Major Features added to Ruffus

version 1.0

Initial Release in Oxford

version 1.0.7

Added proxy_logger module for accessing a shared log across multiple jobs in different processes.

version 1.1.4

Tasks can get their input by automatically chaining to the output from one or more parent tasks using @files_re

version 2.0

• Revamped documentation:

  • Rewritten tutorial
  • Comprehensive manual
  • New syntax help

• Major redesign. New decorators include

  • @split
  • @transform
  • @merge
  • @collate

• Major redesign. Decorator inputs can mix

  • Output from previous tasks
  • glob patterns e.g. *.txt
  • Files names
  • Any other data type

version 2.0.2

• Much prettier /useful output from pipeline_printout
• New tutorial / manual

version 2.0.8

• File names can be in unicode
• File systems with 1 second timestamp granularity no longer cause problems.

version 2.0.9

• Better display of logging output

• Advanced form of @split This is an experimental feature.

  Hitherto, @split only takes 1 set of input (tasks/files/globs) and split these into an indeterminate number of output.

  This is a one->many operation.

  Sometimes it is desirable to take multiple input files, and split each of them further.

  This is a many->many (more) operation.

  It is possible to hack something together using @transform but downstream tasks would not aware that each job in @transform produces multiple outputs (rather than one input, one output per job).

  The syntax looks like:

  @split(get_files, regex(r"(.+).original"), r"\1.*.split")
  def split_files(i, o):
       pass
  

  If get_files() returned A.original, B.original and C.original, split_files() might lead to the following operations:

  A.original
          -> A.1.original
          -> A.2.original
          -> A.3.original
  B.original
          -> B.1.original
          -> B.2.original
  C.original
          -> C.1.original
          -> C.2.original
          -> C.3.original
          -> C.4.original
          -> C.5.original

  Note that each input (A/B/C.original) can produce a number of output, the exact number of which does not have to be pre-determined. This is similar to @split

  Tasks following split_files will have ten inputs corresponding to each of the output from split_files.

  If @transform was used instead of @split, then tasks following split_files would only have 3 inputs.

version 2.0.10

• touch_files_only option for pipeline_run

  When the pipeline runs, task functions will not be run. Instead, the output files for each job (in each task) will be touch-ed if necessary. This can be useful for simulating a pipeline run so that all files look as if they are up-to-date.

  Caveats:

  • This may not work correctly where output files are only determined at runtime, e.g. with @split
  • Only the output from pipelined jobs which are currently out-of-date will be touch-ed. In other words, the pipeline runs as normal, the only difference is that the output files are touch-ed instead of being created by the python task functions which would otherwise have been called.

• Parameter substitution for inputs(...)

  The inputs(...) parameter in @transform, @collate can now take tasks and globs, and these will be expanded appropriately (after regular expression replacement).

  For example:

  @transform("dir/a.input", regex(r"(.*)\/(.+).input"),
                inputs((r"\1/\2.other", r"\1/*.more")), r"elsewhere/\2.output")
  def task1(i, o):
    """
    Some pipeline task
    """
  

  Is equivalent to calling:

  task1(("dir/a.other", "dir/1.more", "dir/2.more"), "elsewhere/a.output")
  

  Here:

  r"\1/*.more"
  

  is first converted to:

  r"dir/*.more"
  

  which matches:

  "dir/1.more"
  "dir/2.more"
  

version 2.1.0

• @jobs_limit Some tasks are resource intensive and too many jobs should not be run at the same time. Examples include disk intensive operations such as unzipping, or downloading from FTP sites.

  Adding:

  @jobs_limit(4)
  @transform(new_data_list, suffix(".big_data.gz"), ".big_data")
  def unzip(i, o):
    "unzip code goes here"
  

  would limit the unzip operation to 4 jobs at a time, even if the rest of the pipeline runs highly in parallel.

