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Add tl;dr to instructions
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config/README.md

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@@ -12,6 +12,16 @@ For example, existing [profiles](https://snakemake.readthedocs.io/en/stable/gett
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are cross-compatible as well, but note that the `--use-conda` flag is deprecated starting with Snakemake 8.
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Instead, use `--software-deployment-method conda`.
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## tl;dr
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- **Needs**:
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- Snakemake 7.19 or later.
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- One FASTA per sample.
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- One BAM per sample.
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- One metadata CSV with columns `ID`, `CollectionDate` (YYYY-MM-DD), `ResidenceCity` and `GISAIDEPI` (can be empty).
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- **Setup**: edit [targets.yaml](/config/targets.yaml) (set `SAMPLES` and `METADATA`, at least) or build it using [`build_targets.py`](/build_targets.py). Leave `CONTEXT_FASTA: null` to auto-download from GISAID (needs `config/gisaid.yaml` with your username and password) or set a local FASTA path if download fails (see GISAID disclaimer).
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- **Run**: `snakemake (--use-conda | --sdm conda) -c4`.
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## Inputs and outputs
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The workflow requires a set of FASTA files (one per target sample), a corresponding set of

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