v3.0.2

CCBR · May 30, 2018 · b286329 · b286329
1 parent 997b26d
commit b286329
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Showing 3 changed files with 5 additions and 4 deletions.
diff --git a/cluster.json b/cluster.json
@@ -545,7 +545,7 @@
     },
     "gatk_realign":
     {
-        "threads": "2",
+        "threads": "1",
         "gres":"lscratch:500",
         "mem": "64g"
     },

diff --git a/rules.json b/rules.json
@@ -2,7 +2,7 @@
     "rules": {
         "avia": ["wgslow","exomeseq-germline","exomeseq-germline-recal","exomeseq-germline-partial","rnaseqvargerm"],
         "rnaseqforfusions": ["rnaseqfusion"],
-        "rnafusioncleanup": ["rnaseqfusion"],
+        "rnafusioncleanup": ["none"],
         "vcf2maf": ["exomeseq-somatic","wgs-somatic"],
         "vcf2maf_tumoronly": ["exomeseq-somatic-tumoronly","wgs-somatic-tumoronly"],
         "maftools": ["exomeseq-somatic","wgs-somatic"],
@@ -81,8 +81,8 @@
         "picard.index.bam": ["none"],
         "picard.markdups": ["bam2recal","initialqc","exomeseq-germline","exomeseq-germline-recal","exomeseq-germline-partial","initialqcgenomeseq"],
         "samtools.mpileup": ["none"],
-        "gatk.realign": ["initialqc","initialqcgenomeseq","bam2recal","exomeseq-pairs","exomeseq-germline-recal","exomeseq-germline-partial","wgslow","rnaseqvargerm"],
-        "gatk.recal": ["initialqc","initialqcgenomeseq","bam2recal","exomeseq-pairs","exomeseq-germline-recal","exomeseq-germline-partial","wgslow","rnaseqvargerm"],
+        "gatk.realign": ["initialqc","initialqcgenomeseq","bam2recal","exomeseq-somatic","exomeseq-somatic-tumoronly","exomeseq-pairs","exomeseq-germline","exomeseq-germline-recal","exomeseq-germline-partial","wgslow","rnaseqvargerm"],
+        "gatk.recal": ["initialqc","initialqcgenomeseq","bam2recal","exomeseq-pairs","exomeseq-germline-recal","exomeseq-germline-partial","wgslow","exomeseq-somatic","exomeseq-somatic-tumoronly","exomeseq-germline","rnaseqvargerm"],
         "samtools.sort": ["none"],
         "novocraft.sort": ["bam2recal","initialqc","exomeseq-germline-partial","initialqcgenomeseq","rnaseqvargerm"],
         "varscan": ["exomeseq-pairs"],

diff --git a/standard-bin.json b/standard-bin.json
@@ -332,6 +332,7 @@
 "tool_parameters":{
         "FASTAWITHADAPTERSETD" : "/data/CCBR_Pipeliner/db/PipeDB/dev/TruSeq_and_nextera_adapters.consolidated.fa",
 	"FASTQ_SCREEN_CONFIG": "/data/CCBR_Pipeliner/db/PipeDB/lib/fastq_screen.conf",
+        "FASTQ_SCREEN_CONFIG2": "/data/CCBR_Pipeliner/db/PipeDB/lib/fastq_screen_2.conf",
         "KRAKENBACDB": "/fdb/kraken/20170202_bacteria",
         "TrimmomaticParameters": "---------------Trimmomatic---------Parameters-------------------",
         "SEEDMISMATCHES": 2,