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Merge pull request /issues/207 from hoytpr/hoyt1
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path typo in fastq text episode 05
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fpsom authored Dec 6, 2019
2 parents d28789d + 7699af6 commit 7b35fe2
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3 changes: 2 additions & 1 deletion episodes/05-automation.md
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Expand Up @@ -331,7 +331,8 @@ mkdir -p sam bam bcf vcf
{: .output}

Then, we use a loop to run the variant calling workflow on each of our FASTQ files. The full list of commands
within the loop will be executed once for each of the FASTQ files in the `data/trimmed_fastq/` directory.
within the loop will be executed once for each of the FASTQ files in the
`data/trimmed_fastq_small/` directory.
We will include a few `echo` statements to give us status updates on our progress.

The first thing we do is assign the name of the FASTQ file we're currently working with to a variable called `fq1` and
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