Make a sample key list to go along with our lane list

At some point I had to add the sample key which could link
lane, library and index together. Some code know expects that
class so I needed to create a "standard" list and pass it in.

diff --git a/htsworkflow/pipelines/runfolder.py b/htsworkflow/pipelines/runfolder.py
index 5d1e16bce460da443da7bebea56220e388770c88..7c06e217de63d5733e524ae551f06eea40528e11 100644 (file)
--- a/htsworkflow/pipelines/runfolder.py
+++ b/htsworkflow/pipelines/runfolder.py
@@ -21,6 +21,7 @@ from htsworkflow.pipelines import ElementTree, \
                                   EUROPEAN_STRPTIME, EUROPEAN_DATE_RE, \
                                   VERSION_RE, USER_RE, \
                                   LANES_PER_FLOWCELL, LANE_LIST
+from htsworkflow.pipelines.samplekey import LANE_SAMPLE_KEYS
 from htsworkflow.util.alphanum import alphanum
 from htsworkflow.util.ethelp import indent, flatten
 from htsworkflow.util.queuecommands import QueueCommands
@@ -753,7 +754,7 @@ def save_raw_data(num_jobs, r, site, raw_format, run_dirname):
                 lanes.append(lane)
     else:
         # assume default list of lanes
-        lanes = LANE_LIST
+        lanes = LANE_SAMPLE_KEYS
 
     run_name = srf.pathname_to_run_name(r.pathname)
     seq_cmds = []

diff --git a/htsworkflow/pipelines/samplekey.py b/htsworkflow/pipelines/samplekey.py
index 0ff6c31fbbb918f4f516150130abde0986c41fdd..60c2dbb1662c2ff660d60083c807cb173ae21a38 100644 (file)
--- a/htsworkflow/pipelines/samplekey.py
+++ b/htsworkflow/pipelines/samplekey.py
@@ -1,3 +1,5 @@
+from htsworkflow.pipelines import LANE_LIST
+
 class SampleKey(object):
     """Identifier for a sample in a particular 'location' on a flowcell.
     """
@@ -72,3 +74,4 @@ class SampleKey(object):
 
         return '<SampleKey(' + ",".join(name) + ')>'
 
+LANE_SAMPLE_KEYS = [ SampleKey(lane=l) for l in LANE_LIST ]
\ No newline at end of file