sample in the run starts with those letters. This is being addressed in this issue.