run_data_managers.yaml

# configuration for fetch and index genomes

data_managers:
    # Data manager ID
    - id: ctat_genome_resource_libs_data_manager
      # tool parameters, nested parameters should be specified using a pipe (|)
      params:
        - 'genome_resource_library|built_library_location': '/export/resources/GRCh38_v27_CTAT_lib_Feb092018/ctat_genome_lib_build_dir'
        - 'genome_resource_library|build_type': 'specify_built_location'
        - 'display_name': 'GRCH38'
        - 'gmap_build': 'true'
      # Items refere to a list of variables you want to run this data manager. You can use them inside the param field with {{ item }}
      # In case of genome for example you can run this DM with multiple genomes, or you could give multiple URLs.
      #items:
        #- ce6
        #- dm3
        #- mm9
      # Name of the data-tables you want to reload after your DM are finished. This can be important for subsequent data managers
      data_table_reload:
        - all_fasta
        - __dbkeys__
#    - id: toolshed.g2.bx.psu.edu/repos/devteam/data_manager_bowtie2_index_builder/bowtie2_index_builder_data_manager/2.2.6
#      params:
#        - 'all_fasta_source': '{{ item.id }}'
#        - 'sequence_name': '{{ item.name }}'
#        - 'sequence_id': '{{ item.id }}'
#      items:
#        - id: ce8
#          name: C. elegans (ce8)
#        - id: dm3
#          name: D. melanogaster Apr. 2006 (BDGP r5/dm3)
#        - id: mm9
#          name: M. musculus July 2007 (NCBI37/mm9)
#      data_table_reload:
#        # Bowtie creates indices for Bowtie and TopHat
#        - bowtie2_indexes
#        - tophat2_indexes