change macs3 to macs2

ATAC-seq_pipeline/envs/macs2.yaml

@@ -4,4 +4,4 @@ channels:
   - r
   - defaults
 dependencies:
-  - macs3=3.0.0a4
+  - macs2=2.2.7.1

ATAC-seq_pipeline/snakefile

@@ -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