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legion.config
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process {
executor='sge'
clusterOptions = '-l mem=20G'
cpus = 1
penv = 'smp'
time = 12.h
memory = 15.Gb
withName: 'star' {
time=48.h
cpus = 4
}
withName: 'splitandtrim' {
cpus = 4
}
withName:workflow_summary_mqc{
memory = 4.Gb
}
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
$fastqc.module = ['fastqc/0.11.5']
$trim_galore.module = ['fastqc/0.11.5','python3/recommended','trim_galore']
$star.module = ['star/2.5.2a']
$markDuplicates.module = ['java/1.8.0_92', 'picard-tools/2.18.9']
$addRG.module = ['java/1.8.0_92', 'picard-tools/2.18.9']
$splitandtrim.module = ['gatk/4.0.8.0']
$recalibrate.module = ['gatk/4.0.8.0']
$variantCall.module = ['gatk/4.0.8.0']
$genotypegvcfs.module = ['gatk/4.0.8.0']
$filterVariants.module = ['gatk/4.0.8.0']
$annotateVariants.module = ['blic-modules','annovar']
$multiqc.module = ['blic-modules','bioconda/4.7.12']
$get_software_versions.module = ['fastqc/0.11.5','python3/recommended','trim_galore', 'java/1.8.0_92', 'picard-tools/2.18.9', 'blic-modules','bioconda/4.7.12', 'star/2.5.2a', 'gatk/4.0.8.0']
}
params {
help = false
// Pipeline Options
name = false
project = false
genome = false
forward_stranded = false
reverse_stranded = false
unstranded = false
splicesites = false
saveReference = false
saveTrimmed = false
saveAlignedIntermediates = false
singleEnd = false
reads = "data/*{1,2}.fastq.gz"
outdir = './results'
email = false
plaintext_email = false
seqCenter = false
multiqc_config = "$baseDir/assets/multiqc_config.yaml"
// Custom trimming options
pico = false
clip_r1 = 0
clip_r2 = 0
three_prime_clip_r1 = 0
three_prime_clip_r2 = 0
// Defaults
sampleLevel = false
clusterOptions = false
maxMultiqcEmailFileSize = 25.MB
readPaths = null
tracedir = "${params.outdir}"
genomes {
'hg19' {
star = '/scratch/scratch/regmr01/Homo_sapiens/NCBI/build37.2/Sequence/STARIndex/'
fasta = '/scratch/scratch/regmr01/Homo_sapiens/NCBI/build37.2/Sequence/WholeGenomeFasta/genome.fa'
gtf = "/scratch/scratch/regmr01/Homo_sapiens/NCBI/build37.2/Annotation/Genes/genes.gtf"
dbsnp = '/scratch/scratch/regmr01/GATK_bundle/2.8/b37/dbsnp_138.b37.vcf'
annovar_anno = '/shared/ucl/depts/cancer/apps/annovar/2018-04-16/hg19'
}
'hg38' {
star = '/scratch/scratch/regmr01/Homo_sapiens/NCBI/GRCh38/Sequence/STARIndex'
fasta = '/scratch/scratch/regmr01/Homo_sapiens/NCBI/GRCh38/Sequence/WholeGenomeFasta/genome.fa'
gtf = "/scratch/scratch/regmr01/Homo_sapiens/NCBI/GRCh38/Annotation/Genes/genes.gtf"
dbsnp = '/scratch/scratch/regmr01/GATK_bundle/hg38bundle/dbsnp_144.hg38.with_chr.vcf.gz'
annovar_anno = '/shared/ucl/depts/cancer/apps/annovar/2018-04-16/hg38'
}
}
}
/////////////////////////////////////////////////////////////////////////
// This should work but it doesn't
// I need to manually remnove the manifest.version instances from main.nf
// otherwise it crashes with confusing StackOverflow errors
//////////////////////////////////////////////////////////////////////////
manifest {
homePage = 'https://github.com/UCL-BLIC/rnaseq_variant_calling'
description = 'UCL-BLIC RNAseq variant calling pipeline'
mainScript = 'main.nf'
version = '1.0.0'
}