2GB for header job is too small
added LD_LIBRARY_PATH for bamindex command, sort the SAM after extracting using -L, as the original sorted order may not be maintained although the chance is close to zero
6GB should be enough
bump up smallJobMemM to 4000
added script launch monitor
Working on bai upload, metadata info in the xml like workflow version, and gtdownload thread number parameterization
Adding pipefail to steps
Merge branch 'feature/bam_slicer_improvements' into feature/brian_data_train_2.0_changes
changed default memory for small jobs to 4G, fix the issue: PANCANCER-42
added flag tryoq=1 for bamtofastq, PANCANCER-34
fix bad read name in bamtofastq step, PANCANCER-45
updated DESCRIPTION part to reference to submission SOP for input BAM preparation: PANCANCER-33
add piece of code to generate md5sum for the bai file in preparation of the upload
updated bwa version number, added markduplicates in the XML as one new PIPE_SECTION, JIRA: PANCANCER-39
prettified xml format in the ANALYSIS_ATTRIBUTE section, added biobambam version there as well
update the workflow version to 2.6.0 from 2.5.0, update PCAP-core to 1.1.1 in the pom.xml
update workflow.properties file to 2.6.0
updated pcap version biobambam version in workflow and gnos_upload_data.pl
added gtdownload options for: timeout and rate limit
change the default rate limit to very high 200, user can choice lowering it if needed