Last updated: 2018-08-08

workflowr checks: (Click a bullet for more information)

• ✖ R Markdown file: uncommitted changes

  The R Markdown file has unstaged changes. To know which version of the R Markdown file created these results, you’ll want to first commit it to the Git repo. If you’re still working on the analysis, you can ignore this warning. When you’re finished, you can run wflow_publish to commit the R Markdown file and build the HTML.

• ✔ Repository version: 5a9a5ba

  Great! You are using Git for version control. Tracking code development and connecting the code version to the results is critical for reproducibility. The version displayed above was the version of the Git repository at the time these results were generated.
  
  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 wflow_publish or wflow_git_commit). 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:

  
  Ignored files:
      Ignored:    .Rproj.user/
  
  Untracked files:
      Untracked:  analysis/analysis_for_joxm.Rmd
      Untracked:  analysis/cell_assignment.Rmd
      Untracked:  analysis/differential_expression.Rmd
      Untracked:  analysis/mutated_genes.Rmd
      Untracked:  data/canopy/
      Untracked:  data/cell_assignment/
      Untracked:  data/de_analysis_FTv62/
      Untracked:  data/donor_info_070818.txt
      Untracked:  data/donor_neutrality.tsv
      Untracked:  data/high-vs-low-exomes.v62.ft.alldonors-filt_lenient.all_filt_sites.vep_most_severe_csq.txt
      Untracked:  data/high-vs-low-exomes.v62.ft.filt_lenient-alldonors.txt.gz
      Untracked:  data/human_H_v5p2.rdata
      Untracked:  data/human_c2_v5p2.rdata
      Untracked:  data/human_c6_v5p2.rdata
      Untracked:  data/sce_merged_donors_cardelino_donorid_all_qc_filt.rds
      Untracked:  data/sce_merged_donors_cardelino_donorid_all_with_qc_labels.rds
      Untracked:  data/sce_merged_donors_cardelino_donorid_unstim_qc_filt.rds
      Untracked:  data/sces/
      Untracked:  docs/figure/
      Untracked:  figures/
  
  Unstaged changes:
      Modified:   analysis/_site.yml
      Modified:   analysis/index.Rmd
  
  

  Note that any generated files, e.g. HTML, png, CSS, etc., are not included in this status report because it is ok for generated content to have uncommitted changes.

Expand here to see past versions:

File	Version	Author	Date	Message
html	9856275	davismcc	2018-08-07	Build site.
Rmd	5fc189d	davismcc	2018-08-07	Start workflowr project.

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This reproducible R Markdown analysis was created with workflowr 1.1.1

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