From b842063c9332a347d7a6d17acc01e8238fff1c65 Mon Sep 17 00:00:00 2001
From: Brandon Fuller <brandonfuller007@gmail.com>
Date: Thu, 14 Nov 2024 13:54:04 -0500
Subject: [PATCH] Fix relative path issue with paths in config

Make it so that all of the paths in config are absolute paths, which
fixes the issue of relative paths breaking when running from a different
directory, i.e. when running unit tests from the test/ directory
---
 lib/common.py               | 8 ++++----
 lib/patterns_targets.py     | 6 +++---
 workflows/chipseq/Snakefile | 4 +++-
 workflows/rnaseq/Snakefile  | 3 ++-
 4 files changed, 12 insertions(+), 9 deletions(-)

diff --git a/lib/common.py b/lib/common.py
index 829cc129..13286298 100644
--- a/lib/common.py
+++ b/lib/common.py
@@ -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
 
 
diff --git a/lib/patterns_targets.py b/lib/patterns_targets.py
index 542d4116..7cca01f7 100644
--- a/lib/patterns_targets.py
+++ b/lib/patterns_targets.py
@@ -46,17 +46,17 @@ 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
diff --git a/workflows/chipseq/Snakefile b/workflows/chipseq/Snakefile
index 90c84d28..a182fe2b 100644
--- a/workflows/chipseq/Snakefile
+++ b/workflows/chipseq/Snakefile
@@ -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
 
 # ----------------------------------------------------------------------------
 #
@@ -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
diff --git a/workflows/rnaseq/Snakefile b/workflows/rnaseq/Snakefile
index 1cde537a..f324b30b 100644
--- a/workflows/rnaseq/Snakefile
+++ b/workflows/rnaseq/Snakefile
@@ -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
 
 # ----------------------------------------------------------------------------
 #
@@ -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: