single.yaml

common: {
  # ============================================================================
  #
  # yaml example file for single channel processing
  #
  # General settings for processing
  # 2015-04-01_LZ2_Stock46
  # Dpse_Dip3_VK33
  #
  # ============================================================================
  # directory that contains the bean shell scripts and Snakefile
  bsh_directory: "/projects/pilot_spim/Christopher/snakemake-workflows/spim_registration/timelapse/",
  # Directory that contains the cuda libraries
  directory_cuda: "/sw/users/schmied/cuda/",
  # Directory that contains the current working Fiji
  fiji-app: "/sw/users/schmied/packages/2015-06-30_Fiji.app.cuda/ImageJ-linux64",
  fiji-prefix: "/sw/users/schmied/packages/xvfb-run -a",       # calls xvfb for Fiji headless mode
  # ============================================================================
  #   Processing switches
  # Description: Use switches to decide which processing steps you need:
  #
  # Options:
  # transformation_switch: "timelapse" standard processing
  # after timelapse registration directly goes into fusion, timelapse_duplicate
  # "timelapse_duplicate" for dual channel processing one channel contains the beads
  #
  # Switches between content based fusion and deconvoltion
  # "deconvolution" > for deconvolution
  # "fusion" > for content based fusion
  # ============================================================================
  #
  # Transformation switch:
  transformation_switch: "timelapse", 
  # Fusion switch:
  fusion_switch: "fusion",
  # ============================================================================
  # xml file names
  # 
  # xml file names without .xml suffix
  # ============================================================================
  first_xml_filename: 'Dpse_Dip3_VK33',       # Name of the xml file for the .czi or .tif files
  hdf5_xml_filename: '"hdf5_Dpse_Dip3_VK33"', # Name of .xml file for the hdf5 data after resave_hdf5
  merged_xml: 'hdf5_Dpse_Dip3_VK33_merge',    # Name of .xml file after merge
  # ============================================================================
  # Describe the dataset
  #
  # Options: number of timepoints
  #          angles
  #          channels
  #          illuminations
  #          pixel size
  # ============================================================================
  ntimepoints: 72,               # number of timepoints of dataset
  angles: "0,72,144,216,288",   # angles
  channels: "green",        # channels
  illumination: "0",            # illuminations
  # ----------------------------------------------------------------------------
  # For .czi datasets
  # master .czi file
  first_czi: "2015-04-01_LZ2_Stock46.czi", 
  # ----------------------------------------------------------------------------
  # For .tif datasets
  # file pattern of .tif files:
  # for multi channel give spim_TL{tt}_Angle{a}_Channel{c}.tif
  # for padded zeros use tt 
  # specify calibration
  image_file_pattern: 'img_TL{{t}}_Angle{{a}}.tif',
  pixel_distance_x: '0.285901069641113',  # Manual calibration x
  pixel_distance_y: '0.285901069641113',  # Manual calibration y
  pixel_distance_z: '1.500000000000000',  # Manual calibration z