v2.1.0

1. add task centrifuge
2. centrifuge can be run as a standalone wdl workflow as well: wf_centrifuge.wdl
3. modify bbduk wdl task to decontaminate for Ecoli and dermacoccus provided by new bbduk contamination database
4. switch to gatk 4.5.0.0: includes hardware acceleration and is significantly faster, changes described in https://github.com/broadinstitute/gatk/releases/tag/4.5.0.0
5. switch to dbest/varpipe4:v2.0.3: includes fix to coverage calculation described in CDCgov/NCHHSTP-DTBE-Varpipe-WGS#16
6. switch to the newest version for multiQC: v1.19
7. add standalone kraken2 wdl workflow: wf_kraken2.wdl

v2.0.5

Add task ptrimmer. This task trims off given primer sequences from input reads.

v2.0.4

Use read 2 from bbduk for read2 in clockwork decontamination.

v2.0.3

1. add task repair
2. add disk size and disk multiplier parameter to workflow
3. add disks to runtime of the tasks
   • bbduk,
   • clockwork decontamination,
   • trimmomatic,
   • varpipe

v2.0.2

1. add disk_size parameter, add disk_multiplier parameter
2. add dynamic calculation of disk size
3. add repair workflow, add repair workflow to beginning of varpipe workflow
4. handle error if structural variant calling by delly fails due to "Sample has not enough data to estimate library parameters"

v2.0.1

1. new docker image varpipe4 v2.0.1: fix QC log generation
2. new docker image snpEff v5.2a
3. switch order of clockwork decontamination and bbduk in read input to varpipe to make clockwork decontamination first

v2.0.0

1. Two new command line parameters
   -d DATABASE, --database DATABASE snpEff database, zip file
   -s SNPEFF_CONFIG, --snpEff_config SNPEFF_CONFIG snpEff config file
   snpEff database and config file not included in docker image starting with v2.0.0
   snpEff database and config file now external parameters
   Note:
   a) new snp_docker.config without snpEff.config
   b) new snp_cdc_docker.config without snpEff.config
2. New snpEff version: 5.1d --> 5.2a

v1.3.1

1. updated variant interpretation to produce laboratorian report
2. updates lims_report
3. added snpit for lineage calling

v1.3.0

Notes:

1. new varpipe docker to deal with CDC regions
2. add lineage task
3. add LIMS report
4. replace variant_interpretation task with interpretation workflow
5. interpretation workflow = variant_interpretation + lineage calling + LIMS report
6. replace delly task with structural variant workflow
7. structural variant workflow = task delly for large deletions + snpEff annotation of larget deletions
8. add concatenation task = concatenate vcf from variant caller and vcf from delly
9. use concatenated vcf for interpretation workflow
10. add snpit as additional lineage caller

v1.2.1

1. new version of variant_interpretation docker image: more robust handling of different gene lists and coverage, one row per chemical in output report
2. additional outputs from collect_targeted_pcr_metrics: theoretical sensitivity, target coverage