  (Thanks to R. Young for suggesting this.)

version 2.1.1

• @transform(.., add_inputs(...))

  add_inputs(...) allows the addition of extra input dependencies / parameters for each job. Unlike inputs(...), the original input parameter is retained:

  from ruffus import *
  @transform(["a.input", "b.input"], suffix(".input"), add_inputs("just.1.more","just.2.more"), ".output")
  def task(i, o):
  ""

  Produces:

  Job = [[a.input, just.1.more, just.2.more] ->a.output]
  Job = [[b.input, just.1.more, just.2.more] ->b.output]

  Like inputs, add_inputs accepts strings, tasks and globs This minor syntactic change promises add much clarity to Ruffus code. add_inputs() is available for @transform, @collate and @split

version 2.2

• Simplifying @transform syntax with suffix(...)

  Regular expressions within ruffus are very powerful, and can allow files to be moved from one directory to another and renamed at will.

  However, using consistent file extensions and @transform(..., suffix(...)) makes the code much simpler and easier to read.

  Previously, suffix(...) did not cooperately well with inputs(...). For example, finding the corresponding header file (“.h”) for the matching input required a complicated regex(...) regular expression and input(...). This simple case, e.g. matching “something.c” with “something.h”, is now much easier in Ruffus.

  For example:

  source_files = ["something.c", "more_code.c"]
  @transform(source_files, suffix(".c"), add_inputs(r"\1.h", "common.h"), ".o")
  def compile(input_files, output_file):
      ( source_file,
        header_file,
        common_header) = input_files
      # call compiler to make object file
  

  This is equivalent to calling:

  compile(["something.c", "something.h", "common.h"], "something.o")
  compile(["more_code.c", "more_code.h", "common.h"], "more_code.o")
  

  The \1 matches everything but the suffix and will be applied to both ``glob``s and file names.

For simplicity and compatibility with previous versions, there is always an implied r”1” before the output parameters. I.e. output parameters strings are always substituted.

• Tasks and glob in inputs(...) / add_inputs(...)

  glob``s and tasks can be added as the prerequisites / input files using ``inputs(...) and add_inputs(...). glob expansions will take place when the task is run.

• Advanced form of @split with regex:

  The standard @split divided one set of inputs into multiple outputs (the number of which can be determined at runtime).

  This is a one->many operation.

  An advanced form of @split has been added which can split each of several files further.

  In other words, this is a many->"many more" operation.

  For example, given three starting files:

  original_files = ["original_0.file",
                    "original_1.file",
                    "original_2.file"]
  

  We can split each into its own set of sub-sections:

  @split(original_files,
     regex(r"starting_(\d+).fa"),                         # match starting files
           r"files.split.\1.*.fa"                         # glob pattern
           r"\1")                                         # index of original file
  def split_files(input_file, output_files, original_index):
      """
          Code to split each input_file
              "original_0.file" -> "files.split.0.*.fa"
              "original_1.file" -> "files.split.1.*.fa"
              "original_2.file" -> "files.split.2.*.fa"
      """
  

  This is, conceptually, the reverse of the @collate(...) decorator

• Ruffus will complain about unescaped regular expression special characters:

  Ruffus uses “1” and “2” in regular expression substitutions. Even seasoned python users may not remember that these have to be ‘escaped’ in strings. The best option is to use ‘raw’ python strings e.g.

  r"\1_substitutes\2correctly\3four\4times"
  

  Ruffus will throw an exception if it sees an unescaped “1” or “2” in a file name, which should catch most of these bugs.

• Prettier output from pipeline_printout_graph

  Changed to nicer colours, symbols etc. for a more professional look. @split and @merge tasks now look different from @transform. Colours, size and resolution are now fully customisable:

  pipeline_printout_graph( #...
                           user_colour_scheme = {
                                                  "colour_scheme_index":1,
                                                  "Task to run"  : {"fillcolor":"blue"},
                                                   pipeline_name : "My flowchart",
                                                   size          : (11,8),
                                                   dpi           : 120)})

  An SVG bug in firefox has been worked around so that font size are displayed correctly.

Fixed Bugs

Full list at “Latest Changes wiki entry”