0.16.0

Changelog

#334 Revise LOHHLA
#336 BCFtools filter vcf edit
#338 Hotfix 0.15.1
#341 Change tags
#342 Germline postprocess maf
#344 Add neoantigen
#347 Install ps in LOHHLA Dockerfile
#348 Bugfix - facets
#349 Revise sigfit Dockerfile
#350 NF Aesthetics
#353 Uniform VEP version
#354 Fix facets PNG channel
#355 Bugfix - WGS regions index
#358 Fix maf anno
#364 Bugfix - Unique Channel Names
#396 Correct reference channel input names

0.15.0

Changelog

#331 Megatron tsv files
#329 Fixed lohhla dockerfile
#326 revise neoantigen Docker image
#314 neoantigen-dev and NetMHCpan Dockerfiles
#320 Fixed vcf2maf Dockerfile

0.14.1

Changelog

Fix references config for missing gnomadWgsVcf file
#321 Add missing resources

0.14.0

Changelog

#308 - Finalizing somatic maf
#306 - Validation for pairing file
#303 - Configurations for scaling issues
#305 - Fix grouping Tumor Normal samples
#309 - Fix process name for Polysolver
#296 - Mutational signatures

0.13.1

Revised juno.config to not include SLA for bsub as the default: #301

0.13.0

Changelog

#278 Small changes to the README.md
#288 Fix delly container
#290 Update container facets suite 1.5.7

0.12.0

Changelog

#262 Generate make_bam_output.tsv outside of process
#263 Fixed grouping for somatic pipeline, added new test files for travis tests
#264 Fixed grouping for germline.nf
#265 Combine make_bam_and_qc.nf, somatic.nf, and germline.nf into one pipeline.nf
#268 add GetBaseCountsMultiSample Dockerfile
#272 Pipefail
#274 Updated comments for pipeline.nf; source code readability
#275 Feature/error_handling

0.11.0

Changelog

#229 - add --rm-dups in vcf combine
#248 - full run TSV files
#245 - thread pool reached the limit error
#228 - Implementation of panel of normal (PoN) annotation of somatic SNVs/indels
#252 - add maxParallelTransfers to solve #128

0.10.1

Changelog

Hotfix Conpair resources and output

0.10.0

Changelog

#208 - Added headers in input tsv files
#218 - Pipeline scripts which connects pipeline steps
#220 - Resource config changes
#214 - Update germline bcftools
#211 - Subdirectories for make_bam_and_qc.nf
#203 - Genome config based on assay type