adding cleansam

workflow/main.nf

 #!/usr/bin/env nextflow
 
 // Default parameter values to run tests
-params.bamdna="$baseDir/../test_data/dna/*.bam"
-params.bamrna="$baseDir/../test_data/rna/*.bam"
+params.bamdna="$baseDir/../test_data/dna/safe/*.bam"
+params.bamrna="$baseDir/../test_data/*.bam"
 rnabams=file(params.bamrna)
 dnabams=file(params.bamdna)
-params.incdna = '1'
+params.incdna = '0'
 
 
 params.design="$baseDir/../test_data/design.txt"
@@ -85,7 +85,8 @@ process gatkbam {
   script:
   """
   module load gatk/3.5 samtools/intel/1.3 speedseq/20160506 picard/1.127
-  java -Xmx4g -jar \$PICARD/picard.jar AddOrReplaceReadGroups INPUT=${rbam} O=${pair_id}.rg_added_sorted.bam SO=coordinate RGID=${pair_id} RGLB=tx RGPL=illumina RGPU=barcode RGSM=${pair_id}
+  java -Xmx4g -jar \$PICARD/picard.jar CleanSam INPUT=${rbam} O=${pair_id}.clean.bam
+  java -Xmx4g -jar \$PICARD/picard.jar AddOrReplaceReadGroups INPUT=${pair_id}.clean.bam O=${pair_id}.rg_added_sorted.bam SO=coordinate RGID=${pair_id} RGLB=tx RGPL=illumina RGPU=barcode RGSM=${pair_id}
   sambamba markdup -t 20 -r ${pair_id}.rg_added_sorted.bam ${pair_id}.dedup.bam
   java -Xmx4g -jar \$GATK_JAR -T SplitNCigarReads -R ${gatkref} -I ${pair_id}.dedup.bam -o ${pair_id}.split.bam -rf ReassignOneMappingQuality -RMQF 255 -RMQT 60 -U ALLOW_N_CIGAR_READS
   java -Xmx4g -jar \$GATK_JAR -l INFO -R ${gatkref} --knownSites ${dbsnp} -I ${pair_id}.split.bam -T BaseRecalibrator -cov ReadGroupCovariate -cov QualityScoreCovariate -cov CycleCovariate -cov ContextCovariate -o ${pair_id}.recal_data.grp -nt 1 -nct 30
@@ -116,6 +117,9 @@ process svcall {
   """
   else
   """
+  module load integrate/0.2.6 samtools/intel/1.3 speedseq/20160506
+  sambamba index ${rbam}
+  sambamba index ${unmap}
   Integrate fusion -reads ${pair_id}.reads.txt -sum ${pair_id}.summary.tsv -ex ${pair_id}.exons.tsv -bk ${pair_id}.breakpoints.tsv -vcf ${pair_id}.bk_sv.vcf -bedpe ${pair_id}.fusions.bedpe ${index_path}/genome.fa ${index_path}/annot.ensembl.txt ${index_path}/bwts/ ${rbam} ${unmap}
   perl $baseDir/scripts/compile_genefusion_results.pl -i ${pair_id} -r ${index_path}
   """