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sra-download -> sra_download -- match code
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meren committed Dec 10, 2023
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10 changes: 5 additions & 5 deletions anvio/docs/workflows/sra-download.md
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The `sra-download` workflow is a Snakemake workflow that downloads FASTQ files from SRA-accessions using [NCBI sra-tools wiki](https://github.com/ncbi/sra-tools/wiki/08.-prefetch-and-fasterq-dump), gzips them using [pigz](https://zlib.net/pigz/), and provides a %(samples-txt)s. You will need to have these tools installed before you start.
The `sra_download` workflow is a Snakemake workflow that downloads FASTQ files from SRA-accessions using [NCBI sra-tools wiki](https://github.com/ncbi/sra-tools/wiki/08.-prefetch-and-fasterq-dump), gzips them using [pigz](https://zlib.net/pigz/), and provides a %(samples-txt)s. You will need to have these tools installed before you start.

Let's get started.

Expand All @@ -9,7 +9,7 @@ Let's get started.
The first step is to make a %(workflow-config)s.

```bash
anvi-run-workflow -w sra-download --get-default-config sra_download_config.json
anvi-run-workflow -w sra_download --get-default-config sra_download_config.json
```

Here's what the %(workflow-config)s file looks like:
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},
"max_threads": "",
"config_version": "3",
"workflow_name": "sra-download"
"workflow_name": "sra_download"
```
#### Modify any of the bells and whistles in the config file
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### List of SRA accessions
The input for the `sra-download` workflow is `SRA_accession_list.txt`. This contains a list of your SRA accession you would like to download and it looks like this:
The input for the `sra_download` workflow is `SRA_accession_list.txt`. This contains a list of your SRA accession you would like to download and it looks like this:
```bash
$ cat SRA_accession_list.txt
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### Run on your local computer
```bash
anvi-run-workflow -w sra-download -c sra_download_config.json
anvi-run-workflow -w sra_download -c sra_download_config.json
```
### Go big and use an HPC!
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