Commit 95060211 authored by Tommy Tang's avatar Tommy Tang
Browse files

4 threads for superEnhancer call

parent 9550d85f
...@@ -274,6 +274,7 @@ rule superEnhancer: ...@@ -274,6 +274,7 @@ rule superEnhancer:
"08peak_macs1/{case}_vs_{control}_macs1_peaks.bed" "08peak_macs1/{case}_vs_{control}_macs1_peaks.bed"
output: "11superEnhancer/{case}_vs_{control}-super/" output: "11superEnhancer/{case}_vs_{control}-super/"
log: "00log/{case}_superEnhancer.log" log: "00log/{case}_superEnhancer.log"
threads: 4
params: params:
jobname = "{case}", jobname = "{case}",
outputdir = os.path.dirname(srcdir("00log")) outputdir = os.path.dirname(srcdir("00log"))
......
idx_bt1: /scratch/genomic_med/apps/annot/indexes/bowtie/hg19 idx_bt1: /scratch/genomic_med/apps/annot/indexes/bowtie/hg19
macs_g: hs macs_g: hs
macs_pvalue: 10e-5 macs_pvalue: 1e-5
macs2_g: hs macs2_g: hs
macs2_pvalue: 10e-5 macs2_pvalue: 1e-5
macs2_pvalue_broad: 10e-5 macs2_pvalue_broad: 1e-5
#superEnhancer genome #superEnhancer genome
rose_g: hg19 rose_g: hg19
#number of reads downsample to #number of reads downsample to, I set to 50 million, if reads number smaller than
target_reads: 15000000 ## 50 million, downsample will keep the orignal reads
target_reads: 50000000
# Path to a JSON file with samples and their corresponding FASTQ files. # Path to a JSON file with samples and their corresponding FASTQ files.
......
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