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<strong>Last updated:</strong> 2021-01-15
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<strong>Checks:</strong> <span class="glyphicon glyphicon-ok text-success" aria-hidden="true"></span> 2 <span class="glyphicon glyphicon-exclamation-sign text-danger" aria-hidden="true"></span> 0
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<p>
<strong>Knit directory:</strong> <code>csna_workflow/</code> <span class="glyphicon glyphicon-question-sign" aria-hidden="true" title="This is the local directory in which the code in this file was executed."> </span>
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<p>
This reproducible <a href="http://rmarkdown.rstudio.com">R Markdown</a> analysis was created with <a
href="https://github.com/jdblischak/workflowr">workflowr</a> (version 1.6.2). The <em>Checks</em> tab describes the reproducibility checks that were applied when the results were created. The <em>Past versions</em> tab lists the development history.
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<p>Great! Since the R Markdown file has been committed to the Git repository, you know the exact version of the code that produced these results.</p>
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<a data-toggle="collapse" data-parent="#workflowr-checks" href="#strongRepositoryversionstrongahrefhttpsgithubcomTheJacksonLaboratoryCSNAtreea684c8adada658929cefc5ba27cf1d2d7c044a66targetblanka684c8aa"> <span class="glyphicon glyphicon-ok text-success" aria-hidden="true"></span> <strong>Repository version:</strong> <a href="https://github.com/TheJacksonLaboratory/CSNA/tree/a684c8adada658929cefc5ba27cf1d2d7c044a66" target="_blank">a684c8a</a> </a>
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Great! You are using Git for version control. Tracking code development and connecting the code version to the results is critical for reproducibility.
</p>
<p>
The results in this page were generated with repository version <a href="https://github.com/TheJacksonLaboratory/CSNA/tree/a684c8adada658929cefc5ba27cf1d2d7c044a66" target="_blank">a684c8a</a>. See the <em>Past versions</em> tab to see a history of the changes made to the R Markdown and HTML files.
</p>
<p>
Note that you need to be careful to ensure that all relevant files for the analysis have been committed to Git prior to generating the results (you can use <code>wflow_publish</code> or <code>wflow_git_commit</code>). workflowr only checks the R Markdown file, but you know if there are other scripts or data files that it depends on. Below is the status of the Git repository when the results were generated:
</p>
<pre><code>
Ignored files:
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Ignored: .Rproj.user/
Untracked files:
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Unstaged changes:
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Deleted: analysis/04_diagnosis_qc_gigamuga_11_batches.Rmd
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Deleted: analysis/17_plot_qtl_mapping.Rmd
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Deleted: analysis/run_02_geneseek2intensity.R
Deleted: analysis/run_03_firstgm2genoprobs.R
Deleted: analysis/run_04_diagnosis_qc_gigamuga_nine_batches.R
Deleted: analysis/run_05_after_diagnosis_qc_gigamuga_nine_batches.R
Deleted: analysis/run_06_final_pr_apr_69K.R
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Deleted: analysis/run_07_recomb_size_founder_prop.R
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Deleted: analysis/run_10_qtl_permu.R
Deleted: analysis/run_11_qtl_blup.R
</code></pre>
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