Merge pull request #818 from maxplanck-ie/dev_ksikora2

Minor fixes for GitHub and other issues

.azure-pipelines/setup.yml

@@ -7,7 +7,10 @@ steps:
 #    installOptions: -c conda-forge -c bioconda --quiet
 #    createOptions: -c conda-forge -c bioconda --quiet --yes
 - bash: |
-    conda create -n foo -q --yes --quiet -c conda-forge -c bioconda snakemake=6.2.1 fuzzywuzzy mock sphinx sphinx-argparse sphinx_rtd_theme flake8 coreutils mamba python=3.9
+    conda install -c conda-forge --yes mamba
+  displayName: Installing mamba in base env
+- bash: |
+    conda create -n foo -q --yes --quiet -c conda-forge -c bioconda snakemake=6.2.1 fuzzywuzzy mock sphinx sphinx-argparse sphinx_rtd_theme flake8 coreutils python=3.9
   displayName: Installing dependencies
 - bash: |
     source activate foo

.azure-pipelines/testCreateEnv.py

@@ -32,7 +32,7 @@ def parse_args():
 elif args.envs_chunk == str(3):
     envs = range(2 * index, length)
 
-for i in range(index):
+for i in envs:
     keys.append(list(cf.set_env_yamls())[i])
 envs_to_test = " ".join(keys)
 sp.check_output("snakePipes createEnvs --only {} --force".format(envs_to_test), shell=True)

conda-recipe/meta.yaml

@@ -1,6 +1,6 @@
 package:
   name: snakepipes
-  version: 2.5.3
+  version: 2.5.4
 
 source:
   path: ../

docs/content/News.rst

@@ -1,6 +1,14 @@
 snakePipes News
 ===============
 
+snakePipes 2.5.4
+----------------
+
+* Fixed a number of minor GitHub issues: #791, #816, #807, #789, #783, #768.
+* Fixed misleading rule name for bamcoverage in atac-seq.
+* Fixed conda env building on microsoft azure.
+* Fixed CSAW report for ChIP-seq.
+
 
 snakePipes 2.5.3
 ----------------

docs/content/running_snakePipes.rst

@@ -35,7 +35,7 @@ All individual jobs of the workflow will be submitted to the Grid engine using t
 
 **To run the workflow locally**, use the parameter ``--local`` for local mode and the parameter ``-j 10`` to specify the maximal number of used CPU threads (here: 10).
 
-**For single-end FASTQ files**, the workflow would automatically recognize them if the file name has no suffix (eg. "sample1.fastq" instead of "sample1_R1.fastq"). However, mixing of single and paired-end files in the same folder is not supported currently.
+**For single-end FASTQ files**, the workflow automatically recognized single suffix (eg. "sample1.fastq" instead of "sample1_R1.fastq") as single-end reads. However, mixing of single and paired-end files in the same folder is not supported currently.
 
 Once the DNA-mapping run is finished sucessfully. We can run the ChIP-seq analysis in the same directory.
 

snakePipes.egg-info/PKG-INFO

@@ -0,0 +1,8 @@
+Metadata-Version: 2.1
+Name: snakePipes
+Version: 2.5.4
+Summary: Snakemake workflows and wrappers for NGS data processing from the MPI-IE
+Home-page: https://github.com/maxplanck-ie/snakepipes
+License: MIT
+Requires-Python: >=3.7
+License-File: LICENSE