Merge branch 'feature/brian_bionimbus_bwa_improvements' into feature/junjun_add_qc
added bam_stats qc step to the workflow
fix command line argument for bam_stats.pl job, also added a pcapPath variable so that the path can be changed easily
fix the input file name for qc step
Merge branch 'feature/brian_bionimbus_bwa_improvements' into feature/junjun_add_qc
added pre-compiled PCAP core 0.3.0 with bam_stats.pl included
added code in gnos_upload_data.pl for collecting qc result and add in analysis.xml file
minor correction in comment
upgrade PCAP core to 1.0.0 which officially supports bam_stats.pl
minor change to the qc_metrics JSON structure
Merge branch 'feature/brian_bionimbus_bwa_improvements' into feature/junjun_add_qc
Merge branch 'feature/brian_bionimbus_bwa_improvements' into feature/junjun_add_qc
Working on the 2.2 version of the workflow, including cleanup code after each step, refactoring the loops, and a few more tweaks
I think this will produce JSON now, still need to test
Just updating the description text and version numbers
A few more changes to title
Working on updated config that points to newer sample data
Trying to model deps better
Adding some missing perl libs
Turning off cleanup while testing Junjun's QC tool