Call SARS-CoV-2 lineages using pangolin across many sequencing runs. Offers the ability to update pangolin/pangoLEARN to ensure that the latest lineage definitions are used. This pipeline is designed to take the output of BCCDC-PHL/ncov2019-artic-nf as its input, and makes some assumptions about directory structures for finding consensus sequences to analyze.
This pipeline also incorporates a 'genome completeness threshold' to assist with quality control. The genome completeness is the proportion of the full SARS-CoV-2 genome for which consensus sequence was successfully generated. That statistic is included in the output. In addition, the genome_completeness_status field indicates whether the sample was above or below a genome completness threshold. The genome completeness threshold is set to 85% by default but can be set to another value using the --genome_completeness_threshold flag.
The --update_pangolin flag controls whether or not pangolin should be updated before proceeding with analysis. The --update_pangolin_data flag controls whether pangolin's data dependencies such as pangoLEARN models and lineage definitions should be updated before proceeding with analysis. Updates are disabled by default.
nextflow run BCCDC-PHL/pangolin-nf \
[--update_pangolin] \
[--update_pangolin_data] \
[--ivar_consensus] \
[--genome_completeness_threshold <genome_completeness_threshold>] \
--analysis_parent_dir <analysis_parent_dir> \
--outdir <outdir>
| run_id | sample_id | genome_completeness | genome_completeness_status | lineage | conflict | pangoLEARN_version | pangolin_version | pango_version | status | note |
|---|---|---|---|---|---|---|---|---|---|---|
| 210330_M01234_0123_000000000-G653A | sample-01 | 95.1 | ABOVE_GENOME_COMPLETENESS_THRESHOLD | B.1 | 0 | 2021-04-28 | 2.4 | v1.1.23 | passed_qc | |
| 210330_M01234_0123_000000000-G653A | sample-02 | 75.2 | BELOW_GENOME_COMPLETENESS_THRESHOLD | P.1 | 0 | 2021-04-28 | 2.4 | v1.1.23 | passed_qc | 15/17 P.1 (B.1.1.28.1) SNPs (1 ref and 0 other) |
| 210330_M01234_0123_000000000-G653A | sample-03 | 0 | BELOW_GENOME_COMPLETENESS_THRESHOLD | None | 0 | 2021-04-28 | 2.4 | v1.1.23 | fail | N_content:1.0 |