Remove version columns from Nextclade TSV

We now check the Nextclade versions using the separate version JSON, so
we no longer need to track version per row.

This is a breaking change for the cache, so will need to be run with the
renew flag to manually force a full-rerun.

workflow/snakemake_rules/nextclade.smk

@@ -218,7 +218,7 @@ rule run_wuhan_nextclade:
  f"--output-translations=data/{database}/nextclade.translation_{{cds}}.upd.fasta"
  ),
  output:
- info=f"data/{database}/nextclade_new_raw.tsv",
+ info=f"data/{database}/nextclade_new.tsv",
  alignment=temp(f"data/{database}/nextclade.aligned.upd.fasta"),
  translations=[
  temp(f"data/{database}/nextclade.translation_{gene}.upd.fasta")
@@ -249,7 +249,7 @@ rule run_21L_nextclade:
  dataset=lambda w: f"data/nextclade_data/sars-cov-2-21L.zip",
  sequences=f"data/{database}/nextclade_21L.sequences.fasta",
  output:
- info=f"data/{database}/nextclade_21L_new_raw.tsv",
+ info=f"data/{database}/nextclade_21L_new.tsv",
  threads:
  workflow.cores * 0.5
  benchmark:
@@ -264,47 +264,13 @@ rule run_21L_nextclade:
  """
 
 
-rule nextclade_tsv_concat_versions:
- input:
- nextclade="data/nextclade",
- tsv=f"data/{database}/nextclade{{reference}}_new_raw.tsv",
- dataset=lambda w: f"data/nextclade_data/sars-cov-2{w.reference.replace('_','-')}.zip",
- output:
- tsv=f"data/{database}/nextclade{{reference}}_new.tsv",
- benchmark:
- f"benchmarks/nextclade_tsv_concat_versions_{database}{{reference}}.txt"
- shell:
- """
- if [ -s {input.tsv} ]; then
- # Get version numbers
- nextclade_version="$({input.nextclade:q} --version)"
- dataset_version="$(unzip -p {input.dataset} pathogen.json | jq -r '.version.tag')"
- timestamp="$(date -u +"%Y-%m-%dT%H:%M:%SZ")"
-
- # Combine input file with version numbers and write to output
- printf "%s\tnextclade_version\tdataset_version\trun_timestamp\n" \
- "$(head -n 1 {input.tsv})" \
- > {output.tsv}
-
- tail -n +2 {input.tsv} | \
- awk -v v1="$nextclade_version" \
- -v v2="$dataset_version" \
- -v v3="$timestamp" \
- -v OFS='\t' '{{print $0, v1, v2, v3}}' \
- >> {output.tsv}
- else
- cp {input.tsv} {output.tsv}
- fi
- """
-
-
 rule nextclade_info:
  """
  Generates nextclade info TSV for all sequences (new + old)
  """
  input:
  old_info=f"data/{database}/nextclade{{reference}}_old.tsv",
- new_info=rules.nextclade_tsv_concat_versions.output.tsv,
+ new_info=f"data/{database}/nextclade{{reference}}_new.tsv",
  output:
  nextclade_info=f"data/{database}/nextclade{{reference}}.tsv",
  benchmark: