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docs: fix Nextflow CLI flag for -quiet in README (#9)
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clintval authored Nov 22, 2023
1 parent cc72b50 commit b4c64f8
Showing 1 changed file with 3 additions and 3 deletions.
6 changes: 3 additions & 3 deletions README.md
Original file line number Diff line number Diff line change
Expand Up @@ -99,21 +99,21 @@ After building the Docker image with `docker compose build`, and after [enabling
When the main Nextflow script is run with `nextflow run main.nf`, you will get the following output:

```console
❯ nextflow --quiet run main.nf
❯ nextflow -quiet run main.nf
samtools 1.17
```

However, upgrade the dotenv variable `SAMTOOLS_VERSION` to `1.18` and you'll see:

```console
❯ nextflow --quiet run main.nf
❯ nextflow -quiet run main.nf
samtools 1.18
```

Conveniently for debugging, local environment variables take precedence over dotenv variables:

```console
❯ SAMTOOLS_VERSION=1.16 nextflow --quiet run main.nf
❯ SAMTOOLS_VERSION=1.16 nextflow -quiet run main.nf
samtools 1.16
```

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