Merge pull request #784 from maxplanck-ie/bugfix_777

fixed macs2 bug , if spike in but not cutnx
maxplanck-ie · Sep 10, 2021 · 6e1e4c6 · 6e1e4c6
2 parents 8a5ee77 + d4e816b
commit 6e1e4c6
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Showing 3 changed files with 3 additions and 3 deletions.
diff --git a/snakePipes/shared/rules/ChIP_peak_calling.snakefile b/snakePipes/shared/rules/ChIP_peak_calling.snakefile
@@ -28,7 +28,7 @@ if pairedEnd:
                 else "",
             genome_size = str(genome_size),
             ext_size =
-                lambda wildcards: " --nomodel --extsize "+get_pe_frag_length(wildcards.chip_sample,
+                lambda wildcards: " --nomodel --extsize "+get_pe_frag_length("filtered_bam/"+wildcards.chip_sample+".filtered.bam",
                                                                             "deepTools_qc/bamPEFragmentSize/fragmentSize.metric.tsv") \
                                                                             if not cutntag else " ",
             peakCaller_options = lambda wildcards: str(peakCallerOptions or '') if not cutntag else " -p 1e-5 ",

diff --git a/snakePipes/shared/rules/ChIP_peak_calling_spikein.snakefile b/snakePipes/shared/rules/ChIP_peak_calling_spikein.snakefile
@@ -30,7 +30,7 @@ if pairedEnd:
                 lambda wildcards: "-c split_bam/"+get_control(wildcards.chip_sample)+"_host.bam" if get_control(wildcards.chip_sample)
                 else "",
             ext_size =
-                lambda wildcards: " --nomodel --extsize "+get_pe_frag_length(wildcards.chip_sample,
+                lambda wildcards: " --nomodel --extsize "+get_pe_frag_length("split_bam/"+wildcards.chip_sample+"_host.bam",
                                                                             "split_deepTools_qc/bamPEFragmentSize/host.fragmentSize.metric.tsv") \
                                                                             if not cutntag else " ",
             peakCaller_options = lambda wildcards: str(peakCallerOptions or '') if not cutntag else " -p 1e-5 ",

diff --git a/snakePipes/workflows/ChIP-seq/internals.snakefile b/snakePipes/workflows/ChIP-seq/internals.snakefile
@@ -64,7 +64,7 @@ def is_allelic(workingdir):
 def get_pe_frag_length(sample, frag_len_file):
     try:
         df = pd.read_csv(frag_len_file, header = None, skiprows = 1, sep = "\t")
-        df = df.loc[df[0] == "filtered_bam/"+sample+".filtered.bam"]
+        df = df.loc[df[0] == sample]
         frag_len = int(df[5].values[0])
         return str(frag_len)
     except: