Merge pull request #306 from jlac/master

repaired missing reference resources for fusion and ranseqvar pipelines
CCBR · Dec 14, 2017 · b13808e · b13808e
2 parents 6b1c988 + c25067a
commit b13808e
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Showing 5 changed files with 36 additions and 60 deletions.
diff --git a/Rules/mutsig_mutect2_tumoronly.rl b/Rules/mutsig_mutect2_tumoronly.rl
@@ -1,5 +1,5 @@
 import glob
-samps = len(glob.glob1(myPath,"*.recal.bam"))
+samps = len(glob.glob1(".","*.recal.bam"))
 
 if samps>10:
   if config['project']['annotation'] == "hg19":

diff --git a/Rules/rnaseqforfusions.rl b/Rules/rnaseqforfusions.rl
@@ -62,14 +62,14 @@ rule rsemcounts:
 rule picard:
   input: file1= "{name}.p2.Aligned.sortedByCoord.out.bam"
   output: outstar1=temp("{name}.star_rg_added.sorted.bam"), outstar2=temp("{name}.star_rg_added.sorted.dmark.bam"),outstar3="{name}.star.duplic"
-  params: rname='pl:picard',batch='--mem=24g --time=10:00:00 --gres=lscratch:800',picardver=config['bin'][pfamily]['PICARDVER']#,picardjarpath=config['bin'][pfamily]['PICARDJARPATH']
-  shell: "module load {params.picardver}; java -Xmx10g  -jar $PICARDJARPATH/AddOrReplaceReadGroups.jar INPUT={input.file1} OUTPUT={output.outstar1} TMP_DIR=/lscratch/$SLURM_JOBID RGID=id RGLB=library RGPL=illumina RGPU=machine RGSM=sample; java -Xmx10g -jar $PICARDJARPATH/MarkDuplicates.jar INPUT={output.outstar1} OUTPUT={output.outstar2} TMP_DIR=/lscratch/$SLURM_JOBID CREATE_INDEX=true VALIDATION_STRINGENCY=SILENT METRICS_FILE={output.outstar3}"
+  params: rname='pl:picard',batch='--mem=24g --time=10:00:00 --gres=lscratch:800'#,picardjarpath=config['bin'][pfamily]['PICARDJARPATH']
+  shell: "module load picard/1.119; java -Xmx10g  -jar $PICARDJARPATH/AddOrReplaceReadGroups.jar INPUT={input.file1} OUTPUT={output.outstar1} TMP_DIR=/lscratch/$SLURM_JOBID RGID=id RGLB=library RGPL=illumina RGPU=machine RGSM=sample; java -Xmx10g -jar $PICARDJARPATH/MarkDuplicates.jar INPUT={output.outstar1} OUTPUT={output.outstar2} TMP_DIR=/lscratch/$SLURM_JOBID CREATE_INDEX=true VALIDATION_STRINGENCY=SILENT METRICS_FILE={output.outstar3}"
 
 rule stats:
   input: file1= "{name}.star_rg_added.sorted.dmark.bam"
   output: outstar1="{name}.RnaSeqMetrics.txt", outstar2="{name}.flagstat.concord.txt", outstar3="{name}.InsertSizeMetrics.txt", outstar4="{name}.InsertSizeHisto.pdf"
-  params: rname='pl:stats',batch='--mem=24g --time=10:00:00 --gres=lscratch:800',picardver=config['bin'][pfamily]['PICARDVER'],refflat=config['references'][pfamily]['REFFLAT'],rrnalist=config['references'][pfamily]['RRNALIST'],picardstrand=config['bin'][pfamily]['PICARDSTRAND']
