Removes the strandedness QC module from all the protocols currently defined in the QC pipeline code, essentially dropping the use of fastq_strand.py for generating the strandedness metric. Instead the strand-specificity metric (generated from RSeQC's infer_experiment.py utility, which is always run when BAM files are produced) will be reported instead.
The intention is to optimise the pipeline by removing the extra computation required when running fastq_strand.py, hopefully making it faster and less resource hungry.
(Note that the functionality of the strandedness QC module is still in place so is available if required.)
Removes the
strandednessQC module from all the protocols currently defined in the QC pipeline code, essentially dropping the use offastq_strand.pyfor generating the strandedness metric. Instead the strand-specificity metric (generated from RSeQC'sinfer_experiment.pyutility, which is always run when BAM files are produced) will be reported instead.The intention is to optimise the pipeline by removing the extra computation required when running
fastq_strand.py, hopefully making it faster and less resource hungry.(Note that the functionality of the
strandednessQC module is still in place so is available if required.)Closes #890.