moved macs format to config

alsmith151 · Mar 28, 2024 · c6606e6 · c6606e6
1 parent 1ddb08e
commit c6606e6
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Showing 2 changed files with 3 additions and 3 deletions.
diff --git a/seqnado/config.py b/seqnado/config.py
@@ -248,7 +248,7 @@ def setup_configuration(assay, genome, template_data):
 
 macs:
     version: 2
-    callpeak:
+    callpeak: -f BAMPE
 
 lanceotron:
     use_input: True

diff --git a/seqnado/workflow/rules/peak_call_chip.smk b/seqnado/workflow/rules/peak_call_chip.smk
@@ -55,7 +55,7 @@ rule macs2_with_input:
         "seqnado_output/logs/macs/{sample}_{treatment}.log",
     shell:
         """
-        macs2 callpeak -t {input.treatment} -c {input.control} -n {params.basename} -f BAMPE {params.options} > {log} 2>&1 &&
+        macs2 callpeak -t {input.treatment} -c {input.control} -n {params.basename} {params.options} > {log} 2>&1 &&
         cat {params.narrow} | cut -f 1-3 > {output.peaks}
         """
 
@@ -78,7 +78,7 @@ rule macs2_no_input:
         "seqnado_output/logs/macs/{sample}_{treatment}.log",
     shell:
         """
-        macs2 callpeak -t {input.treatment} -n {params.basename} -f BAMPE {params.options} > {log} 2>&1 &&
+        macs2 callpeak -t {input.treatment} -n {params.basename} {params.options} > {log} 2>&1 &&
         cat {params.narrow} | cut -f 1-3 > {output.peaks}
         """