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<!DOCTYPE html>
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<strong>Last updated:</strong> 2021-03-15
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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
</p>
<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>
</p>
<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="#strongRepositoryversionstrongahrefhttpsgithubcomTheJacksonLaboratoryCSNAtreefd9720d435774de6687958a9091a1f8bbac40955targetblankfd9720da"> <span class="glyphicon glyphicon-ok text-success" aria-hidden="true"></span> <strong>Repository version:</strong> <a href="https://github.com/TheJacksonLaboratory/CSNA/tree/fd9720d435774de6687958a9091a1f8bbac40955" target="_blank">fd9720d</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/fd9720d435774de6687958a9091a1f8bbac40955" target="_blank">fd9720d</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:
Ignored: .Rhistory
Ignored: .Rproj.user/
Untracked files:
Untracked: analysis/.nfs0000000135a08b9b00002448
Untracked: analysis/.nfs0000000135a08ba50000244a
Untracked: analysis/csna_image.sif
Untracked: analysis/index0.Rmd
Untracked: analysis/rstudio.4.0.3.simg
Untracked: analysis/scripts/
Untracked: analysis/workflow_proc.R
Untracked: analysis/workflow_proc.sh
Untracked: analysis/workflow_proc.stderr
Untracked: analysis/workflow_proc.stdout
Untracked: archived/
Untracked: code/FinalReport2Plink.sh
Untracked: code/csna_qtlmapping_workflow.R
Untracked: code/reconst_utils.R
Untracked: data/69k_grid_pgmap.RData
Untracked: data/FinalReport/
Untracked: data/GCTA/
Untracked: data/GM/
Untracked: data/Jackson_Lab_11_batches/
Untracked: data/Jackson_Lab_12_batches/
Untracked: data/Jackson_Lab_Bubier_MURGIGV01/
Untracked: data/Jackson_Lab_Gagnon/
Untracked: data/RTG/
Untracked: data/cc_do_founders_key.rds
Untracked: data/cc_variants.sqlite
Untracked: data/marker_grid_0.02cM_plus.txt
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Untracked: data/pheno/
Untracked: output/archived_output/
Untracked: output/pdf/
Untracked: output/qtlmapping/
Unstaged changes:
Modified: .Rprofile
Modified: .gitignore
Modified: README.md
Modified: _workflowr.yml
Deleted: analysis/01_geneseek2qtl2.R
Deleted: analysis/02_geneseek2intensity.R
Deleted: analysis/03_firstgm2genoprobs.R
Deleted: analysis/04_diagnosis_qc_gigamuga_11_batches.Rmd
Modified: analysis/04_diagnosis_qc_gigamuga_12_batches.Rmd
Deleted: analysis/04_diagnosis_qc_gigamuga_nine_batches.R
Deleted: analysis/04_diagnosis_qc_gigamuga_nine_batches.Rmd
Deleted: analysis/05_after_diagnosis_qc_gigamuga_11_batches.Rmd
Modified: analysis/05_after_diagnosis_qc_gigamuga_12_batches.Rmd
Deleted: analysis/05_after_diagnosis_qc_gigamuga_nine_batches.R
Deleted: analysis/05_after_diagnosis_qc_gigamuga_nine_batches.Rmd
Deleted: analysis/06_final_pr_apr_69K.R
Deleted: analysis/07.1_html_founder_prop.R
Modified: analysis/07_do_diversity_report.Rmd
Deleted: analysis/07_recomb_size_founder_prop.R
Deleted: analysis/07_recomb_size_founder_prop.Rmd
Deleted: analysis/08_gcta_herit.R
Deleted: analysis/09_qtlmapping.R
Deleted: analysis/10_qtl_permu.R
Deleted: analysis/11_qtl_blup.R
Deleted: analysis/12_plot_69k_qtl_mapping_2.Rmd
Deleted: analysis/12_plot_qtl_mapping_1.Rmd
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Modified: analysis/_site.yml
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Modified: code/README.md
Modified: csna_workflow.Rproj
Modified: data/README.md
Modified: output/README.md
</code></pre>
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