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fix: use relpath for configfiles added to the source archive (thanks to @sposadac for the initial solution) #3240

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merged 4 commits into from
Dec 23, 2024
Merged

fix: use relpath for configfiles added to the source archive (thanks to @sposadac for the initial solution) #3240

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da6f5c8
fix: use relpath for configfiles added to the source archive
johanneskoester Dec 23, 2024
bd13eb1
fix configfile arg
johanneskoester Dec 23, 2024
17a73da
fmt
johanneskoester Dec 23, 2024
ca32992
fix test
johanneskoester Dec 23, 2024
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fix: use relpath for configfiles added to the source archive
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@johanneskoester
johanneskoester committed Dec 23, 2024
commit da6f5c8313e00445294199f713164d04a1415897
2 changes: 1 addition & 1 deletion snakemake/dag.py
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Original file line number Diff line number Diff line change
Expand Up @@ -2907,7 2907,7 @@ def norm_rule_relpath(f, rule):
files.add(env_path)

for f in self.workflow.configfiles:
files.add(f)
files.add(os.path.relpath(f))

# get git-managed files
# TODO allow a manifest file as alternative
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8 changes: 6 additions & 2 deletions snakemake/workflow.py
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Expand Up @@ -295,8 295,12 @@ def get_files():
for f in self.dag.get_sources():
if f.startswith(".."):
logger.warning(
"Ignoring source file {}. Only files relative "
"to the working directory are allowed.".format(f)
f"Ignoring source file {f}! Only files relative "
"to the working directory are allowed. Most likely the "
"spawned jobs will not properly work. Make sure to start "
"the workflow from a directory below which all the sources "
"are located (may be in subfolders) and also ensure that any "
"config files you refer to are inside that directory."
)
continue

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