0.9.0

Changelog

#140 - Implement Conpair
#178 - Update SNV Indel Merge
#75 - Changed config for AWS Batch (require nextflow version 19.05.0)
#195 - Non blocking merge in make_bam_and_qc
#185 - Added isoforms and removed vcf2mafFilterVcf for vcf2maf process

0.8.1

CHANGELOG:

• make_bam_and_qc.nf
Hotfix bam merge step, and improve test to cover both cases, when merge is necessary and when it is not

0.8.0

Improvements and tests

#116 somatic-test: msisensor
#157 Modify Nextflow Trace Setting to get detailed run report

Pipeline Adjustments

make_bam_and_qc.nf
#61 Purge Sarek legacy code
#161 Change make_bam to accept new input format
#162 Implement output of make_bam_and_qc step to be the input for somatic

somatic.nf
#58 Mutational Signatures: create a Docker image for this, and push to Dockerhub
#137 HLA-LOH: Dockerize LOHHLA
#168 Make new bcftools container with ps command
#46 Implement interval file usage
#145 Add callRegions for manta/strelka2
#139 Dockerize Conpair
#146 Add file exclusions for delly
germline.nf
#46 Implement interval file usage
#145 Add callRegions for manta/strelka2

0.7.0

Bug Fixes and QOL Changes

#148 WES samples text file used as input cleaned up
#149 Vcf2Maf container updated to most recent version; improves compatibility with Strelka2
#99 Germline variant calling added to pipeline chart
#142 Concluded initial testing of MarkDuplicates and Samblaster

Pipeline Adjustments

make_bam_and_qc.nf
#144 Adjustments made for MarkDuplicates step

somatic.nf
#132 Added vcf merge for SV variant callers Delly and Manta

germline.nf
#121 Delly
#122 Manta
#135 Strelka2
#147 Merge Manta and Delly VCFs into one using BCFTools
#120 HaplotypeCaller
#150 Merge HaplotypeCaller and Strelka2 output into one MAF using BCFTools and Vcf2Maf

0.6.0

CHANGELOG:

#56 - Performance Enhancement for BAM preprocessing
#54 - Implement Mark Duplicates before and after the merging of BAMs
#90 - HLA Polysolver
#109 - Somatic-test: Implement for delly, manta, and strelka2
#49 - Define sample sheet and pairing design
#92 - Make more informative travis-CI tests
#110 - Remove Lumpy from WES pipeline
#95 - simplify and format the .config files

0.5.0

CHANGELOG:

#88 - refactor mutect2
#87 - fix tag on gatk docker images
#86 - remove makeSampleFIle process
#83 - added Alfred Dockerfile
#82 - fix permissions for EC2 Role
#69 - vcf2maf
#72 - fix Delly
#77 - change Alfred to do both types of bam QCs
#25 - Fastp and Alfred finalized

0.4.0

Changelog:

#14 - BCF merge
#15 - BCF normal
#50 - Fix RG in BAM
#51 - Pipe bwa mem to view
#67 - Autoscaling EBS
#71 - Implement Alfred for BAM QC

0.3.0

CHANGELOG:

#8 - Setup Travis
#27 - interval bed for mutect2
#28 - Refactor containers.config
#37 - corrected sample sheets
#39 - MarkDuplicates remove generating index file

0.2.0

CHANGELOG:

#10 - Create AWS setup environment script
#12 - MSI sensor
#13 - Lumpyexpress
#16 - filtermutect2calls

0.1.0

CHANGELOG:

make_bam_and_qc.nf script (bwa-mem, samtools view, samtools sort, gatk markduplicates, gatk baserecalibrator, gatk applybqsr)
somatic.nf script (delly call, delly filter, snppileup, facets, manta, strelka, mutect2)
config files for aws and lsf (juno)