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
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:
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):