Develop (#625)

* fixed a typo in alignment sieve rule (#623) Please enter the commit message for your changes. Lines starting Co-authored-by: Leily Rabbani <[email protected]> * Atac log (#624) * fixed a typo in alignment sieve rule Please enter the commit message for your changes. Lines starting * ncreased the version Co-authored-by: Leily Rabbani <[email protected]> Co-authored-by: Leily Rabbani <[email protected]>
maxplanck-ie · Apr 24, 2020 · 97706ea · 97706ea
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diff --git a/conda-recipe/meta.yaml b/conda-recipe/meta.yaml
@@ -1,6 +1,6 @@
 package:
   name: snakepipes
-  version: 2.1.0
+  version: 2.1.1
 
 source:
   path: ../

diff --git a/docs/content/News.rst b/docs/content/News.rst
@@ -1,5 +1,8 @@
 snakePipes News
 ===============
+snakePipes 2.1.1
+----------------
+* small bug fix: a typo in atac-seq pipeline
 
 snakePipes 2.1.0
 ----------------
@@ -90,14 +93,14 @@ snakePipes 1.2.3
  * Fixed CSAW QC plot error with single end reads
  * Updated histone HMM environment to a working conda version
  * Salmon_wasabi is now a localrule
- 
+
 
 snakePipes 1.2.2
 ----------------
 
  * Fixed a bug in the ATAC-seq environment where GenomeInfoDbData was missing.
  * Also an occasional issue with CSAW
- 
+
 
 snakePipes 1.2.1
 ----------------
@@ -106,7 +109,7 @@ snakePipes 1.2.1
  * Implemented complex experimental design in RNAseq (differential gene expression), ChIP/ATACseq (differential binding).
  * Fixed an issue with ggplot2 and log transformation in RNAseq report Rmd.
  * fastqc folder is created and its content will be added to multiqc only if fastqc flag is called.
- * fastqc-trimmed folder is created and its content will be added to multiqc only if both fastqc and trim flags are called. 
+ * fastqc-trimmed folder is created and its content will be added to multiqc only if both fastqc and trim flags are called.
 
 snakePipes 1.2.0
 ----------------

diff --git a/snakePipes/__init__.py b/snakePipes/__init__.py
@@ -1 +1 @@
-__version__ = '2.1.0'
+__version__ = '2.1.1'
diff --git a/snakePipes/shared/rules/ATAC.snakefile b/snakePipes/shared/rules/ATAC.snakefile
@@ -16,7 +16,7 @@ rule filterFragments:
         --filterMetrics {output.metrics} \
         --maxFragmentLength {params.maxFragmentSize} \
         --minFragmentLength {params.minFragmentSize} \
-        2 > {log}
+        2> {log}
         """
 
 
@@ -50,9 +50,9 @@ rule filterCoveragePerScaffolds:
     shell: """
         samtools index -@ {threads} {input.bam} 2> {log}
         samtools idxstats {input.bam} | awk -v cutoff={params.count_cutoff} \'$3 > cutoff\' | cut -f 1 > {output.whitelist} 2>> {log}
-        samtools view -@ {threads} -bo {output.bam} {input.bam} $(cat {output.whitelist} | paste -sd\' \') 2>> {log} 
+        samtools view -@ {threads} -bo {output.bam} {input.bam} $(cat {output.whitelist} | paste -sd\' \') 2>> {log}
         samtools index -@ {threads} {output.bam} 2>> {log}
-        
+
         """