jhpce.config

/*
vim: syntax=groovy
-*- mode: groovy;-*-
 * -------------------------------------------------
 *  JHPCE config file
 * -------------------------------------------------
 *
 * A config file designed for the SGE environment on the
 * JHPCE cluster specifically. Takes advantage of lmod modules
 * which are available to JHPCE users, and run particular
 * software versions.
 *
 */

env.OMP_NUM_THREADS = 1
env.OPENBLAS_NUM_THREADS = 2

params {
  gencode_version_human = "25"
  gencode_version_mouse = "M25"
  ensembl_version_rat = "98"
  anno_build = "main" // main or primary (main is canonical seqs only)
  
  //  Number of FASTQ lines to subset when determining strandness for a sample
  num_reads_infer_strand = 2000000
  
  wiggletools_max_threads = 10
  
  //  Note that the "-d", "-i", "-o", and "-s" arguments are internally handled
  //  by SPEAQeasy, and should not be specified here
  bam2wig_args = "-t 4000000000"
  
  //  For variant calling on human samples ('bcftools call')
  bcftools_args = "-mvOz"
  
  //  Note that the "-t" and "--extract" arguments are internally handled
  //  by SPEAQeasy, and should not be specified here
  fastqc_args = ""
  
  //  Note that the "-a", "-o", "-p", and "-T" arguments are internally handled
  //  by SPEAQeasy as appropriate, and should not be specified below
  feat_counts_gene_args = ""
  feat_counts_exon_args = "-O -f"
  
  //  Note that the "-1", "-2", "-p", "--rna-strandness", "--un-conc", "-x", 
  //  "-S", and "-U" arguments are internally handled as applicable by the
  //  pipeline, and should not be specified here. Also note that
  //  "--min-intronlen" is also used by regtools as the "-m" argument (see 
  //  "regtools_args"), and should be kept consistent!
  hisat2_args = "--phred33 --min-intronlen 20"
  
  //  Note that the "-i", "-o", "-t", and "--fr-stranded"/"--rf-stranded"
  //  arguments are handled internally by SPEAQeasy and should not be specified
  //  below
  kallisto_len_mean = "200"
  kallisto_len_sd = "30"
  kallisto_quant_single_args = "--single -l ${kallisto_len_mean} -s ${kallisto_len_sd}"
  kallisto_quant_paired_args = ""
  kallisto_quant_ercc_single_args = "--single -l ${kallisto_len_mean} -s ${kallisto_len_sd}"
  kallisto_quant_ercc_paired_args = ""
  kallisto_index_args = ""
  
  //  Note that the "--gencode", "-i", "-p", and "-t" arguments are
  //  automatically handled by SPEAQeasy, and should not be specified here
  salmon_index_args = "-k 31"
  
  //  Note that the "-1", "-2", "-l", "-o", "-p", and "-r" arguments are
  //  handled internally by SPEAQeasy, and should not be specified below
  salmon_quant_args = ""
  
  //  Arguments passed to 'samtools mpileup' before calling variants on human
  //  samples. Note that the "-f", "-l", "-o", and "-u" arguments are handled
  //  internally by SPEAQeasy, and should not be specified below.
  samtools_args = "-q 0 -Q 13 -d 1000000 -AB"
  
  //  Arguments passed to STAR during alignment (and not during genome index
  //  creation!). Note that the "--genomeDir", "--readFilesIn",
  //  "--readFilesCommand" (used to decompress gzipped files, if applicable),
  //  "--outSAMtype", "--runThreadN" options are handled internally by
  //  SPEAQeasy, and should not be specified below.
  star_args = ""
  
  //  Settings for trimmomatic's adapter trimming. Note that the adapter fasta
  //  specification is in conf/command_paths_short.config. Leave empty
  //  (i.e. "") to instruct SPEAQeasy to not perform adapter trimming.
  trim_adapter_args_single = "2:30:10"
  trim_adapter_args_paired = "2:30:10:1:TRUE"
  
  //  Settings for trimmomatic's quality trimming. Leave empty (i.e. "") to
  //  not perform quality trimming.
  trim_quality_args = "LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:75"
  
  //  Arguments to 'regtools junctions extract'. Note that the "-o" and "-s"
  //  arguments are handled internally, and should not be specified below. Also
  //  note that the "-m" argument is also used by hisat2 as the 
  //  "--min-intronlen" argument (see "hisat2_args"), and should be kept
  //  consistent!
  regtools_args = "-m 20"
  
  wigToBigWig_args = "-clip"
}

executor {
  name = 'sge'
  queueSize = 40
  submitRateLimit = '1 sec'
  exitReadTimeout = '40 min'
}

process {
  
  errorStrategy = { task.exitStatus == 140 ? 'retry' : 'terminate' }
  maxRetries = 1

  cache = 'lenient'

