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maunei / bpipe

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'requires' is undocumented #86

Open GoogleCodeExporter opened 8 years ago

GoogleCodeExporter commented 8 years ago 
The Troubleshooting wiki page mentions a command called 'requires':

 sam_to_fastq = {

    requires run_bar_code : "Id of sequencing machine. Used to name files to ensure uniqueness"

    // Inputs are SAM files with the lane indicated by the form <file name>_L<lane>.sam
    def outputs = [
        file(input.sam).name.replaceAll('_([1-2]).sam$','_' + run_bar_code + '_L$1_R1.fastq'),
        file(input.sam).name.replaceAll('_([1-2]).sam$','_' + run_bar_code + '_L$1_R2.fastq')
    ]
    produce(outputs) {
        exec """
            java -Xmx2g -jar $PICARD_HOME/SamToFastq.jar
                    I=$input.sam
                    F=${output1}
                    F2=${output2}
        """
    }
 }

I looked on the wiki, but the documentation for 'requires' is missing.

Florent

Original issue reported on code.google.com by florent....@gmail.com on 12 Nov 2013 at 5:07