the filename templates were moved from condorfastq to fastqname a while ago

[htsworkflow.git] / htsworkflow / submission / condorfastq.py

diff --git a/htsworkflow/submission/condorfastq.py b/htsworkflow/submission/condorfastq.py
index 17e463351282b7b8091f922760e8b1fd69a2c934..b6c22348f581f5148eeaa33cacfafe65f6ebc963 100644 (file)
--- a/htsworkflow/submission/condorfastq.py
+++ b/htsworkflow/submission/condorfastq.py
@@ -16,7 +16,7 @@ from htsworkflow.pipelines import desplit_fastq
 from htsworkflow.submission.fastqname import FastqName
 from htsworkflow.util.rdfhelp import get_model, dump_model, load_into_model, \
      fromTypedNode, \
-     stripNamespace
+     strip_namespace
 from htsworkflow.util.rdfns import *
 from htsworkflow.util.conversion import parse_flowcell_id
 
@@ -220,8 +220,6 @@ WHERE {
         Also update model with link between illumina result files
         and our target fastq file.
         """
-        fastq_paired_template = '%(lib_id)s_%(flowcell)s_c%(cycle)s_l%(lane)s_r%(read)s.fastq'
-        fastq_single_template = '%(lib_id)s_%(flowcell)s_c%(cycle)s_l%(lane)s.fastq'
         # find what targets we're missing
         needed_targets = {}
         for seq in raw_files:
@@ -347,7 +345,7 @@ class SequenceResult(object):
     ispaired = property(_get_ispaired)
 
     def _get_filetype(self):
-        return stripNamespace(libraryOntology, self._filetype)
+        return strip_namespace(libraryOntology, self._filetype)
     filetype = property(_get_filetype)
 
     def _get_path(self):