Merge pull request #505 from maxplanck-ie/snakemake_5.7

Snakemake 5.7
maxplanck-ie · Oct 10, 2019 · 86e20c4 · 86e20c4
2 parents 7504691 + b9bafec
commit 86e20c4
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Showing 16 changed files with 25 additions and 16 deletions.
diff --git a/azure-pipelines.yml b/azure-pipelines.yml
@@ -89,6 +89,7 @@ jobs:
     displayName: Add conda to PATH
   - bash: |
       if [ -f /Users/vsts/.conda/pkgs/urls.txt ]; then
+        echo "chown"
         sudo chown 501:20 /Users/vsts/.conda/pkgs/urls.txt
       fi
     displayName: Fix OSX permissions

diff --git a/conda-recipe/meta.yaml b/conda-recipe/meta.yaml
@@ -1,6 +1,6 @@
 package:
   name: snakepipes
-  version: 1.3.0
+  version: 1.3.1
 
 source:
   path: ../
@@ -14,7 +14,7 @@ requirements:
     - python >=3
   run:
     - python >=3
-    - snakemake >=5.2.3
+    - snakemake >=5.7
     - pandas
     - graphviz
     - fuzzywuzzy

diff --git a/docs/content/News.rst b/docs/content/News.rst
@@ -1,6 +1,11 @@
 snakePipes News
 ===============
 
+snakePipes 1.3.1
+----------------
+
+ * Support for snakeMake 5.7.0
+
 snakePipes 1.3.0
 ----------------
 

diff --git a/requirements.txt b/requirements.txt
@@ -1,4 +1,4 @@
-snakemake >= 5.2.3
+snakemake >= 5.7.0
 psutil
 pandas
 fuzzywuzzy

diff --git a/setup.py b/setup.py
@@ -10,12 +10,15 @@
 for d in glob('snakePipes/workflows/*'):
     scripts.append(os.path.join(d, os.path.split(d)[1]))
 
+requires = open("requirements.txt").read().strip().split("\n")
+
 setup(
     name='snakePipes',
     version=__version__,  # noqa: F821
     scripts=scripts,
     packages=find_packages(),
     include_package_data=True,
+    install_requires=requires,
     url='https://github.com/maxplanck-ie/snakepipes',
     license='MIT',
     description='Snakemake workflows and wrappers for NGS data processing from the MPI-IE',

diff --git a/snakePipes/__init__.py b/snakePipes/__init__.py
@@ -1 +1 @@
-__version__ = '1.3.0'
+__version__ = '1.3.1'
diff --git a/snakePipes/common_functions.py b/snakePipes/common_functions.py
@@ -49,15 +49,15 @@ def sanity_dict_clean(myDict):
     return myDict
 
 
-def load_configfile(configFile, verbose, info='Config'):
-    with open(configFile, "r") as f:
+def load_configfile(configFiles, verbose, info='Config'):
+    with open(configFiles, "r") as f:
         config = yaml.load(f, Loader=yaml.FullLoader)
 
     config = sanity_dict_clean(config)
 
     if verbose:
         print("\n--- " + info + " ---------------------------------------------------------------------")
-        print("config file: {}".format(configFile))
+        print("config file: {}".format(configFiles))
         for k, v in sorted(config.items()):
             print("{}: {}".format(k, v))
         print("-" * 80, "\n")

diff --git a/snakePipes/workflows/ATAC-seq/Snakefile b/snakePipes/workflows/ATAC-seq/Snakefile
@@ -11,7 +11,7 @@ workflow_rscripts=os.path.join(maindir, "shared", "rscripts")
 globals().update(cf.set_env_yamls())
 
 # load config file
-globals().update(cf.load_configfile(workflow.overwrite_configfile, config["verbose"]))
+globals().update(cf.load_configfile(workflow.overwrite_configfiles[0], config["verbose"]))
 # load organism-specific data, i.e. genome indices, annotation, etc.
 globals().update(cf.load_organism_data(genome, maindir, config["verbose"]))
 

diff --git a/snakePipes/workflows/ChIP-seq/Snakefile b/snakePipes/workflows/ChIP-seq/Snakefile
@@ -11,7 +11,7 @@ workflow_rscripts=os.path.join(maindir, "shared", "rscripts")
 globals().update(cf.set_env_yamls())
 