-  shell: "module load R/3.4.0_gcc-6.2.0;module load {params.picardver}; java -Xmx10g -jar $PICARDJARPATH/CollectRnaSeqMetrics.jar REF_FLAT={params.refflat} INPUT={input.file1} OUTPUT={output.outstar1} RIBOSOMAL_INTERVALS={params.rrnalist}  STRAND_SPECIFICITY=SECOND_READ_TRANSCRIPTION_STRAND TMP_DIR=/lscratch/$SLURM_JOBID  VALIDATION_STRINGENCY=SILENT; java -Xmx10g -jar $PICARDJARPATH/CollectInsertSizeMetrics.jar INPUT={input.file1} OUTPUT={output.outstar3} HISTOGRAM_FILE={output.outstar4} MINIMUM_PCT=0.5 TMP_DIR=/lscratch/$SLURM_JOBID ;module load samtools; samtools flagstat {input.file1} > {output.outstar2}; module load python; python Scripts/bam_count_concord_stats.py {input.file1} >> {output.outstar2} "
+  params: rname='pl:stats',batch='--mem=24g --time=10:00:00 --gres=lscratch:800',refflat=config['references'][pfamily]['REFFLAT'],rrnalist=config['references'][pfamily]['RRNALIST'],picardstrand=config['bin'][pfamily]['PICARDSTRAND']
+  shell: "module load R/3.4.0_gcc-6.2.0;module load picard/1.119; java -Xmx10g -jar $PICARDJARPATH/CollectRnaSeqMetrics.jar REF_FLAT={params.refflat} INPUT={input.file1} OUTPUT={output.outstar1} RIBOSOMAL_INTERVALS={params.rrnalist}  STRAND_SPECIFICITY=SECOND_READ_TRANSCRIPTION_STRAND TMP_DIR=/lscratch/$SLURM_JOBID  VALIDATION_STRINGENCY=SILENT; java -Xmx10g -jar $PICARDJARPATH/CollectInsertSizeMetrics.jar INPUT={input.file1} OUTPUT={output.outstar3} HISTOGRAM_FILE={output.outstar4} MINIMUM_PCT=0.5 TMP_DIR=/lscratch/$SLURM_JOBID ;module load samtools; samtools flagstat {input.file1} > {output.outstar2}; module load python; python Scripts/bam_count_concord_stats.py {input.file1} >> {output.outstar2} "
 
 rule prernaseqc:
   input: expand("{name}.star_rg_added.sorted.dmark.bam", name=samples)
@@ -89,14 +89,14 @@ rule rnaseqc:
   input: "files_to_rnaseqc.txt"
   output: "STAR_QC"
   priority: 2
-  params: rname='pl:rnaseqc',batch='--mem=24g --time=48:00:00',bwaver=config['bin'][pfamily]['BWAVER'],rrnalist=config['references'][pfamily]['RRNALIST'],rnaseqcver=config['bin'][pfamily]['RNASEQCVER'],gtffile=config['references'][pfamily]['GTFFILE'],genomefile=config['references'][pfamily]['GENOMEFILE']
+  params: rname='pl:rnaseqc',batch='--mem=24g --time=48:00:00',rrnalist=config['references'][pfamily]['RRNALIST'],gtffile=config['references'][pfamily]['GTFFILE'],genomefile=config['references'][pfamily]['GENOMEFILE']
   shell: """
-         module load {params.bwaver}
+         module load bwa/0.7.15
          var="{params.rrnalist}"
          if [  $var == "-" ]; then
-                java -jar {params.rnaseqcver} -n 1000 -s {input} -t {params.gtffile} -r {params.genomefile}  -o {output}
+                java -jar /usr/local/apps/rnaseqc/1.1.8/RNA-SeQC_v1.1.8.jar -n 1000 -s {input} -t {params.gtffile} -r {params.genomefile}  -o {output}
          else
