Improve runtest defaults, add changelog, update --version flag, add --force flag, refactor Rlibs

[slsevilla]

Changes

• Adds a --force flag to allow for re-initialization of a workdir
• Fixes error with testrun in DESEQ2
• Decreases the number of samples being run with testrun, essentially running tinytest as default and removing tinytest as an option
• Reads version from VERSION file instead of github repo link
• Added a CHANGELOG
• Refactor R library handling
• Adds missing mm10 parameters
• Removes some testing from annotation report gopeaks due to latency

Issues

• fixes Use version file instead of git commit tag #96
• fixes Consider allowing workdir to already existing during init #97
• fixes carlisle --version should print version number #112
• fixes rumode testrun produces error with DESEQ2 #113
• fixes Improve runmode testrun by updating params, adding mm10 #115
• fixes add CHANGELOG #116
• fixes RLibs Path for all RMD files #118
• fixes Pipeline does not launch for mm10 due to missing parameters #121
• fixes GO enrichment is lagging with 'gopeaks' peak caller, during linking distal enhancers #125

PR Checklist

(Strikethrough any points that are not applicable.)

• This comment contains a description of changes with justifications, with any relevant issues linked.
• Update docs if there are any API changes.
• Update CHANGELOG.md with a short description of any user-facing changes and reference the PR number. Guidelines: https://keepachangelog.com/en/1.1.0/

[kopardev]

Everything looks good to me. Also, delete the "test_dev" GHA WF as it refers to some 9999.9999 version which does not exist and include that in this PR.

[kelly-sovacool]

My test run failed in the GO enrichment rule:

Quitting from lines 19-52 [setup] (_go_enrichment.Rmd)
Error in `install.packages()`:
! unable to install packages
Backtrace:
  1. BiocManager::install(new.packages, INSTALL_opts = "--no-lock")
  2. BiocManager:::.install(...)
  3. BiocManager:::.install_repos(...)
  4. BiocManager:::.inet_install.packages(...)
  6. base::tryCatch(...)
  7. base (local) tryCatchList(expr, classes, parentenv, handlers)
  8. base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
  9. value[[3L]](cond)
 10. BiocManager:::.inet_error(e)
Execution halted

Must be failing on chipenrich:

CARLISLE/workflow/scripts/_go_enrichment.Rmd

Line 26 in f41e914

list.of.bioconductor.packages=c("chipenrich")

The good news is all other jobs passed!

[slsevilla]

Finished testing these changes - everything went to completion. ready for you to test again @kelly-sovacool !

[kelly-sovacool]

test run submitted

bash /data/CCBR_Pipeliner/Pipelines/CARLISLE/carlisle-dev-sovacool/carlisle --runmode=init --workdir=/data/sovacoolkl/carlisle_test_iss-113_2
bash /data/CCBR_Pipeliner/Pipelines/CARLISLE/carlisle-dev-sovacool/carlisle --runmode=runtest --workdir=/data/sovacoolkl/carlisle_test_iss-113_2

[kelly-sovacool]

all jobs in my test run completed successfully 🎉