myriad.config

///////////////
// LC ISSUES //
///////////////////////////////////////////////////////////////////////////////////////////////
// *** STEP 7 deepTools : change  '--normalizeUsingRPKM' for '--normalizeUsing RPKM (twice)' //
//	----> no longer needed in nf-core <---                        			     //
// *** * Parse software version numbers: dont print trim_galore or multiQC versions as these //
//		need python3 and clashes with other software that needs python2              //
//		CHANGE TO: "echo "unknown"  > v_trim_galore.txt"                             //
//	----> no longer needed after installing multiQC and MACS2 with bioconda              //
// *** ADD "--nomodelExtsize" option to MACS and Saturation analysis                         // 
// *** ADD bigwig conversion **TESTING**                                                     // 
// *** 'post_peak_calling_processing.r' -> change a few things regarding annotations         // 
// *** Install new Deeptools 3.1, as I'm getting "ValueError: left cannot be >= right"       //
//		errors in plotPCA (https://github.com/nf-core/chipseq/pull/50)               //
///////////////////////////////////////////////////////////////////////////////////////////////

process {

  executor='sge'
  clusterOptions = '-l mem=48G'

  cpus = 1
  penv = "smp"
  time = 12.h

  beforeScript = 'source $HOME/.bashrc;module load blic-modules bioconda/4.5.11'
  echo = true

  withName: bwa {
    cpus = 1
    time = 48.h
    memory = 64.Gb
    module = ['bwa/0.7.12']
  }

  withName: picard {
    module = ['java/1.8.0_92', 'picard-tools/2.18.9']
  }
  withName: ngsplot {
    module = ['blic-modules','ngsplot/2.61']
  }
  withName: get_software_versions {
    module = ['java/1.8.0_92','bwa/0.7.12/gnu-4.9.2','picard-tools/2.18.9']
  }


}

params {

  genomes {

    'GRCh37'      { bwa = "/scratch/scratch/regmr01/Homo_sapiens/UCSC/hg19/Sequence/BWAIndex/"
                    blacklist = "/scratch/scratch/regmr01/blacklist_regions/wgEncodeHg19ConsensusSignalArtifactRegions.bed"
                    gtf = "/scratch/scratch/regmr01/Homo_sapiens/UCSC/hg19/Annotation/Archives/archive-2015-07-17-14-32-32/Genes/genes.gtf"
                    fasta = "/scratch/scratch/regmr01/Homo_sapiens/UCSC/hg19/Sequence/WholeGenomeFasta/genome.fa"
                  }
    'GRCh38'      { bwa = "/scratch/scratch/regmr01/Homo_sapiens/UCSC/hg38/Sequence/BWAIndex/"
                   blacklist = "/scratch/scratch/regmr01/blacklist_regions/hg38.blacklist.bed"
                    gtf = "/scratch/scratch/regmr01/Homo_sapiens/UCSC/hg38/Annotation/Archives/archive-2015-08-14-08-18-15/Genes/genes.gtf"
                    fasta = "/scratch/scratch/regmr01/Homo_sapiens/UCSC/hg38/Sequence/WholeGenomeFasta/genome.fa"
                  }
    'GRCm38'      { bwa = "/scratch/scratch/regmr01/Mus_musculus/UCSC/mm10/Sequence/BWAIndex/"
                    blacklist = "/scratch/scratch/regmr01/blacklist_regions/mm10.blacklist.bed"
                    gtf = "/scratch/scratch/regmr01/Mus_musculus/UCSC/mm10/Annotation/Archives/archive-2015-07-17-14-33-26/Genes/genes.gtf"
                    fasta = "/scratch/scratch/regmr01/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa"
                  }
  }
}

//env {
//     NXF_HOME = '/home/regmr01/Scratch/.nextflow'
//}