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datacarpentry / wrangling-genomics

Data Wrangling and Processing for Genomics
https://datacarpentry.org/wrangling-genomics/
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Create docs directory #255

Closed ErinBecker closed 3 months ago

ErinBecker commented 4 months ago

The read_qc.sh script is inconsistent in creating new directories. Before creating the results/fastqc_untrimmed_reads directory, there is a note that says:

"Our next line will create a new directory to hold our FastQC output files. Here we are using the -p option for mkdir again. It is a good idea to use this option in your shell scripts to avoid running into errors if you do not have the directory structure you think you do."

But then the last line in the script cats the summaries to a new file within the /docs/ directory without first creating that directory. This will run without error for most learners, if they have been following along with the materials, but will fail if someone is using the script independently of the lesson. This PR adds a command to create that /docs/ directory, to be on the safe side and consistent with advice earlier in the episode.

github-actions[bot] commented 4 months ago

Thank you!

Thank you for your pull request :smiley:

:robot: This automated message can help you check the rendered files in your submission for clarity. If you have any questions, please feel free to open an issue in {sandpaper}.

If you have files that automatically render output (e.g. R Markdown), then you should check for the following:

Rendered Changes

:mag: Inspect the changes: https://github.com/datacarpentry/wrangling-genomics/compare/md-outputs..md-outputs-PR-255

The following changes were observed in the rendered markdown documents:

 05-automation.md | 1 +
 md5sum.txt       | 2 +-
 2 files changed, 2 insertions(+), 1 deletion(-)
What does this mean? If you have source files that require output and figures to be generated (e.g. R Markdown), then it is important to make sure the generated figures and output are reproducible. This output provides a way for you to inspect the output in a diff-friendly manner so that it's easy to see the changes that occur due to new software versions or randomisation.

:stopwatch: Updated at 2024-06-14 19:15:06 +0000

aidamiro commented 3 months ago

This looks good. Thanks @ErinBecker for your recommendation!