Indriya

Components changes

• mapping_patlas: refactored to remove temporary files used to create
  sam and bam files and added data to .report.json. Updated databases to pATLAS
  version 1.5.2.
• mash_screen and mash_dist: added data to .report.json. Updated databases
  to pATLAS version 1.5.2.

New components

• Added component fasterq_dump
• Added component mash_sketch_fasta
• Added component mash_sketch_fastq
• Added component downsample_fastq for FastQ read sub sampling using seqtk
• Added component momps for typing of Legionella pneumophila
• Added component split_assembly
• Added component mafft
• Added component raxml
• Added component viral_assembly
• Added component progressive_mauve
• Added component dengue_typing

Minor/Other changes

• Added check for params.accessions that enables to report a proper
  error when it is set to null.
• Added build option to export component parameters information in JSON format.
• Fixed minor issue preventing the maxbin2 and split_assembly components
  from being used multiples times in a pipeline
• Added a catch to the filter_poly process for cases where the input file is empty.
• spades template now reports the exit code of spades' execution

Bug fixes

• Removed the need for the nf process templates to have an empty line
  at the beginning of the template files.
• Fixed issue when the inspect mode was executed on a pipeline directory
  with failed processes but with the work directory removed (the log files
  where no longer available).
• Fixed issue when the inspect mode was executed on a pipeline without the
  memory directory defined.
• Fixed issue in the inspect mode, where there is a rare race condition between
  tags in the log and trace files.
• Fixed bug on midas_species process where the output file was not being
  linked correctly, causing the process to fail
• Fixed bug on bowtie where the reference parameter was missing the pid
• Fixed bug on filter_poly where the tag was missing