Cuneiform (programming language): Difference between revisions

Revision as of 19:41, 2 November 2016

Revision as of 23:05, 26 November 2016

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A hello-world script:

<sourcepre>

deftask greet( out : person )in python *{

out = "Hello "+person

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greet( person: "Peter" "Robert" );

</sourcepre>

This script defines a task <code>greet</code> in [[Python (programming language)|Python]] which prepends the string <code>"Hello "</code> to its argument <code>person</code>.

The task has one output variable <code>out</code>.

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Command line tools can be integrated by defining a task in [[Bash (Unix shell)|Bash]]:

<sourcepre>

deftask samtools-view( bam( File ) : sam( File ) )in bash *{

samtools view -bS $sam > $bam

}*

</sourcepre>

In this example a task <code>samtools-view</code> is defined.

It calls the tool [[SAMtools]], consuming an input file in SAM format and producing an output file in BAM format.