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Update phylo workflow #3

Merged
merged 3 commits into from
May 16, 2024
Merged

Update phylo workflow #3

merged 3 commits into from
May 16, 2024

Commits on May 14, 2024

  1. Convert nextalign run to nextclade run #2 

    * `output.insertions` will be a TSV file now
* `--reference` is now spelled `--input-ref`
* `--genemap` is now spelled `--input-annotation`
* `--retry-reverse-complement` is no longer supported
* `--output-insertions` is now spelled `--output-tsv`

Note: dropping `--retry-reverse-complement` is the one that I am most
unsure about, but this version completes this step.
    @genehack
    genehack committed May 14, 2024
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  2. change gene=* to gene_name=* in hku1/genemap.gff #2 

    Initially, the workflow failed with the following error:

```
Error:
   0: When reading genome annotation
   1: When reading file: "config/hku1/genemap.gff"
   2: Attempted to parse the genome annotation as JSON and as GFF, but both attempts failed:
      JSON error: invalid type: string "NC_006577.2\tfeature\tsource\t1\t29926\t.\t+\t.\tgene=nuc NC_006577.2\tfeature\tgene\t206\t13600
\t.\t+\t.\tgene=ORF1a NC_006577.2\tfeature\tgene\t13600\t21753\t.\t+\t.\tgene=ORF1b NC_006577.2\tfeature\tgene\t21773\t22933\t.\t+\t.\tg
ene=HE NC_006577.2\tfeature\tgene\t22942\t27012\t.\t+\t.\tgene=Spike NC_006577.2\tfeature\tgene\t22978\t25221\t.\t+\t.\tgene=S1 NC_00657
7.2\tfeature\tgene\t27051\t27380\t.\t+\t.\tgene=S2 NC_006577.2\tfeature\tgene\t27051\t27380\t.\t+\t.\tgene=ORF4 NC_006577.2\tfeature\tge
ne\t27373\t27621\t.\t+\t.\tgene=E NC_006577.2\tfeature\tgene\t27633\t28304\t.\t+\t.\tgene=M NC_006577.2\tfeature\tgene\t28320\t29645\t.\
t+\t.\tgene=N NC_006577.2\tfeature\tgene\t28342\t28959\t.\t+\t.\tgene=N2", expected struct GeneMap at line 2 column 1

      GFF3 error: When processing gene, 'N': When processing feature group 'N' ('N') of type 'gene': genes must consist of exactly one f
eature: Expected exactly one element, but found: 2
   2:

Location:
   /workdir/packages/nextclade/src/gene/gene_map.rs:56
```

While looking at the referenced file, and comparing it to the other
`genemap.gff` files in the config, I noticed that all the others used
`gene_name` for everything after the first `gene` line. I changed this
file to match, and the workflow got past the point where it was
previously erroring out.

I have no idea why this worked; hopefully somebody will explain in the
code review.
    @genehack
    genehack committed May 14, 2024
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  3. snakefmt applied to phylogenetic/rules/prepare_sequences.smk #2

    @genehack
    genehack committed May 14, 2024
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