It seems that the way can_run method of rna autoqc check method is, in many cases the check will be submited to LSF for execution for non-tophat alignment. At run time the check will detect this (by examining the bam file header) and exit early without any error. The advantage of this approach is that the check does not implement its own logic about applicability of the rna analisis. The drawback is that a json file will be present. This json file will be archived. The SeqQC viewer will render it unnecessary.
Th elogin about what type of alignment is being performed is in npg_pipeline::archive::file::generation::seq_alignment. It would be logical to conditionally invoke a qc script for rna analysis there.
mgcam
commented
7 years ago
It seems that the way can_run method of rna autoqc check method is, in many cases the check will be submited to LSF for execution for non-tophat alignment. At run time the check will detect this (by examining the bam file header) and exit early without any error. The advantage of this approach is that the check does not implement its own logic about applicability of the rna analisis. The drawback is that a json file will be present. This json file will be archived. The SeqQC viewer will render it unnecessary.
Th elogin about what type of alignment is being performed is in npg_pipeline::archive::file::generation::seq_alignment. It would be logical to conditionally invoke a qc script for rna analysis there.