dragen v4.2.4

1. Use dragen v4.2.4 for demux and alignment
2. version 9 dragen hash table
3. Turn off data_transfer task in json

Replace RIS local docker registry images and fix a bug of filtering variants

1. Replace all RIS local docker registry images
2. Fix a bug of filtering variants that exist in prior cases but get ALT read count lower than threshold
3. Remove unneeded remove_rundir task and several redundant variables in workflow, set GenotypeVcf in analysis sub workflow
4. Update launcher.pl with new sample naming and X_Plus info_string

Fix a multiallelic site bug and change QC coverage threshold

1. Add "-m none" to bcftools merge command line to fix multlallelic variants
2. Lower average target alignment coverage from 4000 to 2500, Change metrics target bases > 2000x to > 1250x
3. Update launcher script and script paths in workflow.

Use dragen 4.0.3, demux setting change, remove strand bias filter, and other updates

1. Use dragen version 4.0.3
2. Change dragen demux setting to trim 1 base from 5' and 2 bases from 3'
3. Remove StrandBias filter
4. Add "--qc-coverage-ignore-overlaps true" to dragen align command
5. Add "-F x" to the bcftools merge command of MyeloseqHDAnalysis.wdl to preserves 'PASS' filter if one of the merged files has 'PASS'
6. Several updates for filterHaloplex.py (refer to https://jira.wustl.edu/browse/CI-934)
7. application.conf and WDL workflow updates to be compatible for dragen-3 and dragen-4

Update Coverage Bed and launcher.pl

1. Update coverage bed with different BRAF ensembl transcript ID and exon_15
2. Update launcher.pl to better handle exception columns and positive control samples.

Improve UMI collapsing, Add QC review status and others

1. Update dragen align command to correctly handle UMI collapse
2. Add QC review status, change several QC metrics thresholds and report these metrics accordingly
3. Check small demux_fastq size as sign of potential wrong index and stop the workflow
4. Make launcher.pl to use Illumina run folder and align input files on storage1 as dragen demux/align command inputs
5. Make launcher.pl to handle special cases of RESEQ, RESEARCH, NOTRANSFER properly
6. Remove unneeded output files from data_transfer

Drop freebayes, Update variant filtering, Include prior MRNs for DB querying

1. Remove freebayes from variant calling
2. Update filterHaloplex.py for better variant filtering
3. Include prior MRNs for query_DB task

Refer to https://jira.wustl.edu/browse/CI-779

Initial Release

This is the initial release of MyeloseqHD analysis wdl workflow.