Merge pull request #217 from maxplanck-ie/Fix_awk_QC

Fix peak QC awk command in ChIP and ATAC workflows
maxplanck-ie · Jul 25, 2018 · aa0a79d · aa0a79d
2 parents e17068c + 60e0c3b
commit aa0a79d
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Showing 4 changed files with 6 additions and 6 deletions.
diff --git a/conda-recipe/meta.yaml b/conda-recipe/meta.yaml
@@ -1,6 +1,6 @@
 package:
   name: snakepipes
-  version: 1.0.0_alpha4
+  version: 1.0.0_alpha5
 
 source:
   path: ../

diff --git a/snakePipes/__init__.py b/snakePipes/__init__.py
@@ -1 +1 @@
-__version__ = '1.0.0-a4'
+__version__ = '1.0.0-a5'
diff --git a/snakePipes/shared/rules/ATAC_qc.snakefile b/snakePipes/shared/rules/ATAC_qc.snakefile
@@ -79,8 +79,8 @@ rule MACS2_peak_qc:
         frip=`bc -l <<< "$reads_in_peaks/$mapped_reads"`
 
         # compute peak genome coverage
-        peak_len=`awk '{{total=$3-$2}}END{{print total}}' {params.peaks}`
-        genome_size=`awk '{{total=$3-$2}}END{{print total}}' {params.peaks}`
+        peak_len=`awk '{{total+=$3-$2}}END{{print total}}' {params.peaks}`
+        genome_size=`awk '{{total+=$3-$2}}END{{print total}}' {params.peaks}`
         genomecov=`bc -l <<< "$peak_len/$genome_size"`
 
         # write peak-based QC metrics to output file

diff --git a/snakePipes/shared/rules/MACS2.snakefile b/snakePipes/shared/rules/MACS2.snakefile
@@ -114,8 +114,8 @@ rule MACS2_peak_qc:
         frip=`bc -l <<< "$reads_in_peaks/$mapped_reads"`
 
         # compute peak genome coverage
-        peak_len=`awk '{{total=$3-$2}}END{{print total}}' {params.peaks}`
-        genome_size=`awk '{{total=$3-$2}}END{{print total}}' {params.peaks}`
+        peak_len=`awk '{{total+=$3-$2}}END{{print total}}' {params.peaks}`
+        genome_size=`awk '{{total+=$3-$2}}END{{print total}}' {params.peaks}`
         genomecov=`bc -l <<< "$peak_len/$genome_size"`
 
         # write peak-based QC metrics to output file