---
# Example file for specifying run information to bcbio_nextgen.py
# In a fully Galaxy automated setup this information can be retrieved
# from the Galaxy server based on user inputs. This allows you to
# run the automated pipeline separately or from other external programs

# If your folder naming is not standard Illumina style
# (110729_SN728_0036_A81UJUABXX) you should specify the date and a unique name
# to use for naming the output files.
fc_date: '110812'
fc_name: unique_name
details:
  # For each flowcell, you specify either the lane if the files follow standard
  # naming conventions (1_110729_A81UJUABXX) or the names of the files if they
  # are differently named. Can specify either one file for single end or two for
  # paired.
  - files: [/path/to/1_1-fastq.txt, /path/to/1_2-fastq.txt]
    description: 'Sample 1'
    genome_build: GRCh37
    analysis: variant
    algorithm:
      aligner: novoalign
      variantcaller: gatk
      quality_format: Standard
  - description: 'Multiplex example'
    analysis: Minimal
    genome_build: hg19
    multiplex:
      - barcode_type: Illumina
        barcode_id: 1
        name: 'One Barcode Sample'
        sequence: ATCACG
      - barcode_type: Illumina
        barcode_id: 2
        name: 'Another Barcode Sample'
        sequence: CGATGT 
# Information on uploading back into Galaxy. Need the user name to upload as
# and the Galaxy Data Library to write to. These are not needed if not
# interoperating with Galaxy.
galaxy_user: chapmanb@test.com
galaxy_library: Upload Folder Name
