bcbio_sample.yaml

---
# 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 YAML files 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 can optionally specify a date and a unique name
# to use for naming the output files and project directories.
fc_date: '110812'
fc_name: unique_name
# Directory to upload final results to. Also supports Galaxy and S3 upload.
upload:
  dir: ../final
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: variant2
    algorithm:
      aligner: novoalign
      variantcaller: gatk