Monkeypox

[fanninpm]

Most of the current workflow should be compatible with the references for hMPXV. However, pangolin seems to be exclusive to SARS-CoV-2.

• The URL for the iVar GFF is https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/014/621/545/GCF_014621545.1_ASM1462154v1/GCF_014621545.1_ASM1462154v1_genomic.gff.gz.
• The sequencing protocol (including the primers) is located at https://dx.doi.org/10.17504/protocols.io.5qpvob1nbl4o/v2.

[friesac]

Yeah, Nextclade should call the clades for us and pangolin can be removed for hmpxv.

[fanninpm]

Code changes to make:

• modules/local/bbtools.nf:
  • (in general) possibly tweaking a few parameters
  • BBMAP_ALIGN (and BBMAP_INDEX): find a way to store the index on-disk instead of in-memory
• modules/local/ivar.nf: perhaps tweaking a few parameters related to ivar and samtools
• modules/local/misc.nf:
  • DATA_PREP:
  • make --schema-name argument customizable
  • in the future, use edirect to download iVar GFF (if the GFF straight from NCBI gives better iVar results than the GFF from nextclade_data)
  • LINEAGE_EXCEL: make pangolin input optional
  • SPIKE_GENE_COVERAGE: see #10
  • TRAFFIC_LIGHT_PLOT: in the future, explain what it represents
• modules/local/nextclade.nf: make name and reference (accession) customizable
• modules/local/vadr.nf: move params.vadr_{mdir,options,reference,trim_options} out to main.nf or a subworkflow
• main.nf: implement logic for handling SARS-CoV-2 vs. hMPXV

[friesac]

• modules/local/misc.nf:

  • DATA_PREP:

  • make --schema-name argument customizable

  • in the future, use edirect to download iVar GFF (if the GFF straight from NCBI gives better iVar results than the GFF from nextclade_data)

  • LINEAGE_EXCEL: make pangolin input optional

Yeah, the LINEAGE_EXCEL file would not need to be created, or anything like it, for this initial conversion of taking fastq data and turning it into a consensus fasta.

• SPIKE_GENE_COVERAGE: see Generalize SPIKE_GENE_COVERAGE to cover all genes #10

Can we just ignore edits/improvements to SPIKE_GENE_COVERAGE process while trying to get to hmpxv conversion?

[fanninpm]

As discussed today, we should name these primers something like "hMPXV_YSPH".