Sample location (#31)

* Manually merged master and sample_location branch.

* Fixed a bug causing pipelines without samples to fail.

docs/conf.py

@@ -26,7 +26,7 @@
 # The short X.Y version
 version = u''
 # The full version, including alpha/beta/rc tags
-release = u'0.9.1'
+release = u'0.9.2'
 
 
 # -- General configuration ---------------------------------------------------

snakelines.snake

@@ -1,4 +1,4 @@
-SNAKELINES_VERSION = '0.9.1'
+SNAKELINES_VERSION = '0.9.2'
 
 import os
 import sys

src/common.snake

@@ -26,15 +26,19 @@ for sample_configuration in sample_configurations:
     # Filter samples according to the user configuration
     samples = []
     if 'name' in sample_configuration:
-        wildcards = glob_wildcards('reads/original/{sample, %s}_R1.fastq.gz' % sample_configuration['name'])
-        assert len(wildcards.sample) > 0, 'No samples in reads/original/ match configured pattern {}'.format(sample_configuration['name'])
+        location = sample_configuration.get('location', DEFAULT_SAMPLE_LOCATION)
+        location = location.replace('{}', '{sample, %s}' % sample_configuration['name'])
+        wildcards = glob_wildcards(location)
         samples = wildcards.sample
+        assert len(wildcards.sample) > 0, 'No samples in {} match configured pattern {}'.format(location, sample_configuration['name'])
+
 
     reference = sample_configuration.get('reference', None)
-    pipeline.add(samples, reference,
-                 sample_configuration.get('panel', None),
-                 sample_configuration.get('prebuilt', False),
-                 bool(extract_from_config(config, ['reference', 'download', reference], [])))
+    pipeline.add(samples,
+                reference,
+                sample_configuration.get('panel', None),
+                sample_configuration.get('prebuilt', False),
+                bool(extract_from_config(config, ['reference', 'download', reference], [])))
 
 if pipeline.is_empty():
     print('No samples to analyse', file=sys.stderr)