seacr mode

maxplanck-ie · Apr 22, 2024 · 186b772 · 186b772
1 parent 2c35a46
commit 186b772
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Showing 2 changed files with 4 additions and 4 deletions.
diff --git a/snakePipes/shared/rules/ChIP_peak_calling.snakefile b/snakePipes/shared/rules/ChIP_peak_calling.snakefile
@@ -279,7 +279,7 @@ rule SEACR_peaks_lenient:
         script=os.path.join(maindir, "shared","tools/SEACR-1.3/SEACR_1.3.sh")
     conda: CONDA_SEACR_ENV
     shell: """
-        bash {params.script} {input.chip} {input.control} {params.fdr} "norm" "lenient" {params.prefix} 2>{log}
+        bash {params.script} {input.chip} {input.control} {params.fdr} "norm" "relaxed" {params.prefix} 2>{log}
         """
 
 rule SEACR_peak_stringent_qc:

diff --git a/snakePipes/shared/rules/ChIP_peak_calling_spikein.snakefile b/snakePipes/shared/rules/ChIP_peak_calling_spikein.snakefile
@@ -255,7 +255,7 @@ rule SEACR_peaks_stringent:
                  else []
     output:
         "SEACR/{chip_sample}_host.stringent.bed"
-    log: "SEACR/logs/{chip_sample}.log"
+    log: "SEACR/logs/{chip_sample}_stringent.log"
     params:
         fdr = lambda wildcards,input: fdr if not input.control else "",
         prefix = os.path.join(outdir,"SEACR/{chip_sample}_host"),
@@ -272,14 +272,14 @@ rule SEACR_peaks_lenient:
                  else []
     output:
         "SEACR/{chip_sample}_host.lenient.bed"
-    log: "SEACR/logs/{chip_sample}.log"
+    log: "SEACR/logs/{chip_sample}_lenient.log"
     params:
         fdr = lambda wildcards,input: fdr if not input.control else "",
         prefix = os.path.join(outdir,"SEACR/{chip_sample}_host"),
         script=os.path.join(maindir, "shared","tools/SEACR-1.3/SEACR_1.3.sh")
     conda: CONDA_SEACR_ENV
     shell: """
-        bash {params.script} {input.chip} {input.control} {params.fdr} "non" "lenient" {params.prefix} 2>{log}
+        bash {params.script} {input.chip} {input.control} {params.fdr} "non" "relaxed" {params.prefix} 2>{log}
         """