GitLab

Fixed arguments for pepr peak calling.  Updated params in peak_call module to correctly reflect the output files produced by hidden domains.

Small updates to many yaml files.  All peak callers now generating successfully.  Adjusted file_list input loding.  Fixed chip-job-ccat-format-bed to create correct number of columns.

Updated peak call yaml to include puncatte music.  Added python script to handle directory / file management.

Updated yaml files to mark final_output.  Final output implies both transfer=true and should_save=true

Added transfer=true to sorted peak results.  Added transfer=false to module_generator download results.

Updated gem peak calling to list & sort both results.  Updated peak_call generator to correctly get ouput file from gem.

Added correct commands for parsing jobs.  Fixed naming conventions for ccat, and updated the prefix.

Gem ONLY accepts chr_fasta files with names chr1.fa, chr2.fa... We can't prefix them with our unique genome prefix, so we are now staging them into separate directories based on assembly.

Cleaned up peak call generator and yaml files to include default distribution arguments.  Removed gene annotation argument from peakranger.

Fixed several more yaml job files.  Removed unnecessary duplicate cp_bed_tagalign files.  Updated peak_call.yaml accordingly.

Added peakranger to peak call yaml.  Added jamm and peakranger to peak call generator.  Fixed prefix issues with peak call generation.

Add unique param names/files for converting bed to tagalign
for control and exp files. This is needed to avoid issues with
parsing due to repeated names.

Added peak call generator.  Adjusted gem_callpeak yaml removing redundant genome_dir.  Updated peak_call module yaml accordingly, changed some names in macs2 file names.

Updated all yaml files to support type argument.  Heavily updated workflow_job parsing and verbosity.

Added db_save_results yaml job, and script.  Updated workflow information tracking to create correct meta data files for saving information to the database.  Conf adjusted to support yaml files, and arbitrary result files.  workflow_job can now return a dictionary of all arguments used.