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Corrects some syncing behaviour #307

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Merged
sven1103 merged 6 commits into from
Apr 10, 2019
Merged

Corrects some syncing behaviour #307

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4ab80b8
Merge pull request #305 from nf-core/dev
sven1103 Apr 9, 2019
c6deebe
Corrects blacklist filtering
sven1103 Apr 9, 2019
b807637
Uses meta information from dev branch instead of master
sven1103 Apr 9, 2019
8e32e69
Enables single pipeline sync via command line
sven1103 Apr 9, 2019
ef8d987
Updates changelog
sven1103 Apr 9, 2019
adce02e
Corrects markdown error
sven1103 Apr 10, 2019
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5 changes: 5 additions & 0 deletions CHANGELOG.md
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Original file line number Diff line number Diff line change
@@ -1,5 +1,10 @@
# nf-core/tools: Changelog

## v1.7dev

#### Syncing
* Can now sync a targeted pipeline via command-line

## v1.6

#### Syncing
Expand Down
8 changes: 6 additions & 2 deletions bin/sync
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Original file line number Diff line number Diff line change
Expand Up @@ -55,7 +55,7 @@ def filter_blacklisted_pipelines_from_list(pipelines, blacklisted_pipelines):
def fetch_black_listed_pipelines_from_file(file_path):
with open(file_path) as fh:
blacklist = json.load(fh)
return blacklist
return blacklist.get('pipelines')


def fetch_nfcore_workflows_from_website(url):
Expand Down Expand Up @@ -100,7 +100,11 @@ def main():

pipelines = fetch_nfcore_workflows_from_website(NF_CORE_PIPELINE_INFO)

filtered_pipelines = filter_blacklisted_pipelines_from_list(pipelines, blacklisted_pipeline_names)
if len(sys.argv) > 1:
pipeline_to_sync = sys.argv[1]
filtered_pipelines = [pipeline for pipeline in pipelines if pipeline_to_sync in pipeline.get('name')]
else:
filtered_pipelines = filter_blacklisted_pipelines_from_list(pipelines, blacklisted_pipeline_names)

for pipeline in filtered_pipelines:
print("Update template branch for pipeline '{pipeline}'... ".format(pipeline=pipeline['name']))
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6 changes: 2 additions & 4 deletions bin/syncutils/template.py
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Original file line number Diff line number Diff line change
Expand Up @@ -42,8 +42,8 @@ def context_from_nextflow(self, nf_project_dir):
Returns: A cookiecutter-readable context (Python dictionary)
"""
# Check if we are on "master" (main pipeline code)
if self.repo.active_branch.name != "master":
self.repo.git.checkout("origin/master", b="master")
if self.repo.active_branch.name != "dev":
self.repo.git.checkout("origin/dev", b="dev")

# Fetch the config variables from the Nextflow pipeline
config = utils.fetch_wf_config(wf_path=nf_project_dir)
Expand All @@ -66,8 +66,6 @@ def update_child_template(self, templatedir, target_dir, context=None):
shutil.rmtree(os.path.join(target_dir, f))
except:
os.remove(os.path.join(target_dir, f))
print(target_dir)
print(context.get('author'))
# Create the new template structure
nf_core.create.PipelineCreate(
name=context.get('pipeline_name'),
Expand Down