This example shows how to write a pipeline with two simple Bash processes, so that the results produced by the first process are consumed by the second process.
Line 1 The script starts with a shebang declaration. This allows you to launch your pipeline just like any other Bash script.
Line 3: Declares a pipeline parameter named params.in that is initialized with the value $HOME/sample.fa. This value can be overridden when launching the pipeline, by simply adding the option --in <value> to the script command line.
Lines 8-19: The process that splits the provided file.
Line 10: Opens the input declaration block. The lines following this clause are interpreted as input definitions.
Line 11: Declares the process input file, which will be named input.fa in the process script.
Line 13: Opens the output declaration block. The lines following this clause are interpreted as output declarations.
Line 14: Files whose names match the pattern seq_* are declared as the output of this process.
Lines 16-18: The actual script executed by the process to split the input file.
Lines 24-35: The second process, which receives the splits produced by the previous process and reverses their content.
Line 26: Opens the input declaration block. Lines following this clause are interpreted as input declarations.
Line 27: Defines the process input file.
Line 29: Opens the output declaration block. Lines following this clause are interpreted as output declarations.
Line 30: The standard output of the executed script is declared as the process output.
Lines 32-34: The actual script executed by the process to reverse the content of the input files.
Lines 40-44: The workflow that connects everything together!
Line 41: First, the input file specified by params.in is passed to the splitSequences process.
Line 42: The outputs of splitSequences are passed as inputs to the reverse process, which processes each split file in parallel.
Line 43: Finally, each output emitted by reverse is printed.