Commit 5fdddbc3 authored by WJH58's avatar WJH58
Browse files

change macs3 to macs2

parent b337f46f
......@@ -4,4 +4,4 @@ channels:
- r
- defaults
dependencies:
- macs3=3.0.0a4
- macs2=2.2.7.1
......@@ -54,7 +54,7 @@ SORTED_INDEXED = expand(WORKING_DIR + "index/{samples}.sorted.bam.bai", samples
GENOME_INFO = expand(WORKING_DIR + "genome_info/{samples}.genome.info", samples = SAMPLES),
GAPPED_PEAK = expand(RESULT_DIR + "peaks/{samples}_peaks.gappedPeak", samples = SAMPLES),
NAME_LOG = expand(RESULT_DIR + "peaks/{samples}.log", samples = SAMPLES),
NARROWPEAK = expand(RESULT_DIR + "macs3/{samples}_peaks.narrowPeak", samples = SAMPLES)
NARROWPEAK = expand(RESULT_DIR + "macs2/{samples}_peaks.narrowPeak", samples = SAMPLES)
rule all:
input:
......@@ -254,19 +254,19 @@ rule call_narrow_peaks:
input:
map_sorted = WORKING_DIR + "sort/{samples}.sorted.bam"
output:
narrowPeak = RESULT_DIR + "macs3/{samples}_peaks.narrowPeak"
narrowPeak = RESULT_DIR + "macs2/{samples}_peaks.narrowPeak"
params:
name = "{samples}",
format = str(config['macs2']['format']),
genomesize = str(config['macs2']['genomesize']),
outdir = str(config['macs2']['outdir'])
log:
RESULT_DIR + "logs/macs3/{samples}_peaks.narrowPeak.log"
RESULT_DIR + "logs/macs2/{samples}_peaks.narrowPeak.log"
conda:
"envs/macs2.yaml"
shell:
"""
macs3 callpeak -t {input} {params.format} {params.genomesize} --name {params.name} --nomodel --bdg -q 0.05 --outdir {params.outdir}/ 2>{log}
macs2 callpeak -t {input} {params.format} {params.genomesize} --name {params.name} --nomodel --bdg -q 0.05 --outdir {params.outdir}/ 2>{log}
"""
#bdg: create bedgraph output files
#format=BAMPE: only use properly-paired read alignments
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