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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.

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:    .DS_Store
    Ignored:    .Rhistory
    Ignored:    .Rproj.user/
    Ignored:    code/log/

Untracked files:
    Untracked:  .Rprofile
    Untracked:  ._.DS_Store
    Untracked:  .gitignore
    Untracked:  README.md
    Untracked:  _workflowr.yml
    Untracked:  analysis/
    Untracked:  apaQTL.Rproj
    Untracked:  code/._SnakefilePAS
    Untracked:  code/._bed2saf.py
    Untracked:  code/._callPeaksYL.py
    Untracked:  code/._chooseAnno2SAF.py
    Untracked:  code/._cluster.json
    Untracked:  code/._config.yaml
    Untracked:  code/._config2.yaml
    Untracked:  code/._configOLD.yaml
    Untracked:  code/._convertNumeric.py
    Untracked:  code/._filter5perc.R
    Untracked:  code/._filter5percPheno.py
    Untracked:  code/._filterpeaks.py
    Untracked:  code/._fixFChead.py
    Untracked:  code/._make5percPeakbed.py
    Untracked:  code/._makeFileID.py
    Untracked:  code/._makePheno.py
    Untracked:  code/._mergeAllBam.sh
    Untracked:  code/._mergeByFracBam.sh
    Untracked:  code/._mergePeaks.sh
    Untracked:  code/._namePeaks.py
    Untracked:  code/._peak2PAS.py
    Untracked:  code/._peakFC.sh
    Untracked:  code/._pheno2countonly.R
    Untracked:  code/._quantassign2parsedpeak.py
    Untracked:  code/.snakemake/
    Untracked:  code/README.md
    Untracked:  code/Snakefile
    Untracked:  code/SnakefilePAS
    Untracked:  code/cluster.json
    Untracked:  code/config.yaml
    Untracked:  code/configOLD.yaml
    Untracked:  code/environment.yaml
    Untracked:  code/snakelog.out
    Untracked:  code/snakemake.batch
    Untracked:  data/
    Untracked:  output/

Unstaged changes:
    Modified:   code/bed2saf.py
    Modified:   code/callPeaksYL.py
    Modified:   code/chooseAnno2SAF.py
    Modified:   code/convertNumeric.py
    Modified:   code/filter5perc.R
    Modified:   code/filter5percPheno.py
    Modified:   code/filterpeaks.py
    Modified:   code/fixFChead.py
    Modified:   code/make5percPeakbed.py
    Modified:   code/makeFileID.py
    Modified:   code/makePheno.py
    Modified:   code/mergeAllBam.sh
    Modified:   code/mergeByFracBam.sh
    Modified:   code/mergePeaks.sh
    Modified:   code/namePeaks.py
    Modified:   code/peak2PAS.py
    Modified:   code/peakFC.sh
    Modified:   code/pheno2countonly.R
    Modified:   code/quantassign2parsedpeak.py
    Modified:   code/submit-snakemake.sh

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.