-                java -jar {params.rnaseqcver} -n 1000 -s {input} -t {params.gtffile} -r {params.genomefile} -rRNA {params.rrnalist}  -o {output}
+                java -jar /usr/local/apps/rnaseqc/1.1.8/RNA-SeQC_v1.1.8.jar -n 1000 -s {input} -t {params.gtffile} -r {params.genomefile} -rRNA {params.rrnalist}  -o {output}
          fi
          """
 

diff --git a/hg19.json b/hg19.json
@@ -155,17 +155,17 @@
     "RRNALIST": "/data/CCBR_Pipeliner/db/PipeDB/dev/Hg19.rRNA.interval_list_v3",
 #    "FASTQ_SCREEN_CONFIG": "/data/CCBR_Pipeliner/db/PipeDB/lib/fastq_screen.conf",
 #    "FASTAWITHADAPTERSETC": "/data/CCBR_Pipeliner/dev/RNA-Seq-pipeline/ver2/TruSeq_and_nextera_adapters_new.fa",
-#    "FASTAWITHADAPTERSETC": "/data/CCBR_Pipeliner/db/PipeDB/dev/TruSeq_and_nextera_adapters_new.fa",
+    "FASTAWITHADAPTERSETC": "/data/CCBR_Pipeliner/db/PipeDB/dev/TruSeq_and_nextera_adapters_new.fa",
 #    "GTFFILE2": "/data/CCBR_Pipeliner/db/PipeDB/lib/hs37d5/annotation/gencode.v19.annotation.gtf",
-#    "FUSIONGTFFILE": "/data/CCBR_Pipeliner/db/PipeDB/lib/GENCODE_GRCh37_ref_annot.gtf",
+    "FUSIONGTFFILE": "/data/CCBR_Pipeliner/db/PipeDB/lib/GENCODE_GRCh37_ref_annot.gtf",
 #    "REFFLAT2": "/data/CCBR_Pipeliner/db/PipeDB/lib/hs37d5/annotation/refFlatHg19.txt",
 #    "SALMONREF": "/data/CCBR_Pipeliner/db/PipeDB/Rnaseq/rsem1.3.0/human_gencode.transcripts.fa",
 #    "STARREF": "/data/CCBR_Pipeliner/db/PipeDB/lib/Star_refs/hs37d5/genes-",
 #    "RRNALIST2": "/data/CCBR_Pipeliner/db/PipeDB/lib/hs37d5/annotation/gencode.v19.annotation.gtf.rRNA.interval_list",
-#    "STARFUSIONLIB": "/data/CCBR_Pipeliner/db/PipeDB/lib/GRCh37_gencode_v19_CTAT_lib_July272016_prebuilt",
-#    "FUSCATCHDAT": "/usr/local/apps/fusioncatcher/0.99.7b/fusioncatcher/data/ensembl_v86",
-#    "FUSCATCHCONFIG": "/data/CCBR_Pipeliner/db/PipeDB/lib/hg19_hg38_configuration.cfg",
-#    "FASTQ_SCREEN_CONFIG": "/data/CCBR_Pipeliner/db/PipeDB/lib/fastq_screen.conf",
+    "STARFUSIONLIB": "/data/CCBR_Pipeliner/db/PipeDB/lib/GRCh37_gencode_v19_CTAT_lib_July272016_prebuilt",
+    "FUSCATCHDAT": "/usr/local/apps/fusioncatcher/0.99.7b/fusioncatcher/data/ensembl_v86",
+    "FUSCATCHCONFIG": "/data/CCBR_Pipeliner/db/PipeDB/lib/hg19_hg38_configuration.cfg",
+    "FASTQ_SCREEN_CONFIG": "/data/CCBR_Pipeliner/db/PipeDB/lib/fastq_screen.conf",
 #    "GENOME": "/data/CCBR_Pipeliner/db/PipeDB/lib/hs37d5.fa",
 #    "INDELSITES": "/fdb/GATK_resource_bundle/b37/Mills_and_1000G_gold_standard.indels.b37.vcf",
 #    "KNOWNANCESTRY": "/data/CCBR_Pipeliner/db/PipeDB/lib/1k_genomes_phase3_autosomes.vcf.gz",
@@ -177,23 +177,18 @@
 #    "THETASNPS": "/data/CCBR_Pipeliner/db/PipeDB/lib/hg19_theta_SNPfile.txt",
 #    "INDELSITES2": "/fdb/GATK_resource_bundle/b37/1000G_phase1.indels.b37.vcf",
 #    "ALVIEWGENOME": "hg19",
-#    "ONCOFUSEBUILD": "hg19",
