v 2.4 to be released as production

patidarr · Jan 4, 2017 · cf1b41c · cf1b41c
1 parent 68876f2
commit cf1b41c
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Showing 4 changed files with 6 additions and 7 deletions.
diff --git a/config/config_cluster.json b/config/config_cluster.json
@@ -66,7 +66,7 @@
                 "job_gatk"       : "--partition=batch --time=30:00:00 --mem=40G  --cpus-per-task=2  ",
                 "job_HC"         : "--partition=batch --time=30:00:00 --mem=20G  --cpus-per-task=2  ",
                 "job_gatk_RNA"   : "--partition=mmem,hmem  --time=30:00:00 --mem=150G --cpus-per-task=2  ",
-                "job_bam2mpg"    : "--partition=mmem,hmem --time=24:00:00 --mem=80G  --cpus-per-task=10 ",
+                "job_bam2mpg"    : "--partition=mmem,hmem --time=24:00:00 --mem=80G  --cpus-per-task=8 ",
                 "job_mutect"     : "--partition=batch --time=24:00:00 --mem=10G  --cpus-per-task=2  ",
                 "job_strelka"    : "--partition=batch --time=10:00:00 --mem=45G  --cpus-per-task=16 ",
                 "job_platypus"   : "--partition=batch --time=10:00:00 --mem=40G  --cpus-per-task=16 ",
@@ -88,7 +88,7 @@
                 "job_annot"      : "--partition=batch --time=03:00:00 --mem=05G  --cpus-per-task=2  ",
                 "job_bamUtil"    : "--partition=batch --time=20:00:00 --mem=05G  --cpus-per-task=2  ",
                 "job_igvtools"   : "--partition=batch --time=05:00:00 --mem=10G  --cpus-per-task=1  ",
-                "job_novoalign"  : "--partition=mmem,hmem --time=20:00:00 --mem=60G  --cpus-per-task=16 ",
+                "job_novoalign"  : "--partition=mmem,hmem --time=20:00:00 --mem=60G  --cpus-per-task=8 ",
                 "job_deFuse"     : "--partition=mmem,hmem  --time=20:00:00 --mem=180G --cpus-per-task=10 "
         }
 }
diff --git a/config/config_common.json b/config/config_common.json
@@ -1,7 +1,7 @@
 {
-	"pipeline_version"	: "v2.3",
+	"pipeline_version"	: "v2.4",
 	"mails"			: "-c patidarr@mail.nih.gov",
-	"mails"			: "-c patidarr@mail.nih.gov -c weij@mail.nih.gov -c sivasish.sindiri@nih.gov -c manoj.tyagi@nih.gov -c khanjav@mail.nih.gov -c wangc@mail.nih.gov",
+	"mail"			: "-c patidarr@mail.nih.gov -c weij@mail.nih.gov -c manoj.tyagi@nih.gov -c khanjav@mail.nih.gov -c wangc@mail.nih.gov",
 	"platform"		: "Illumina",
 	"samtools"		: "0.1.19",
 	"samtools_old"		: "0.1.19",

diff --git a/config/config_common_tgen.json b/config/config_common_tgen.json
@@ -1,7 +1,7 @@
 {
 	"group"			: "clinomics",
 	"host"			: "login01",
-	"mail"			: "-c patidarr@mail.nih.gov",
+	"mails"			: "-c patidarr@mail.nih.gov",
 	"annovar_data"		: "/projects/Clinomics/Tools/ref/hg19/annotation/",
 	"genotypeDest"		: "/data/khanlab/projects/Genotyping/GenotypeFiles/",
 	"bwaIndex"		: "/projects/Clinomics/Tools/ref/hg19/Index/bwa/ucsc.hg19.fasta",

diff --git a/ngs_pipeline.snakefile b/ngs_pipeline.snakefile
@@ -281,8 +281,7 @@ for subject in SUBJECT_ANNO.keys():
 		for varFile in SUBJECT_ANNO[subject][group]:
 			varFiles.append(varFile)
 ###########################################################################
-localrules: Khanlab_Pipeline, RNASeq
-#IGV_Session, DBinput, AttachAnnotation, Expressed, vcf2txt, symlink_tophatBam, copyNovoBam, Actionable_Germline, Actionable_RNAseq, Actionable_Somatic, Actionable_Variants, Actionable_fusion, Sub_Fusion, makeConfig, TargetInterval, QC_Summary_Patient,QC_Summary,UnionSomaticCalls,TOPHAT_LINK, SampleGT,QC_Sum, FormatInput, RNASeqQC_1,RNASeqQC1 RNASeqQC_2,RNASeqQC_3, Cuff_Mat
+localrules: Khanlab_Pipeline, RNASeq, IGV_Session, DBinput, AttachAnnotation, Expressed, vcf2txt, symlink_tophatBam, copyNovoBam, Actionable_Germline, Actionable_RNAseq, Actionable_Somatic, Actionable_Variants, Actionable_fusion, Sub_Fusion, makeConfig, TargetInterval, QC_Summary_Patient,QC_Summary,UnionSomaticCalls,TOPHAT_LINK, SampleGT,QC_Sum, FormatInput, RNASeqQC_1,RNASeqQC1 RNASeqQC_2,RNASeqQC_3, Cuff_Mat
 #Circos, CoveragePlot, BoxPlot_Hotspot, makeConfig,Ideogram
 ###########################################################################
 #                               Rule Book				  #