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nextflow.config
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// List of parameters that can be passed to this workflow
params.infile = ""
params.output_dir = ""
params.prefix = ""
params.demofile = ""
params.read_length = 75
params.stranded = true
params.ref_fasta = "/restricted/projectnb/cbmhive/references/ucsc/hg19/base_random/hg19.fa"
params.ref_dir = "/restricted/projectnb/cbmhive/references/STAR/ucsc/hg19/base_random/"
params.gatk_jar = "/share/pkg/gatk/3.5/install/GenomeAnalysisTK.jar"
params.picard_jar = "/share/pkg/picard/2.8.0/install/lib/picard.jar"
params.gold_indels1 = "/restricted/projectnb/cbmhive/references/ucsc/hg19/base_random/1000G_phase1.indels.hg19.sites.vcf"
params.gold_indels2 = "/restricted/projectnb/cbmhive/references/ucsc/hg19/base_random/Mills_and_1000G_gold_standard.indels.hg19.sites.vcf"
params.dbsnp = "/restricted/projectnb/cbmhive/references/ucsc/hg19/base_random/dbsnp_138.hg19.vcf"
params.infile_header = true
params.gene_gtf = "/restricted/projectnb/cbmhive/references/RSEM/ucsc/hg19/Ensembl/Homo_sapiens.GRCh37.75/base_random/Homo_sapiens.GRCh37.75.ucsc.base_random.gtf"
params.gene_bed = "/restricted/projectnb/cbmhive/references/RSEM/ucsc/hg19/Ensembl/Homo_sapiens.GRCh37.75/base_random/Homo_sapiens.GRCh37.75.ucsc.base_random.bed"
params.rsem_ref = "/restricted/projectnb/cbmhive/references/RSEM/ucsc/hg19/Ensembl/Homo_sapiens.GRCh37.75/base_random/Homo_sapiens.GRCh37.75.ucsc.base_random"
params.create_SE_Rscript = "/restricted/projectnb/decamp/Scripts/RNA/Alignment/Nextflow/createSEfromRSEM.R"
params.inferAncestry = "/restricted/projectnb/decamp/Scripts/RNA/Alignment/Nextflow/inferAncestry.R"
// Project used for SGE cluster
PROJECT = 'decamp'
process {
// Global cluster parameters
executor='sge'
scratch=true
// Specific cluster parameters for each process
$runSTAR_1pass.clusterOptions = "-P ${PROJECT} -l h_rt=24:00:00 -l mem_total=30G -pe omp 12"
$runSTAR_GenomeGenerate.clusterOptions = "-P ${PROJECT} -l h_rt=24:00:00 -l mem_total=30G -pe omp 12"
$runSTAR_2pass.clusterOptions = "-P ${PROJECT} -l h_rt=24:00:00 -l mem_total=30G -pe omp 12"
$runRSEM.clusterOptions = "-P ${PROJECT} -l h_rt=24:00:00 -l mem_total=5G -pe omp 12"
$runAddReadGroupInfo.clusterOptions = "-P ${PROJECT} -l h_rt=24:00:00 -l mem_total=5G"
$runMarkDuplicates.clusterOptions = "-P ${PROJECT} -l h_rt=48:00:00 -l mem_total=94G -pe omp 5"
$runSplitNCigarReads.clusterOptions = "-P ${PROJECT} -l h_rt=24:00:00 -l mem_total=5G -pe omp 5"
$runRealignerTargetCreator.clusterOptions = "-P ${PROJECT} -l h_rt=96:00:00 -l mem_total=94G -pe omp 5"
$runIndelRealigner.clusterOptions = "-P ${PROJECT} -l h_rt=192:00:00 -l mem_total=94G -pe omp 5"
$runBaseRecalibrator.clusterOptions = "-P ${PROJECT} -l h_rt=96:00:00 -l mem_total=94G -pe omp 2"
$runPrintReads.clusterOptions = "-P ${PROJECT} -l h_rt=24:00:00 -l mem_total=25G"
$runBaseRecalibratorPostRecal.clusterOptions = "-P ${PROJECT} -l h_rt=48:00:00 -l mem_total=5g"
$runAnalyzeCovariates.clusterOptions = "-P ${PROJECT} -l h_rt=12:00:00 -l mem_total=5G"
$runHTC.clusterOptions = "-P ${PROJECT} -l h_rt=96:00:00 -l mem_total=25G"
$runFilterVariants.clusterOptions = "-P ${PROJECT} -l h_rt=24:00:00 -l mem_total=10G"
$runCombineVariants.clusterOptions = "-P ${PROJECT} -l h_rt=24:00:00 -l mem_total=10G"
$runDepthOfCoverage.clusterOptions = "-P ${PROJECT} -l h_rt=24:00:00 -l mem_total=10G"
$runCollectMultipleMetrics.clusterOptions = "-P ${PROJECT} -l h_rt=24:00:00 -l mem_total=25G"
$runHybridCaptureMetrics.clusterOptions = "-P ${PROJECT} -l h_rt=24:00:00 -l mem_total=10G"
$runFastQC.clusterOptions = "-P ${PROJECT} -l h_rt=24:00:00 -l mem_total=5G"
$runOxoGMetrics.clusterOptions = "-P ${PROJECT} -l h_rt=24:00:00 -l mem_total=10G"
$runMultiQCFastq.clusterOptions = "-P ${PROJECT} -l h_rt=24:00:00 -l mem_total=1G"
$runMultiQCLibrary.clusterOptions = "-P ${PROJECT} -l h_rt=24:00:00 -l mem_total=1G"
$runMultiQCSample.clusterOptions = "-P ${PROJECT} -l h_rt=24:00:00 -l mem_total=1G"
$runRSeQC.clusterOptions = "-P ${PROJECT} -l h_rt=96:00:00 -l mem_total=5G"
$runCreateSE.clusterOptions = "-P ${PROJECT} -l h_rt=96:00:00 -l mem_total=10G"
//inferAncestry.clusterOptions = "-P ${PROJECT} -l h_rt=96:00:00 -l mem_total=5G"
}