  withName: PullAssemblyFasta {
    cpus = 1
    clusterOptions = '-l mf=2G,h_vmem=2G'
  }
  withName: buildHISATindex {
    cpus = 4
    penv = 'local'
    module = 'hisat2/2.2.1'
    clusterOptions = '-l mf=15G,h_vmem=15G -R y'
  }
  withName: BuildStarIndex {
    cpus = 8
    penv = 'local'
    module = 'star/2.7.8a'
    clusterOptions = '-l mf=8G,h_vmem=8G,h_fsize=100G -R y'
  }
  withName: PullGtf {
    cpus = 1
    clusterOptions = '-l mf=2G,h_vmem=2G'
  }
  withName: BuildAnnotationObjects {
    cpus = 1
    module = 'conda_R/4.3'
    clusterOptions = '-l mf=15G,h_vmem=15G'
  }
  withName: PullTranscriptFasta {
    cpus = 1
    module = 'conda_R/4.3'
    clusterOptions = '-l mf=2G,h_vmem=2G'
  }
  withName: buildSALMONindex  {
    cpus = 6
    penv = 'local'
    module = 'salmon/1.2.1'
    clusterOptions = '-l mf=10G,h_vmem=10G'
  }
  withName: BuildKallistoIndex {
    cpus = 1
    module = 'kallisto/0.46.1'
    clusterOptions = '-l mf=20G,h_vmem=20G'
  }
  withName: PreprocessInputs {
    cpus = 1
    module = 'conda_R/4.3'
    clusterOptions = '-l mf=2G,h_vmem=2G,h_fsize=50G'
  }
  withName: CompleteManifest {
    cpus = 1
    module = 'conda_R/4.3'
    clusterOptions = '-l mf=2G,h_vmem=2G,h_fsize=50G'
  }
  withName: ERCC {
    cpus = 4
    penv = 'local'
    module = 'kallisto/0.46.1'
    clusterOptions = '-l mf=2G,h_vmem=2G'
  }
  withName: QualityUntrimmed { 
    cpus = 2
    penv = 'local'
    module = 'fastqc/0.11.8'
    clusterOptions = '-l mf=2G,h_vmem=2G -R y'
  }
  withName: Trimming {
    cpus = 2
    penv = 'local'
    module = 'trimmomatic/0.39'
    clusterOptions = '-l mf=4G,h_vmem=4G,h_fsize=80G -R y'
  }
  withName: QualityTrimmed {
    cpus = 2
    penv = 'local'
    module = 'fastqc/0.11.8'
    clusterOptions = '-l mf=2G,h_vmem=2G -R y'
  }
  withName: SingleEndHISAT {
    cpus = 4
    penv = 'local'
    module = 'hisat2/2.2.1:samtools/1.10'
    clusterOptions = '-l mf=4G,h_vmem=4G,h_fsize=500G -R y'
  }
  withName: PairedEndHISAT {
    cpus = 4
    penv = 'local'
    module = 'hisat2/2.2.1:samtools/1.10'
    clusterOptions = '-l mf=4G,h_vmem=4G,h_fsize=500G -R y'
  }
  withName: AlignStar {
    cpus = 4
    penv = 'local'
    module = 'star/2.7.8a'
    clusterOptions = '-l mf=8G,h_vmem=8G -R y'
  }
  withName: BamSort {
    cpus = 1
    module = 'samtools/1.10'
    clusterOptions = '-l mf=8G,h_vmem=8G,h_fsize=150G -R y'
  }
  withName: InferStrandness {
    cpus = 1
    module = 'conda_R/4.3:kallisto/0.46.1'
    clusterOptions = '-l mf=8G,h_vmem=8G,h_fsize=20G -R y'
  }
  withName: FeatureCounts {
    cpus = 2
    penv = 'local'
    module = 'featurecounts/2.0.0'
    clusterOptions = '-l mf=4G,h_vmem=4G,h_fsize=200G -R y'
  }
  withName: PrimaryAlignments {
    cpus = 1
    module = 'samtools/1.10'
    clusterOptions = '-l mf=4G,h_vmem=4G,h_fsize=50G -R y'
  }
  withName: Junctions {
    cpus = 1
    module = 'regtools/0.5.33g'
    clusterOptions = '-l mf=2G,h_vmem=2G'
  }
  withName: Coverage {
    cpus = 2
    penv = 'local'
    module = 'rseqc/3.0.1'
    clusterOptions = '-l mf=10G,h_vmem=10G,h_fsize=100G'
  }
  withName: WigToBigWig {
    cpus = 1
    module = 'ucsctools'
    clusterOptions = '-l mf=20G,h_vmem=20G,h_fsize=30G'
  }
  withName: MeanCoverage {
    cpus = 5
    penv = 'local'
    module = 'wiggletools/1.2.1:ucsctools'
    clusterOptions = '-l mf=10G,h_vmem=10G -R y'
  }
  withName: TXQuantSalmon {
    cpus = 2
    penv = 'local'
    module = 'salmon/1.2.1'
    clusterOptions = '-l mf=20G,h_vmem=20G -R y'
  }
  withName: TXQuantKallisto {
    cpus = 4
    penv = 'local'
    module = 'kallisto/0.46.1'
    clusterOptions = '-l mf=4G,h_vmem=4G -R y'
  }
  withName: CountObjects {
    cpus = 2
    penv = 'local'
    module = 'conda_R/4.3'
    clusterOptions = '-l mf=25G,h_vmem=25G,h_fsize=100G -R y'
  }
  withName: CoverageObjects {
    cpus = 4
    penv = 'local'
    module = 'conda_R/4.3'
    clusterOptions = '-l mf=4G,h_vmem=4G,h_fsize=50G -R y'
  }
  withName: VariantCalls {
    cpus = 1
    module = 'samtools/1.10:bcftools/1.10.2:htslib/1.10.2'
    clusterOptions = '-l mf=2G,h_vmem=2G'
  }
  withName: VariantsMerge {
    cpus = 1
    module = 'bcftools/1.10.2:htslib/1.10.2'
    clusterOptions = '-l mf=2G,h_vmem=2G'
  }
  withName: ExpressedRegions {
    cpus = 4
    penv = 'local'
    module = 'conda_R/4.3'
    clusterOptions = '-l mf=6G,h_vmem=6G,h_fsize=100G -R y'
  }
}