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Fix relative path issue with paths in config #420

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Fix relative path issue with paths in config #420

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b842063
Fix relative path issue with paths in config
b-full Nov 14, 2024
715c849
Merge branch 'v1.12rc' into fix_config_paths
daler Jan 2, 2025
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8 changes: 4 additions & 4 deletions lib/common.py
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Original file line number Diff line number Diff line change
Expand Up @@ -64,13 +64,13 @@ def resolve_config(config, workdir=None):
if isinstance(config, str):
config = yaml.load(open(config), Loader=yaml.FullLoader)

def rel(pth):
if workdir is None or os.path.isabs(pth):
def abs_path(pth):
if os.path.isabs(pth):
return pth
return os.path.join(workdir, pth)
for key in PATH_KEYS:
if key in config:
config[key] = rel(config[key])
if key in config and workdir:
config[key] = abs_path(config[key])
return config


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6 changes: 3 additions & 3 deletions lib/patterns_targets.py
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Original file line number Diff line number Diff line change
Expand Up @@ -47,17 +47,17 @@ def __init__(self, config, patterns, workdir=None):
as relative to `workdir`
"""
self.path = None
self.workdir = '.'
self.workdir = None
if workdir is not None:
config = os.path.join(workdir, config)
patterns = os.path.join(workdir, patterns)
self.workdir = workdir

if isinstance(config, str):
self.path = config
config = os.path.join(workdir, config)

self.config = common.load_config(
common.resolve_config(config, workdir))
common.resolve_config(config, self.workdir))

stranded = self.config.get('stranded', None)
self.stranded = None
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4 changes: 3 additions & 1 deletion workflows/chipseq/Snakefile
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Original file line number Diff line number Diff line change
Expand Up @@ -10,6 +10,7 @@ import pybedtools
from lib import common, utils, helpers, aligners, chipseq
from lib.patterns_targets import ChIPSeqConfig
from lib.utils import autobump, gb, hours
from pathlib import Path

# ----------------------------------------------------------------------------
#
Expand All @@ -30,7 +31,8 @@ helpers.preflight(config)

c = ChIPSeqConfig(
config,
config.get('patterns', 'config/chipseq_patterns.yaml')
config.get('patterns', 'config/chipseq_patterns.yaml'),
Path('.').resolve()
)

SAMPLES = c.sampletable.iloc[:, 0].values
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3 changes: 2 additions & 1 deletion workflows/rnaseq/Snakefile
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Original file line number Diff line number Diff line change
Expand Up @@ -9,6 +9,7 @@ import pandas as pd
from lib import common, utils, helpers, aligners
from lib.utils import autobump, gb, hours
from lib.patterns_targets import RNASeqConfig
from pathlib import Path

# ----------------------------------------------------------------------------
#
Expand All @@ -27,7 +28,7 @@ include: '../references/Snakefile'
# Verify configuration of config and sampletable files
helpers.preflight(config)

c = RNASeqConfig(config, config.get('patterns', 'config/rnaseq_patterns.yaml'))
c = RNASeqConfig(config, config.get('patterns', 'config/rnaseq_patterns.yaml'), Path('.').resolve())

SAMPLES = c.sampletable.iloc[:, 0].values
wildcard_constraints:
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