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legion.config
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///////////////
// 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=24G'
cpus = 2
penv = "smp"
time = 12.h
beforeScript = 'source $HOME/.bashrc;module unload compilers;module unload mpi;module load r/recommended;module unload python2;module unload python3;module unload python'
echo = true
withName: bwa {
cpus = 6
time = 48.h
memory = 64.Gb
}
$fastqc.module = ['blic-modules','bioconda/4.7.12']
$trim_galore.module = ['blic-modules','bioconda/4.7.12']
$bwa.module = ['samtools/1.3.1/gnu-4.9.2', 'bwa/0.7.12/gnu-4.9.2']
$bwa_mapped.module = ['samtools/1.3.1/gnu-4.9.2']
$samtools.module = ['samtools/1.3.1/gnu-4.9.2', 'bedtools/2.25.0']
$picard.module = ['java/1.8.0_92', 'picard-tools/2.18.9', 'bedtools/2.25.0','samtools/1.3.1/gnu-4.9.2']
$macs.module = ['python2/recommended']
$deepTools.module = ['blic-modules','bioconda/4.7.12']
$bigwigs.module = ['bedtools/2.25.0','blic-modules','bioconda/4.7.12']
$saturation.module = ['blic-modules','bioconda/4.5.11','samtools/1.3.1/gnu-4.9.2']
$phantompeakqualtools.module = ['samtools/1.3.1/gnu-4.9.2', 'blic-modules', 'phantompeakqualtools/1.14']
$ngsplot.module = ['samtools/1.3.1/gnu-4.9.2', 'blic-modules','ngsplot/2.61']
$multiqc.module = ['blic-modules','bioconda/4.7.12']
$get_software_versions.module = ['samtools/1.3.1/gnu-4.9.2','java/1.8.0_92','bwa/0.7.12/gnu-4.9.2','picard-tools/2.18.9','python2/recommended','bedtools/2.25.0','blic-modules','bioconda/4.7.12']
}
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'
//}