Merge branch 'master' of mus.cacr.caltech.edu:htsworkflow

[htsworkflow.git] / htsworkflow / pipelines / runfolder.py

diff --git a/htsworkflow/pipelines/runfolder.py b/htsworkflow/pipelines/runfolder.py
index 4a2b4cdc3704fccb1b7fbdd5f48211c86851b6c4..3389c2d9ab8ad6f3ffc4b2378c0c8fcd7ff8139a 100644 (file)
--- a/htsworkflow/pipelines/runfolder.py
+++ b/htsworkflow/pipelines/runfolder.py
@@ -555,7 +555,10 @@ def extract_results(runs, output_base_dir=None, site="individual", num_jobs=1, r
             lanes.append(lane)
 
         run_name = srf.pathname_to_run_name(r.pathname)
-        if raw_format == 'qseq':
+        seq_cmds = []
+        if raw_format == 'fastq':
+            srf.copy_hiseq_project_fastqs(run_name, r.bustard.pathname, site, cycle_dir)
+        elif raw_format == 'qseq':
             seq_cmds = srf.make_qseq_commands(run_name, r.bustard.pathname, lanes, site, cycle_dir)
         elif raw_format == 'srf':
             seq_cmds = srf.make_srf_commands(run_name, r.bustard.pathname, lanes, site, cycle_dir, 0)