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Releases: CCBR/CHARLIE

CHARLIE 0.11.1

25 Nov 14:03
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  • CHARLIE was falsely throwing a file permissions error for tempdir values containing bash variables. (#118, @kelly-sovacool)
  • Singularity bind paths were not being set properly. (#119, @kelly-sovacool)
  • Update docker containers to set $PYTHONPATH. (#119, #125, @kelly-sovacool)
    • Otherwise, this environment variable can be carried over and cause package conflicts when singularity is not run with -C.
    • Also use python -E to ensure the $PYTHONPATH is not carried over. (#129, @kelly-sovacool)
  • Fix reconfig to correctly replace variables in the config file. (#121, @kelly-sovacool)
  • Prevent using excessive memory when copying reference files. (#126, @kelly-sovacool)
  • Fix missing output files due to file system latency and use real (absolute) paths where possible. (#130, @kelly-sovacool)
  • Update documentation to reflect biowulf usage and improved test dataset. (#132, @kelly-sovacool)

CHARLIE 0.11.0

16 Sep 21:37
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  • Major updates to convert CHARLIE from a biowulf-specific to a platform-agnostic pipeline (#102, @kelly-sovacool):
    • All rules now use containers instead of envmodules.
    • Default config and cluster config files are provided for use on biowulf and FRCE.
    • New entry TEMPDIR in the config file sets the temporary directory location for rules that require transient storage.
    • New --singcache argument to provide a singularity cache dir location. The singularity cache dir is automatically set inside /data/$USER/ or $WORKDIR/ if --singcache is not provided.
  • Minor documentation improvements. (#114, @kelly-sovacool)

v0.10.1

23 Dec 19:36
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  • strand are reported together, strand from all callers are reported,
  • both + and - flanking sites are reported,
  • rev-comp function updated,
  • updated versions of tools to match available tools on BIOWULF.

v0.9.0

27 Apr 16:57
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Significant upgrades since the last release:

  • updates to wrapper script, many new arguments/options added
  • new per-sample counts table format
  • new all-sample master counts matrix with min-nreads filtering and ntools column to show number of tools supporting the circRNA call
  • new version of Snakemake
  • cluster_status script added for forced completion of pipeline upon TIMEOUTs
  • updated flowchart from lucid charts
  • added circRNAfinder, find_circ, circExplorer2_bwa and other tools
  • optimized execution and resource requirements
  • updated viral annotations (Thanks Sara!)
  • new method to extract linear counts, create linear BAMs using circExplorer2 outputs
  • new job reporting using jobby and its derivatives
  • separated creation of BWA and BOWTIE2 index from creation of STAR index to speed things up
  • parallelized find_circ
  • better cleanup (eg. deleting _STARgenome folders, etc.) for much smaller digital footprint
  • multitude of comments throughout the snakefiles including listing of output file column descriptions
  • preliminary GH actions added

v0.7.0

19 Nov 02:37
ed60ef4
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  • 5 circRNA callers
  • all-sample counts matrix with annotations

v0.6.9

27 Apr 01:10
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  • Optimized pysam scripts
  • fixed premature completion of singularity rules

v0.6.5

26 May 19:49
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  • updated config.yaml to use the latest HSV-1 annotations received from Sarah (050421)

v0.6.4

24 May 21:40
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  • create linear reads BAM file
  • create linear reads BigWigs for each region in the .regions file.

v0.6.3

18 May 20:10
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  • QOS not working for Taka... removed from cluster.json
  • recall rule requires python/3.7 ... env module updated

v0.6.2

11 May 12:53
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BSJ files are in BSJ subfolder... bug fix for v0.6.1