qc/pipeline: remove redundant imports.

Author: pjbriggs

auto_process_ngs/qc/pipeline.py

@@ -36,12 +36,8 @@
 import tempfile
 import shutil
 import random
-from bcftbx.JobRunner import SimpleJobRunner
 from bcftbx.FASTQFile import FastqIterator
-from bcftbx.TabFile import TabFile
 from bcftbx.utils import mkdir
-from bcftbx.utils import mkdirs
-from bcftbx.utils import find_program
 from bcftbx.ngsutils import getreads
 from bcftbx.ngsutils import getreads_subset
 from ..analysis import AnalysisFastq
@@ -57,10 +53,7 @@
 from ..pipeliner import PipelineParam as Param
 from ..pipeliner import ListParam
 from ..pipeliner import PipelineFailure
-from ..tenx.cellplex import CellrangerMultiConfigCsv
 from ..tenx.multiome import MultiomeLibraries
-from ..tenx.utils import add_cellranger_args
-from ..utils import get_organism_list
 from ..utils import normalise_organism_name
 from .modules.cellranger_atac_count import CellrangerAtacCount
 from .modules.cellranger_arc_count import CellrangerArcCount
@@ -75,8 +68,6 @@
 from .modules.rseqc_infer_experiment import RseqcInferExperiment
 from .modules.sequence_lengths import SequenceLengths
 from .modules.strandedness import Strandedness
-from .protocols import determine_qc_protocol
-from .protocols import fetch_protocol_definition
 from .protocols import parse_qc_module_spec
 from .reporting import report as reportqc
 from .utils import get_bam_basename