From cf1b41c51603db4537cd4e5241d80639f55efef7 Mon Sep 17 00:00:00 2001 From: patidarr Date: Wed, 4 Jan 2017 11:25:09 -0500 Subject: [PATCH] v 2.4 to be released as production --- config/config_cluster.json | 4 ++-- config/config_common.json | 4 ++-- config/config_common_tgen.json | 2 +- ngs_pipeline.snakefile | 3 +-- 4 files changed, 6 insertions(+), 7 deletions(-) diff --git a/config/config_cluster.json b/config/config_cluster.json index 0838464..e4903da 100644 --- 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 index b2edbf2..fd14469 100644 --- 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 index 72348c3..4630bb9 100644 --- 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 index 7f6b1e3..518eb8f 100644 --- 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 #