Move downloaded Nextclade executable to data/nextclade

Avoids clash of downloaded Nextclade executable with the Nextclade
command available in the environment.

Includes the side-effect of the downloaded executable being removed
as part of `bin/clean` when running the workflow without the
`keep_all_files=True` config param. This ensures that the workflow will
start from a clean slate.

workflow/snakemake_rules/nextclade.smk

@@ -65,7 +65,7 @@ if config.get("s3_dst") and config.get("s3_src"):
 
  rule use_nextclade_cache:
  input:
- nextclade="./nextclade",
+ nextclade="data/nextclade",
  nextclade_dataset=lambda w: f"data/nextclade_data/sars-cov-2{w.reference.replace('_','-')}.zip",
  params:
  dst_source=config["s3_dst"],
@@ -166,40 +166,40 @@ rule get_sequences_without_nextclade_annotations:
 rule download_nextclade_executable:
  """Download Nextclade"""
  output:
- nextclade="nextclade",
+ nextclade="data/nextclade",
  benchmark:
  f"benchmarks/download_nextclade_executable_{database}.txt"
  shell:
  """
  if [ "$(uname)" = "Darwin" ]; then
- curl -fsSL "https://github.com/nextstrain/nextclade/releases/latest/download/nextclade-x86_64-apple-darwin" -o "nextclade"
+ curl -fsSL "https://github.com/nextstrain/nextclade/releases/latest/download/nextclade-x86_64-apple-darwin" -o {output.nextclade:q}
 
  else
- curl -fsSL "https://github.com/nextstrain/nextclade/releases/latest/download/nextclade-x86_64-unknown-linux-gnu" -o "nextclade"
+ curl -fsSL "https://github.com/nextstrain/nextclade/releases/latest/download/nextclade-x86_64-unknown-linux-gnu" -o {output.nextclade:q}
  fi
- chmod +x nextclade
+ chmod +x {output.nextclade:q}
 
- if ! command -v ./nextclade &>/dev/null; then
+ if ! command -v {output.nextclade:q} &>/dev/null; then
  echo "[ERROR] Nextclade executable not found"
  exit 1
  fi
 
- NEXTCLADE_VERSION="$(./nextclade --version)"
+ NEXTCLADE_VERSION="$({output.nextclade:q} --version)"
  echo "[ INFO] Nextclade version: $NEXTCLADE_VERSION"
  """
 
 
 rule download_nextclade_dataset:
  """Download Nextclade dataset"""
  input:
- "nextclade",
+ nextclade="data/nextclade",
  output:
  dataset="data/nextclade_data/{dataset_name}.zip",
  benchmark:
  f"benchmarks/download_nextclade_dataset_{database}_{{dataset_name}}.txt"
  shell:
  """
- ./nextclade dataset get --name="{wildcards.dataset_name}" --output-zip={output.dataset} --verbose
+ {input.nextclade:q} dataset get --name="{wildcards.dataset_name}" --output-zip={output.dataset} --verbose
  """
 
 
@@ -210,7 +210,7 @@ rule run_wuhan_nextclade:
  metrics which will ultimately end up in metadata.tsv.
  """
  input:
- nextclade_path="nextclade",
+ nextclade_path="data/nextclade",
  dataset="data/nextclade_data/sars-cov-2.zip",
  sequences=f"data/{database}/nextclade.sequences.fasta",
  params:
@@ -245,7 +245,7 @@ rule run_21L_nextclade:
  Like wuhan nextclade, but TSV only, no alignments output
  """
  input:
- nextclade_path="nextclade",
+ nextclade_path="data/nextclade",
  dataset=lambda w: f"data/nextclade_data/sars-cov-2-21L.zip",
  sequences=f"data/{database}/nextclade_21L.sequences.fasta",
  output:
@@ -266,6 +266,7 @@ 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:
@@ -276,7 +277,7 @@ rule nextclade_tsv_concat_versions:
  """
  if [ -s {input.tsv} ]; then
  # Get version numbers
- nextclade_version="$(./nextclade --version)"
+ nextclade_version="$({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")"