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Create docs directory #255

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1 change: 1 addition & 0 deletions episodes/05-automation.md
Original file line number Diff line number Diff line change
Expand Up @@ -158,6 +158,7 @@

```output
echo "Saving summary..."
mkdir -p ~/dc_workshops/docs
cat */summary.txt > ~/dc_workshop/docs/fastqc_summaries.txt
```

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We can extend these principles to the entire variant calling workflow. To do this, we will take all of the individual commands that we wrote before, put them into a single file, add variables so that the script knows to iterate through our input files and write to the appropriate output files. This is very similar to what we did with our `read_qc.sh` script, but will be a bit more complex.

Download the script from [here](files/run_variant_calling.sh). Download to `~/dc_workshop/scripts`.

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[uninformative link text]: [here](files/run_variant_calling.sh)

```bash
curl -O https://datacarpentry.org/wrangling-genomics/files/run_variant_calling.sh
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