nf-core · sven1103 · Dec 3, 2018 · Dec 3, 2018 · Dec 3, 2018
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -1,6 +1,8 @@
 # nf-core/tools: Changelog
 
 ## v1.4dev
+
+#### Template pipeline
 * Institutional custom config profiles moved to github `nf-core/configs`
     * These will now be maintained centrally as opposed to being shipped with the pipelines in `conf/`
     * Load `base.config` by default for all profiles
@@ -9,8 +11,11 @@
     * Added parameter `--custom_config_version` for custom config version control. Can use this parameter to provide commit id for reproducibility. Defaults to `master`  
     * Deleted custom configs from template in `conf/` directory i.e. `uzh.config`, `binac.config` and `cfc.config`
 * Added `local.md` to cookiecutter template in `docs/configuration/`. This was referenced in `README.md` but not present.
+* Major overhaul of docs to add/remove parameters, unify linking of files and added description for providing custom configs where necessary
+
+#### Tools helper code
 * Make Travis CI tests fail on pull requests if the `CHANGELOG.md` file hasn't been updated
-* Major overhaul of docs to add/remove parameters, unify linking of files and added description for providing custom contigs where necessary
+* Minor bugfixing in Python code (eg. removing unused import statements)
 
 ## [v1.3](https://github.com/nf-core/tools/releases/tag/1.3) - 2018-11-21
 * `nf-core create` command line interface updated

diff --git a/bin/sync b/bin/sync
@@ -1,15 +1,10 @@
 #!/usr/bin/env python
 
-from cookiecutter.main import cookiecutter
-import git
 import json
 import os
 import requests
 from requests.auth import HTTPBasicAuth
-import shutil
 import sys
-import subprocess
-import tempfile
 import syncutils.template
 
 # Set the default nf-core pipeline template branch
@@ -53,7 +48,7 @@ def main():
     pipelines = res.json().get('remote_workflows')
     if not pipelines:
         print("Pipeline information was empty!")
-    
+
     # TODO: Remove this line, once we go for production
     pipelines = [
         {
@@ -82,21 +77,20 @@ def main():
         else:
             print("Created pull-request for pipeline \'{pipeline}\' successfully."
                 .format(pipeline=pipeline["name"]))
-    
+
     for pipeline, exception in sync_errors:
         print("Sync for pipeline {name} failed.".format(name=pipeline))
         print(exception)
 
     for pipeline, return_code, content in pr_errors:
-        print("Pull-request for pipeline \'{pipeline}\' failed," 
+        print("Pull-request for pipeline \'{pipeline}\' failed,"
                 " got return code {return_code}."
                 .format(pipeline=pipeline, return_code=return_code))
         print(content)
-    
+
     if pr_errors or sync_errors: sys.exit(1)
-    
+
     sys.exit(0)
-            
+
 if __name__ == "__main__":
     main()
-
diff --git a/bin/syncutils/template.py b/bin/syncutils/template.py
@@ -3,8 +3,6 @@
 import git
 import os
 import shutil
-import sys
-from cookiecutter.main import cookiecutter
 
 import nf_core.create
 
@@ -29,7 +27,7 @@ def __init__(self, pipeline, branch=TEMPLATE_BRANCH, repo_url=""):
         self.templatedir = tempfile.mkdtemp()
         self.repo = git.Repo.clone_from(self.repo_url, self.tmpdir)
         assert self.repo
-    
+
     def sync(self):
         """Execute the template update.
         """
@@ -49,7 +47,7 @@ def context_from_nextflow(self, nf_project_dir):
 
         # Fetch the config variables from the Nextflow pipeline
         config = utils.fetch_wf_config(wf_path=nf_project_dir)
-        
+
         # Checkout again to configured template branch
         self.repo.git.checkout("origin/{branch}".format(branch=self.branch),
             b="{branch}".format(branch=self.branch))

diff --git a/nf_core/create.py b/nf_core/create.py
@@ -9,7 +9,6 @@
 import git
 import logging
 import os
-import re
 import shutil
 import sys
 import tempfile

diff --git a/nf_core/download.py b/nf_core/download.py
@@ -8,7 +8,6 @@
 import logging
 import hashlib
 import os
-import re
 import requests
 import requests_cache
 import subprocess
@@ -77,8 +76,8 @@ def download_workflow(self):
                         self.pull_singularity_image(container)
 
     def fetch_workflow_details(self, wfs):
-        """ Fetch details of nf-core workflow to download 
-        
+        """ Fetch details of nf-core workflow to download
+
         params:
         - wfs   A nf_core.list.Workflows object
         """

diff --git a/nf_core/lint.py b/nf_core/lint.py
@@ -11,7 +11,6 @@
 import os
 import re
 import shlex
-import subprocess
 import tempfile
 
 import click

diff --git a/nf_core/utils.py b/nf_core/utils.py
@@ -3,7 +3,6 @@
 Common utility functions for the nf-core python package.
 """
 
-import logging
 import os
 import subprocess