add stderr log to macs2 - add spp file as input instead of params

Snakefile

@@ -667,7 +667,7 @@ if config["macs2"]["do"]:
             macs2_options += " --nomodel "
             macs2_shift_file = os.path.join(analysis_dir, "05-QC/PhantomPeakQualTools/{{SAMPLE}}_{}_sort{}_spp.out".format(ref, biasedRegions))
         else:
-            macs2_shift_file = "Empty"
+            macs2_shift_file = "{}/{{SAMPLE}}_{}_sort{}.bam".format(biasedRegions_dir, ref, biasedRegions)
         if paired :
             macs2_pe_mode = "no"
         else:
@@ -675,7 +675,8 @@ if config["macs2"]["do"]:
 
         macs2_input_bam = "{}/{{SAMPLE}}_{}_sort{}.bam".format(biasedRegions_dir, ref, biasedRegions)
         macs2_control = INPUTtoIP
-        macs2_log = os.path.join(analysis_dir, "06-PeakCalling/macs2/{}/logs/{{SAMPLE}}.out".format(model_dir))
+        macs2_log_out = os.path.join(analysis_dir, "06-PeakCalling/macs2/{}/logs/{{SAMPLE}}.out".format(model_dir))
+        macs2_log_err = os.path.join(analysis_dir, "06-PeakCalling/macs2/{}/logs/{{SAMPLE}}.err".format(model_dir))
         macs2_output = os.path.join(analysis_dir, "06-PeakCalling/macs2/{}/{{SAMPLE}}_peaks.{}Peak".format(model_dir, model))
         macs2_output_prefix = os.path.join(analysis_dir, "06-PeakCalling/macs2/{}/{{SAMPLE}}".format(model_dir))
 

workflow/rules/macs2.rules

@@ -26,16 +26,17 @@
 rule macs2:
     input:
         bam = macs2_input_bam,
-        control = macs2_control
+        control = macs2_control,
+        shift_file = macs2_shift_file
     params:
         gsize = config["macs2"]["genomeSize"],
         options = macs2_options,
         pe_mode = macs2_pe_mode,
         prefix = macs2_output_prefix,
-        shift_file = macs2_shift_file,
         read_length = 146
     log:
-        out = macs2_log
+        out = macs2_log_out,
+        err = macs2_log_err
     output:
         macs2_output
     singularity:
@@ -46,20 +47,20 @@ rule macs2:
 
         #if [[ "{input.control}" == "NA" ]] ; then input="" ; else input="{input.control}" ; fi
 
-        if [[ {params.shift_file} != "Empty" ]] ; then
-            if [[ -e {params.shift_file} ]] ; then
-                shift=$(awk '{{print $3}}' {params.shift_file} | awk -F ',' '{{if ($1=={params.read_length}){{print $2}}  else {{print $1}} }}')
+        if [[ {input.shift_file} == "*_spp.out"  ]] ; then
+            if [[ -e {input.shift_file} ]] ; then
+                shift=$(awk '{{print $3}}' {input.shift_file} | awk -F ',' '{{if ($1=={params.read_length}){{print $2}}  else {{print $1}} }}')
                 if [[ {params.pe_mode} == "yes" ]] ; then
-                    macs2 callpeak -t {input.bam} -c {input.control} -f BAMPE -g {params.gsize} -n {params.prefix} {params.options} --extsize ${{shift}} 2> {log.out}
+                    macs2 callpeak -t {input.bam} -c {input.control} -f BAMPE -g {params.gsize} -n {params.prefix} {params.options} --extsize ${{shift}} > {log.out} 2> {log.err}
                 else
-                    macs2 callpeak -t {input.bam} -c {input.control} -f BAM -g {params.gsize} -n {params.prefix} {params.options} --extsize ${{shift}} 2> {log.out}
+                    macs2 callpeak -t {input.bam} -c {input.control} -f BAM -g {params.gsize} -n {params.prefix} {params.options} --extsize ${{shift}}> {log.out} 2> {log.err}
                 fi
             fi
         else
             if [[ {params.pe_mode} == "yes" ]] ; then
-                macs2 callpeak -t {input.bam} -c {input.control} -f BAMPE -g {params.gsize} -n {params.prefix} {params.options} 2> {log.out}
+                macs2 callpeak -t {input.bam} -c {input.control} -f BAMPE -g {params.gsize} -n {params.prefix} {params.options} > {log.out} 2> {log.err}
             else
-                macs2 callpeak -t {input.bam} -c {input.control} -f BAM -g {params.gsize} -n {params.prefix} {params.options} 2> {log.out}
+                macs2 callpeak -t {input.bam} -c {input.control} -f BAM -g {params.gsize} -n {params.prefix} {params.options} > {log.out} 2> {log.err}
             fi
         fi
         """