 # load config file
-globals().update(cf.load_configfile(workflow.overwrite_configfile, config["verbose"]))
+globals().update(cf.load_configfile(workflow.overwrite_configfiles[0], config["verbose"]))
 # load organism-specific data, i.e. genome indices, annotation, etc.
 globals().update(cf.load_organism_data(genome, maindir, config["verbose"]))
 

diff --git a/snakePipes/workflows/DNA-mapping/Snakefile b/snakePipes/workflows/DNA-mapping/Snakefile
@@ -8,7 +8,7 @@ maindir = os.path.dirname(os.path.dirname(workflow.basedir))
 globals().update(cf.set_env_yamls())
 
 # load config file
-globals().update(cf.load_configfile(workflow.overwrite_configfile, config["verbose"]))
+globals().update(cf.load_configfile(workflow.overwrite_configfiles[0], config["verbose"]))
 # load organism-specific data, i.e. genome indices, annotation, etc.
 globals().update(cf.load_organism_data(genome, maindir, config["verbose"]))
 

diff --git a/snakePipes/workflows/HiC/Snakefile b/snakePipes/workflows/HiC/Snakefile
@@ -9,7 +9,7 @@ maindir = os.path.dirname(os.path.dirname(workflow.basedir))
 globals().update(cf.set_env_yamls())
 
 # load config file
-globals().update(cf.load_configfile(workflow.overwrite_configfile, config["verbose"]))
+globals().update(cf.load_configfile(workflow.overwrite_configfiles[0], config["verbose"]))
 # load organism-specific data, i.e. genome indices, annotation, etc.
 globals().update(cf.load_organism_data(genome, maindir, config["verbose"]))
 

diff --git a/snakePipes/workflows/RNA-seq/Snakefile b/snakePipes/workflows/RNA-seq/Snakefile
@@ -9,7 +9,7 @@ maindir = os.path.dirname(os.path.dirname(workflow.basedir))
 globals().update(cf.set_env_yamls())
 
 # load config file
-globals().update(cf.load_configfile(workflow.overwrite_configfile, config["verbose"]))
+globals().update(cf.load_configfile(workflow.overwrite_configfiles[0], config["verbose"]))
 # load organism-specific data, i.e. genome indices, annotation, etc.
 globals().update(cf.load_organism_data(genome, maindir, config["verbose"]))
 

diff --git a/snakePipes/workflows/WGBS/Snakefile b/snakePipes/workflows/WGBS/Snakefile
@@ -15,7 +15,7 @@ workflow_rscripts=os.path.join(maindir, "shared", "rscripts")
 globals().update(cf.set_env_yamls())
 
 # load config file
-globals().update(cf.load_configfile(workflow.overwrite_configfile, config["verbose"]))
+globals().update(cf.load_configfile(workflow.overwrite_configfiles[0], config["verbose"]))
 # load organism-specific data, i.e. genome indices, annotation, etc.
 globals().update(cf.load_organism_data(genome, maindir, config["verbose"]))
 

diff --git a/snakePipes/workflows/createIndices/Snakefile b/snakePipes/workflows/createIndices/Snakefile
@@ -8,7 +8,7 @@ maindir = os.path.dirname(os.path.dirname(workflow.basedir))
 globals().update(cf.set_env_yamls())
 
 # load config file
-globals().update(cf.load_configfile(workflow.overwrite_configfile, config["verbose"]))
+globals().update(cf.load_configfile(workflow.overwrite_configfiles[0], config["verbose"]))
 
 ### include modules of other snakefiles ########################################
 ################################################################################

diff --git a/snakePipes/workflows/preprocessing/Snakefile b/snakePipes/workflows/preprocessing/Snakefile
@@ -9,7 +9,7 @@ maindir = os.path.dirname(os.path.dirname(workflow.basedir))
 globals().update(cf.set_env_yamls())
 
 # load config file
-globals().update(cf.load_configfile(workflow.overwrite_configfile, config["verbose"]))
+globals().update(cf.load_configfile(workflow.overwrite_configfiles[0], config["verbose"]))
 
 # do workflow specific stuff now
 include: os.path.join(workflow.basedir, "internals.snakefile")

diff --git a/snakePipes/workflows/scRNAseq/Snakefile b/snakePipes/workflows/scRNAseq/Snakefile
@@ -9,7 +9,7 @@ workflow_rscripts=os.path.join(maindir, "shared", "rscripts")
 globals().update(cf.set_env_yamls())
 
 # load config file
-globals().update(cf.load_configfile(workflow.overwrite_configfile, config["verbose"]))
+globals().update(cf.load_configfile(workflow.overwrite_configfiles[0], config["verbose"]))
 # load organism-specific data, i.e. genome indices, annotation, etc.
 globals().update(cf.load_organism_data(genome, maindir, config["verbose"]))