+    "ONCOFUSEBUILD": "hg19",
 #    "EXONS": "/data/CCBR_Pipeliner/db/PipeDB/lib/hg19.exons.bed",
 #    "ANNDIR": "/data/CCBR_Pipeliner/db/PipeDB/AnnovarDB/",
-#    "STRELKA_CONFIG": "/data/CCBR_Pipeliner/db/PipeDB/lib/strelka_demo_config.ini",
-#    "CNVKIT_TARGETS": "/data/CCBR_Pipeliner/db/PipeDB/lib/human_SSv5_cnvkit_targets.bed",
-#    "CNVKIT_ANTITARGETS": "/data/CCBR_Pipeliner/db/PipeDB/lib/human_SSv5_cnvkit_antitargets.bed",
-#    "CNVKITACCESS": "/data/CCBR_Pipeliner/db/PipeDB/lib/access-5k-mappable.grch37.bed",
-#    "DELLY_EXCLUSIONS": "/data/CCBR_Pipeliner/db/PipeDB/lib/delly.human.hg19.excl.tsv",
 #    "tg_GS_INDELS": "/fdb/GATK_resource_bundle/hg19-2.8/Mills_and_1000G_gold_standard.indels.hg19.vcf.gz",
 #    "tg_PHASE_INDELS": "/fdb/GATK_resource_bundle/hg19-2.8/1000G_phase1.indels.hg19.vcf.gz",
 #    "SNP138": "/fdb/GATK_resource_bundle/hg19-2.8/dbsnp_138.hg19.vcf.gz",
 #    "HAPMAP": "/fdb/GATK_resource_bundle/hg19-2.8/hapmap_3.3.hg19.vcf.gz",
 #    "B1K": "/fdb/GATK_resource_bundle/hg19-2.8/1000G_phase1.snps.high_confidence.hg19.vcf.gz",
 #    "OMNI": "/fdb/GATK_resource_bundle/hg19-2.8/1000G_omni2.5.hg19.vcf.gz",
 #    "adapter.file": "/data/CCBR_Pipeliner/db/PipeDB/dev/TruSeq_and_nextera_adapters.ngsqc.dat",
-#    "fastqc.adapters": "/data/CCBR_Pipeliner/db/PipeDB/dev/fastqc.adapters",
-#    "trimmomatic.adapters": "/data/CCBR_Pipeliner/db/PipeDB/dev/adapters2.fa",
+    "fastqc.adapters": "/data/CCBR_Pipeliner/db/PipeDB/dev/fastqc.adapters",
+    "trimmomatic.adapters": "/data/CCBR_Pipeliner/db/PipeDB/dev/adapters2.fa",
 #    "ORGANISM": "HUMAN",
 #    "AVIASET": "hg19",
 #    "ADAPTER1": "AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC",
@@ -203,15 +198,7 @@
 #    "DB29": "/data/CCBR_Pipeliner/db/PipeDB/snpEff_db/dbNSFP2.9.txt.gz",
 #    "SNPEFF_CONFIG": "/usr/local/apps/snpEff/4.2/snpEff.config",
 #    "SELECTDB": "SIFT_score,SIFT_pred,Polyphen2_HVAR_score,Polyphen2_HVAR_pred,LRT_score,LRT_pred,GERP++_RS,MutationAssessor_score,MutationAssessor_pred,1000Gp1_AF,1000Gp1_EUR_AF,ESP6500_EA_AF,ESP6500_AA_AF",
-#    "SNPEFF_GENOME": "GRCh37.75",
-#    "HAPMAP_DBNSFP": "/data/CCBR_Pipeliner/db/PipeDB/lib/snpEff_db/hapmap.bed",
 #    "REGULOMEDB": "/data/CCBR_Pipeliner/db/PipeDB/lib/snpEff_db/RegulomeDB.bed",
-#    "MUTECTCOSMIC": "/data/CCBR_Pipeliner/db/PipeDB/lib/COSMIC_v82_GRCh37.vcf.gz",
-#    "MUTECTSNP": "/fdb/muTect/dbsnp_137.b37.vcf",
-#    "MUTECTGENOME": "/fdb/muTect/human_g1k_v37.fasta",
-#    "MUTECTVARIANTS": "--dbsnp /fdb/muTect/dbsnp_137.b37.vcf --cosmic /data/CCBR_Pipeliner/db/PipeDB/lib/COSMIC_v82_GRCh37.vcf.gz",
-#    "ADMIXTUREKEY": "/data/CCBR_Pipeliner/db/PipeDB/lib/1k_genomes_superpop_key.txt",
-#    "ADMIXTUREREFS": "5",
 #>>>>>>> FETCH_HEAD
     },
     "rnaseqvargerm": {

