From 1c62310139ce92424276ea55751318a64a8538ab Mon Sep 17 00:00:00 2001 From: Diane Trout Date: Thu, 19 Jul 2012 11:14:29 -0700 Subject: [PATCH] Update save_raw_data to SampleKey api --- htsworkflow/pipelines/gerald.py | 5 ++++- htsworkflow/pipelines/runfolder.py | 2 +- 2 files changed, 5 insertions(+), 2 deletions(-) diff --git a/htsworkflow/pipelines/gerald.py b/htsworkflow/pipelines/gerald.py index eb37cc4..e0d84cf 100644 --- a/htsworkflow/pipelines/gerald.py +++ b/htsworkflow/pipelines/gerald.py @@ -439,7 +439,10 @@ class LaneSpecificRunParameters(collections.MutableMapping): if k.matches(lookup_key): results.append(k) if len(results) > 1: - raise ValueError("More than one key matched query %s" % (str(lookup_key),)) + errmsg = "Key %s matched multiple keys: %s" + raise ValueError(errmsg % (str(lookup_key), + ",".join((str(x) for x in results)))) + elif len(results) == 1: return results[0] else: diff --git a/htsworkflow/pipelines/runfolder.py b/htsworkflow/pipelines/runfolder.py index 1e46e17..67dc505 100644 --- a/htsworkflow/pipelines/runfolder.py +++ b/htsworkflow/pipelines/runfolder.py @@ -630,7 +630,7 @@ def extract_results(runs, output_base_dir=None, site="individual", num_jobs=1, r def save_raw_data(num_jobs, r, site, raw_format, cycle_dir): lanes = [] - for lane in range(1, 9): + for lane in r.gerald.lanes: lane_parameters = r.gerald.lanes.get(lane, None) if lane_parameters is not None and lane_parameters.analysis != 'none': lanes.append(lane) -- 2.30.2