Param Param!

Improvements

• The parameter system has been revamped, and parameters are now component-specific
  and independent by default. This allows a better fine-tuning of the parameters
  and also the execution of the same component multiple times (for instance in a fork)
  with different parameters. The old parameter system that merged identical parameters
  is still available by using the --merge-params flag when building the pipeline.
• Added a global --clearAtCheckpoint parameter that, when set to true, will remove
  temporary files that are no longer necessary for downstream steps of the pipeline
  from the work directory. This option is currently supported for the trimmomatic,
  fastqc_trimmomatic, skesa and spades components.

New components

• maxbin2: An automatic tool for binning metagenomic sequences.
• bowtie2: Align short paired-end sequencing reads to long reference
  sequences.
• retrieve_mapped: Retrieves the mapped reads of a previous bowtie2 mapping process.

New recipes

• plasmids: A recipe to perform mapping, mash screen on reads
  and also mash dist for assembly based approaches (all to detect
  plasmids). This also includes annotation with abricate for the assembly.
• plasmids_mapping: A recipe to perform mapping for plasmids.
• plasmids_mash: A recipe to perform mash screen for plasmids.
• plasmids_assembly: A recipe to perform mash dist for plasmid
  assemblies.

Minor/Other changes

• Added "smart" check when the user provides a typo in pipeline string
  for a given process, outputting some "educated" guesses to the
  terminal.http://192.92.149.169:80/inspect/5b585070ed1cb0dbb9a696c724b7f9ed7844e1afe5188ef3aa44c7c3cc5b539d
• Added "-cr" option to show current recipe pipeline_string.
• Changed the way recipes were being parsed by proc_collector for the
  usage of -l and -L options.
• Added check for non-ascii characters in colored_print.
• Fixed log when a file with the pipeline is provided to -t option
  instead of a string.

Bug fixes

• Fixed pipeline names that contain new line characters.
• Fixed pipeline generation when automatic dependencies were added right after a fork
• Template: sistr.nf: Fixed comparison that determined process status.
• Fixed issue with --version option.