diff --git a/hg38.json b/hg38.json
@@ -145,18 +145,17 @@
      "RSEMREF": "/data/CCBR_Pipeliner/db/PipeDB/Rnaseq/rsem1.3.0/hg38_R26/human_gencode",
      "STARDIR": "/fdb/STAR_indices/2.5.2b/GENCODE/Gencode_human/release_26/genes-",
      "RRNALIST": "/data/CCBR_Pipeliner/db/PipeDB/dev/Hg38.rRNA.interval_list_R26",
-#     "FASTQ_SCREEN_CONFIG": "/data/CCBR_Pipeliner/db/PipeDB/lib/fastq_screen.conf",
-#     "FUSIONGTFFILE": "/fdb/GENCODE/Gencode_human/release_26/gencode.v26.annotation.gtf",
+     "FASTQ_SCREEN_CONFIG": "/data/CCBR_Pipeliner/db/PipeDB/lib/fastq_screen.conf",
+     "FUSIONGTFFILE": "/fdb/GENCODE/Gencode_human/release_26/gencode.v26.annotation.gtf",
 #     "REFFLAT2": "/data/CCBR_Pipeliner/db/PipeDB/dev/refFlatHg38_R26.txt",
 #     "SALMONREF": "/data/CCBR_Pipeliner/db/PipeDB/Rnaseq/rsem1.3.0/hg38_R26/human_gencode.transcripts.fa",
 #     "FASTAWITHADAPTERSETC": "/data/CCBR_Pipeliner/dev/RNA-Seq-pipeline/ver2/TruSeq_and_nextera_adapters_new.fa",
-#     "FASTAWITHADAPTERSETC": "/data/CCBR_Pipeliner/db/PipeDB/dev/TruSeq_and_nextera_adapters_new.fa",
+     "FASTAWITHADAPTERSETC": "/data/CCBR_Pipeliner/db/PipeDB/dev/TruSeq_and_nextera_adapters_new.fa",
 #     "STARREF": "/fdb/STAR_indices/2.5.2b/GENCODE/Gencode_human/release_26/genes-",
 #     "RRNALIST2": "/data/CCBR_Pipeliner/db/PipeDB/dev/Hg38.rRNA.interval_list_R26",
-#    "STARFUSIONLIB": "/data/CCBR_Pipeliner/db/PipeDB/lib/GRCh38_gencode_v24_CTAT_lib_Mar292017_prebuilt",
-#    "FUSCATCHDAT": "/usr/local/apps/fusioncatcher/0.99.7b/fusioncatcher/data/ensembl_v86",
-#    "FUSCATCHCONFIG": "/data/CCBR_Pipeliner/db/PipeDB/lib/hg19_hg38_configuration.cfg",
-#    "FASTQ_SCREEN_CONFIG": "/data/CCBR_Pipeliner/db/PipeDB/lib/fastq_screen.conf",
+    "STARFUSIONLIB": "/data/CCBR_Pipeliner/db/PipeDB/lib/GRCh38_gencode_v24_CTAT_lib_Mar292017_prebuilt",
+    "FUSCATCHDAT": "/usr/local/apps/fusioncatcher/0.99.7b/fusioncatcher/data/ensembl_v86",
+    "FUSCATCHCONFIG": "/data/CCBR_Pipeliner/db/PipeDB/lib/hg19_hg38_configuration.cfg",
 #    "GENOME": "/fdb/GENCODE/Gencode_human/release_26/GRCh38.primary_assembly.genome.fa",
 #    "INDELSITES": "/fdb/GATK_resource_bundle/hg38bundle/Mills_and_1000G_gold_standard.indels.hg38.vcf.gz",
 #    "KNOWNANCESTRY": "/data/CCBR_Pipeliner/db/PipeDB/lib/1k_genomes_phase3_autosomes.hg38.vcf.gz",
@@ -168,39 +167,29 @@
 #    "THETASNPS": "/data/CCBR_Pipeliner/db/PipeDB/lib/hg38_theta_SNPfile.txt",
 #    "INDELSITES2": "/data/CCBR_Pipeliner/db/PipeDB/lib/ALL.wgs.1000G_phase3.GRCh38.ncbi_remapper.20150424.shapeit2_indels.vcf.gz",
 #    "ALVIEWGENOME": "hg38",
-#    "ONCOFUSEBUILD": "hg38",
+    "ONCOFUSEBUILD": "hg38",
 #    "EXONS": "/data/CCBR_Pipeliner/db/PipeDB/lib/hg38_exons.bed",
 #    "ANNDIR": "/data/CCBR_Pipeliner/db/PipeDB/AnnovarDB/",
-#    "STRELKA_CONFIG": "/data/CCBR_Pipeliner/db/PipeDB/lib/strelka_demo_config.ini",
