message: chore: format .env file
diff: -DEV_CLI_OPTIONS="--sequences=data/sars-cov-2/sequences.fasta --reference=data/sars-cov-2/reference.fasta --genemap=data/sars-cov-2/genemap.gff --genes=E,M,N,ORF1a,ORF1b,ORF3a,ORF6,ORF7a,ORF7b,ORF8,ORF9b,S --output-dir=tmp/ --output-basename=nextalign --include-reference --verbose"
  +DEV_CLI_OPTIONS=" \
  +--verbose \
  +--sequences=data/sars-cov-2/sequences.fasta \
  +--reference=data/sars-cov-2/reference.fasta \
  +--genemap=data/sars-cov-2/genemap.gff \
  +--genes=E,M,N,ORF1a,ORF1b,ORF3a,ORF6,ORF7a,ORF7b,ORF8,ORF9b,S \
  +--output-dir=tmp/ \
  +--output-basename=nextalign \
  +--include-reference \
  +"
  -DEV_NEXTCLADE_CLI_OPTIONS="--verbose --in-order --input-fasta=data/sars-cov-2/sequences.fasta --input-root-seq=data/sars-cov-2/reference.fasta --genes=E,M,N,ORF1a,ORF1b,ORF3a,ORF6,ORF7a,ORF7b,ORF8,ORF9b,S --input-gene-map=data/sars-cov-2/genemap.gff --input-tree=data/sars-cov-2/tree.json --input-qc-config=data/sars-cov-2/qc.json --input-pcr-primers=data/sars-cov-2/primers.csv --output-json=tmp/nextclade.json --output-csv=tmp/nextclade.csv --output-tsv=tmp/nextclade.tsv --output-tree=tmp/nextclade.auspice.json --output-dir=tmp/ --output-basename=nextclade --include-reference"
  +DEV_NEXTCLADE_CLI_OPTIONS=" \
  +--verbose \
  +--in-order \
  +--input-fasta=data/sars-cov-2/sequences.fasta \
  +--input-root-seq=data/sars-cov-2/reference.fasta \
  +--genes=E,M,N,ORF1a,ORF1b,ORF3a,ORF6,ORF7a,ORF7b,ORF8,ORF9b,S \
  +--input-gene-map=data/sars-cov-2/genemap.gff \
  +--input-tree=data/sars-cov-2/tree.json \
  +--input-qc-config=data/sars-cov-2/qc.json \
  +--input-pcr-primers=data/sars-cov-2/primers.csv \
  +--output-json=tmp/nextclade.json \
  +--output-csv=tmp/nextclade.csv \
  +--output-tsv=tmp/nextclade.tsv \
  +--output-tree=tmp/nextclade.auspice.json \
  +--output-dir=tmp/ \
  +--output-basename=nextclade \
  +--include-reference \
  +"
  