now includes header in output
Now checks Experiment for ALIGNED_CONTROL. Old fastqs rm now does not exit if files are absent. Now uses run_system_cmd_no_retry for split
Now evals calling Aligner->run so we can process the error using throw_no_retry. Also added check_analysis_can_run as this is a link analysis
Moved input fastq removal to end, to prevent removing input before a possible job failure. This was causing problems when trying to rerun a job.
now resets dangling link analyses which have exited early and not run/dataflown
added run_system_cmd_no_retry. get_alignment_files_by_ResultSet_formats now checks for appropriate ALIGNED(_CONTROL) status. check_analysis_can_run fixed.
Now bypasses control alignment if it has already been done.
now sets run_controls dynamically based on presence of result_set_groups. Checks for appropriate ALIGNED(_CONTROL) status. Added no_tidy clause for bam file rm.
added chack_analysis_can_run as this is a link analysis