-#    "CNVKITACCESS": "/data/CCBR_Pipeliner/db/PipeDB/lib/access-5k-mappable.grch37.bed",
-#    "DELLY_EXCLUSIONS": "/data/CCBR_Pipeliner/db/PipeDB/lib/delly.human.hg38.excl.tsv",
 #    "tg_GS_INDELS": "/fdb/GATK_resource_bundle/hg38bundle/Mills_and_1000G_gold_standard.indels.hg38.vcf.gz",
 #    "tg_PHASE_INDELS": "/data/CCBR_Pipeliner/db/PipeDB/lib/ALL.wgs.1000G_phase3.GRCh38.ncbi_remapper.20150424.shapeit2_indels.vcf.gz",
 #    "SNP138": "/fdb/GATK_resource_bundle/hg38bundle/dbsnp_138.hg38.vcf.gz",
 #    "HAPMAP": "/fdb/GATK_resource_bundle/hg38bundle/hapmap_3.3.hg38.vcf.gz",
 #    "B1K": "/fdb/GATK_resource_bundle/hg38bundle/1000G_phase1.snps.high_confidence.hg38.vcf.gz",
 #    "OMNI": "/fdb/GATK_resource_bundle/hg38bundle/1000G_omni2.5.hg38.vcf.gz",
 #    "adapter.file": "/data/CCBR_Pipeliner/db/PipeDB/dev/TruSeq_and_nextera_adapters.ngsqc.dat",
-#    "fastqc.adapters": "/data/CCBR_Pipeliner/db/PipeDB/dev/fastqc.adapters",
-#    "trimmomatic.adapters": "/data/CCBR_Pipeliner/db/PipeDB/dev/adapters2.fa",
+    "fastqc.adapters": "/data/CCBR_Pipeliner/db/PipeDB/dev/fastqc.adapters",
+    "trimmomatic.adapters": "/data/CCBR_Pipeliner/db/PipeDB/dev/adapters2.fa",
 #    "ORGANISM": "HUMAN",
 #    "AVIASET": "hg38",
 #    "ADAPTER1": "AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC",
 #    "ADAPTER2": "AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT",
 #    "nextera1": "CTGTCTCTTATACACATCTCCGAGCCCACGAGAC",
 #    "nextera2": "CTGTCTCTTATACACATCTGACGCTGCCGACGA",
 #    "DB29": "/data/CCBR_Pipeliner/db/PipeDB/snpEff_db/dbNSFP2.9.txt.gz",
-#    "SNPEFF_CONFIG": "/usr/local/apps/snpEff/4.2/snpEff.config",
 #    "SELECTDB": "SIFT_score,SIFT_pred,Polyphen2_HVAR_score,Polyphen2_HVAR_pred,LRT_score,LRT_pred,GERP++_RS,MutationAssessor_score,MutationAssessor_pred,1000Gp1_AF,1000Gp1_EUR_AF,ESP6500_EA_AF,ESP6500_AA_AF",
 #    "SNPEFF_GENOME": "GRCh38.82",
 #    "HAPMAP_DBNSFP": "/data/CCBR_Pipeliner/db/PipeDB/lib/snpEff_db/hapmap.bed",
 #    "REGULOMEDB": "/data/CCBR_Pipeliner/db/PipeDB/lib/snpEff_db/RegulomeDB.bed",
-#    "MUTECTCOSMIC": "/data/CCBR_Pipeliner/db/PipeDB/lib/COSMIC_82_hg38.vcf.gz",
-#    "MUTECTSNP": "/fdb/GATK_resource_bundle/hg38bundle/dbsnp_138.hg38.vcf.gz",
-#    "MUTECTGENOME": "/data/CCBR_Pipeliner/db/PipeDB/lib/GRCh38.d1.vd1.fa",
-#    "MUTECTVARIANTS": "--dbsnp /fdb/GATK_resource_bundle/hg38bundle/dbsnp_138.hg38.vcf.gz --cosmic /data/CCBR_Pipeliner/db/PipeDB/lib/COSMIC_82_hg38.vcf.gz",
-#    "ADMIXTUREKEY": "/data/CCBR_Pipeliner/db/PipeDB/lib/1k_genomes_superpop_key.txt",
-#    "ADMIXTUREREFS": "5",
     },
     "rnaseqvargerm": {
     "GENOMEFILE": "/fdb/GENCODE/Gencode_human/release_19/GRCh37.p13.genome.fa",

