JAFFA_direct.groovy

/***********************************************************
 ** This is the JAFFA pipeline file for fusion detection
 ** without read assembly. Run like so:
 **    bpipe run <path_to_this_file> <path_to_fastq/fasta_files>
 ** See our website for details	on running options:
 ** https://code.google.com/p/jaffa-project/.
 **
 ** Author: Nadia Davidson <nadia.davidson@mcri.edu.au>
 ** Last Update: 6th Feb 2014
 *********************************************************/

codeBase = file(bpipe.Config.config.script).parentFile.absolutePath
load codeBase+"/JAFFA_stages.groovy"

common_steps = segment { filter_transcripts +
                 extract_fusion_sequences +
                 align_transcripts_to_genome }

get_unmapped_as_fasta = segment { prepare_reads + get_unmapped }


// below is the pipeline for a fasta file
if(args[0].endsWith(fastaSuffix)) {
   run { run_check + fastaInputFormat * [
	     align_transcripts_to_annotation +
	     common_steps + 
	     make_fasta_reads_table +
	     get_final_list ] + compile_all_results
   } 
// or you can provide the reads and they will be 
// filtered and converted to fasta before running
// the same pipeline as above
} else {
  if(readLayout=="single"){ fastqInputFormat="%.gz" }
  run { run_check + fastqInputFormat * [
	    get_unmapped_as_fasta +
	    align_reads_to_annotation +
	    common_steps +
	    make_simple_reads_table +
	    get_final_list ] + compile_all_results 
   }
}