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nextflow.config
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nextflow.config
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process {
errorStrategy = { task.exitStatus in [1,143,137,104,134,139] ? 'retry' : 'terminate' }
maxRetries = 3
maxErrors = '-1'
}
executor.$local.cpus = 32
executor.$local.memory = '256 GB'
params {
// tracedir = '$baseDir/trace'
// reference genomes
genomes {
'hg38' {
bwa = '/athena/elementolab/scratch/asd2007/reference/hg38/BWAIndex/'
bt2 = '/athena/elementolab/scratch/asd2007/reference/hg38/BT2index/genome.fasta'
fasta = '/athena/elementolab/scratch/asd2007/reference/hg38/BWAIndex/genome.fa'
annotation_config = "conf/hg38.config"
chrsz = '/athena/elementolab/scratch/asd2007/reference/hg38/hg38.chrom.sizes'
picardconf = "/athena/elementolab/scratch/asd2007/reference/hg38/picardmetrics.conf"
PROM = "/athena/elementolab/scratch/asd2007/reference/hg38/ataqc/reg2map_honeybadger2_dnase_prom_p2.hg19_to_hg38.bed.gz"
ROADMAP_META = "/athena/elementolab/scratch/asd2007/reference/hg38/ataqc/hg38_dnase_avg_fseq_signal_metadata.txt"
species_browser = "hg38"
DNASE_BED = "/athena/elementolab/scratch/asd2007/reference/hg38/ataqc/reg2map_honeybadger2_dnase_all_p10_ucsc.bed.gz"
blacklist = "/athena/elementolab/scratch/asd2007/reference/hg38/hg38.blacklist.bed.gz"
BLACK = "/athena/elementolab/scratch/asd2007/reference/hg38/hg38.blacklist.bed.gz"
PICARDCONF = "/athena/elementolab/scratch/asd2007/reference/hg38/picardmetrics.conf"
REF = "/athena/elementolab/scratch/asd2007/reference/hg38/BWAIndex/genome.fa"
REFbt2="/athena/elementolab/scratch/asd2007/reference/hg38/bowtie2_index/GRCh38_no_alt_analysis_set_GCA_000001405.15.fasta"
bwt2_idx="/athena/elementolab/scratch/asd2007/reference/hg38/bowtie2_index/GRCh38_no_alt_analysis_set_GCA_000001405.15.fasta"
RG="hg38"
spec = 'hs'
SPEC = 'hs'
REFGen="/athena/elementolab/scratch/asd2007/reference/hg38/GRCh38_no_alt_analysis_set_GCA_000001405.15.fasta"
seq="/athena/elementolab/scratch/asd2007/reference/hg38/seq"
gensz="hs"
bwt2_idx="/athena/elementolab/scratch/asd2007/reference/hg38/bowtie2_index/GRCh38_no_alt_analysis_set_GCA_000001405.15.fasta"
REF_FASTA="/athena/elementolab/scratch/asd2007/reference/hg38/GRCh38_no_alt_analysis_set_GCA_000001405.15.fasta"
species_browser='hg38'
TSS_ENRICH="/athena/elementolab/scratch/asd2007/reference/hg38/ataqc/hg38_gencode_tss_unique.bed.gz"
DNASE='/athena/elementolab/scratch/asd2007/reference/hg38/ataqc/reg2map_honeybadger2_dnase_all_p10_ucsc.hg19_to_hg38.bed.gz'
PROM='/athena/elementolab/scratch/asd2007/reference/hg38/ataqc/reg2map_honeybadger2_dnase_prom_p2.hg19_to_hg38.bed.gz'
ENH='/athena/elementolab/scratch/asd2007/reference/hg38/ataqc/reg2map_honeybadger2_dnase_enh_p2.hg19_to_hg38.bed.gz'
REG2MAP='/athena/elementolab/scratch/asd2007/reference/hg38/ataqc/hg38_dnase_avg_fseq_signal_formatted.txt.gz'
REG2MAP_BED="/athena/elementolab/scratch/asd2007/reference/hg38/ataqc/hg38_celltype_compare_subsample.bed.gz"
ROADMAP_META="/athena/elementolab/scratch/asd2007/reference/hg38/ataqc/hg38_dnase_avg_fseq_signal_metadata.txt"
ENCODEDHS='/athena/elementolab/scratch/asd2007/reference/hg38/ataqc/reg2map_honeybadger2_dnase_all_p10_ucsc.hg19_to_hg38.bed.gz'
}
'mm10' {
bwa = '/athena/elementolab/scratch/asd2007/reference/mm10/BWAIndex/'
bt2 = '/athena/elementolab/scratch/asd2007/reference/mm10/BT2index/'
fasta = '/athena/elementolab/scratch/asd2007/reference/mm10/BWAIndex/genome.fa'
RG = 'mm10'
spec = 'mm'
annotation_config = "conf/mm10.config"
SPEC = 'mm'
REFGen = '/athena/elementolab/scratch/asd2007/bin/bcbio/genomes/Mmusculus/mm10/seq/'
PICARDCONF="/athena/elementolab/scratch/asd2007/reference/mm10/picardmetrics.conf"
picardconf="/athena/elementolab/scratch/asd2007/reference/mm10/picardmetrics.conf"
chrsz = '/athena/elementolab/scratch/asd2007/reference/mm10/mm10.chrom.sizes'
seq = '/athena/elementolab/scratch/asd2007/reference/mm10/seq'
gensz = 'mm'
bwt2_idx = "/athena/elementolab/scratch/asd2007/reference/mm10/BT2index/genome.fasta.gz"
fasta = '/athena/elementolab/scratch/asd2007/reference/mm10/bwa_index/mm10_no_alt_analysis_set_ENCODE.fasta'
ref_fa = '/athena/elementolab/scratch/asd2007/reference/mm10/mm10_no_alt_analysis_set_ENCODE.fasta'
REF = '/athena/elementolab/scratch/asd2007/reference/mm10/BWAIndex/genome.fa'
blacklist = "/athena/elementolab/scratch/asd2007/reference/mm10/mm10.blacklist.bed.gz"
BLACK = "/athena/elementolab/scratch/asd2007/reference/mm10/mm10.blacklist.bed.gz"
species_browser = 'mm10'
TSS_ENRICH = '/athena/elementolab/scratch/asd2007/reference/mm10/ataqc/mm10_gencode_tss_unique.bed.gz'
DNASE = '/athena/elementolab/scratch/asd2007/reference/mm10/ataqc/mm10_univ_dhs_ucsc.bed.gz'
PROM = '/athena/elementolab/scratch/asd2007/reference/mm10/ataqc/tss_mm10_master.bed.gz'
ENH = '/athena/elementolab/scratch/asd2007/reference/mm10/ataqc/mm10_enh_dhs_ucsc.bed.gz'
REG2MAP = '/athena/elementolab/scratch/asd2007/reference/mm10/ataqc/mm10_dnase_avg_fseq_signal_formatted.txt.gz'
REG2MAP_BED = '/athena/elementolab/scratch/asd2007/reference/mm10/ataqc/mm10_celltype_compare_subsample.bed.gz'
ROADMAP_META = '/athena/elementolab/scratch/asd2007/reference/mm10/ataqc/mm10_dnase_avg_fseq_signal_metadata.txt'
ENCODEDHS = "/athena/elementolab/scratch/asd2007/reference/mm10/ataqc/mm10_univ_dhs_ucsc.bed.gz"
}
}
}
env {
PICARDROOT="/home/asd2007/Tools/picard/build/libs"
}
//process.shell = ['/bin/bash', '-euo', 'pipefail']