diff --git a/mm10.json b/mm10.json
@@ -132,17 +132,17 @@
 "KARYOBEDS": "/data/CCBR_Pipeliner/db/PipeDB/dev/karyobeds/mm.vM12/",
 "RSEMREF": "/data/CCBR_Pipeliner/db/PipeDB/Rnaseq/rsem1.3.0/mouse_gencode",
 "RRNALIST": "/data/CCBR_Pipeliner/db/PipeDB/dev/gencode.vM12.annotation.rRNA.interval_list",
-#"FASTQ_SCREEN_CONFIG": "/data/CCBR_Pipeliner/db/PipeDB/lib/fastq_screen.conf",
-#"FUSIONGTFFILE": "/fdb/STAR_indices/2.5.2b/GENCODE/Gencode_mouse/release_M12/genes.gtf",
+"FASTQ_SCREEN_CONFIG": "/data/CCBR_Pipeliner/db/PipeDB/lib/fastq_screen.conf",
+"FUSIONGTFFILE": "/fdb/STAR_indices/2.5.2b/GENCODE/Gencode_mouse/release_M12/genes.gtf",
 #"STARREF": "/fdb/STAR_indices/2.5.2b/GENCODE/Gencode_mouse/release_M12/genes-",
 # "RSEMREF": "/data/CCBR_Pipeliner/db/PipeDB/dev/rsemref/mouse_gencode",
 # "SALMONREF": "/data/CCBR_Pipeliner/db/PipeDB/dev/rsemref/mouse_gencode.transcripts.fa",
 #"SALMONREF": "/data/CCBR_Pipeliner/db/PipeDB/Rnaseq/rsem1.3.0/mouse_gencode.transcripts.fa",
-#"FASTAWITHADAPTERSETC": "/data/CCBR_Pipeliner/db/PipeDB/dev/TruSeq_and_nextera_adapters_new.fa",
-#"STARFUSIONLIB": "/data/CCBR_Pipeliner/db/PipeDB/lib/mm10_gencode_vM12_TrinityResource",
-#"FUSCATCHDAT": "/fdb/fusioncatcher/mus_musculus",
-#"FUSCATCHCONFIG": "/data/CCBR_Pipeliner/db/PipeDB/lib/fusioncatcher_mm10_configuration.cfg",
-#"ONCOFUSEBUILD": "mm10",
+"FASTAWITHADAPTERSETC": "/data/CCBR_Pipeliner/db/PipeDB/dev/TruSeq_and_nextera_adapters_new.fa",
+"STARFUSIONLIB": "/data/CCBR_Pipeliner/db/PipeDB/lib/mm10_gencode_vM12_TrinityResource",
+"FUSCATCHDAT": "/fdb/fusioncatcher/mus_musculus",
+"FUSCATCHCONFIG": "/data/CCBR_Pipeliner/db/PipeDB/lib/fusioncatcher_mm10_configuration.cfg",
+"ONCOFUSEBUILD": "mm10",
 #    "BWAGENOME": "/fdb/igenomes/Mus_musculus/UCSC/mm10/Sequence/BWAIndex/genome.fa",
 #    "GENOME": "/fdb/STAR_indices/2.5.2b/GENCODE/Gencode_mouse/release_M12/ref.fa",
 #    "CHROMS": "/data/CCBR_Pipeliner/db/PipeDB/lib/mm10_chromosomes",
@@ -156,8 +156,8 @@
 #    "CNVKITGENOME": "/data/CCBR_Pipeliner/db/PipeDB/lib/genome.fa",
 #    "SNPSITES": "/data/CCBR_Pipeliner/db/PipeDB/lib/mm10_allstrains_dbSNP142.vcf.gz",
 #    "adapter.file": "/data/CCBR_Pipeliner/db/PipeDB/dev/TruSeq_and_nextera_adapters.ngsqc.dat",
-#    "fastqc.adapters": "/data/CCBR_Pipeliner/db/PipeDB/dev/fastqc.adapters",
-#    "trimmomatic.adapters": "/data/CCBR_Pipeliner/db/PipeDB/dev/adapters2.fa",
+    "fastqc.adapters": "/data/CCBR_Pipeliner/db/PipeDB/dev/fastqc.adapters",
+    "trimmomatic.adapters": "/data/CCBR_Pipeliner/db/PipeDB/dev/adapters2.fa",
 #    "ADAPTER1": "AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC", 
 #    "ADAPTER2": "AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT",
 #    "nextera1": "CTGTCTCTTATACACATCTCCGAGCCCACGAGAC",