1.2.0

1. Re-organize the result and DAG representation enhancement #707
2. Re-positioning processes to more proper place #717
3. Avoid duplicated normal runs #718
4. check for identical fastq files and fix groovy exit function #721
5. remove unused facets output and change result directory name #719
6. Bugfix/neoantigen truncating maf #722
7. Bugfix/fix lohhla naming addresses #711 with some simple sed/mv action #723
8. Bugfix/facets labels #724
9. bugfix facets_seg_and_neoantigen_txt #725
10. add SomaticAggregateLOHHLA and fix germline final maf #726
11. conpair Duplicate when 1 normal used many times #727
12. QC Duplicate when 1 normal used many times #728
13. Fix sample name was dropped from an input file for LOHHLA resultin in partial outputs #731
14. Add --somatic, --germline, --QC, --aggregate and build aggregation entry point so that standalone aggregation can be done on a group of structured T/N sample results, Disable --QC by default #729
15. Enable --mapping [tsv] only (no --pairing [tsv]) as input for BAM generation and BAM QC, removed --bamPairing [tsv] parameter and replaced by --bamMapping [tsv] + --pairing [tsv] for doing somatic/germline/qc starting from BAM #740
16. Comprehensive checks for inputs #743
17. Bugfix/small grch37 reference path #746
18. Feature/check duplicate files #747
19. Bugfix/lohhla 1.1.4 #748, solving two bugs mentioned in #658
20. Fix AWS support previously broke by using groovy file I/O for fastq content checking
21. Make the check for same read groups within sample and the check for unique fastq read names across samples compatible with the above change in bullet 21. #745
22. Documentation update #750

1.1.0

Changelog

Feature/fix_DAG #685
feature/normalNoWaitForTumor #698
feature/removeAssayFromInput #699
bugfix QcConpairAll and QcAlfred #701
feature/update-docs #710
Bugfix FACETS PNG output #716

Parameter name change: --bam_pairing to --bamPairing, --conpair_all to --conpairAll
Required Nextflow version advanced from 19.07.0 to 19.10.0, just for DAG generation

1.0.3

Merge pull request #705 from mskcc/bugfix/facets_TN_swap

bugfix/facets_TN_swap

1.0.2

Adding a unit-less number to the memory settings that have a unit does not work. #697

1.0.1

Changelog

feature/sparkRetryMem #677
Minor documentation change, specify where filter cutoffs are #678
Fix travis badge token #679
Wrong output from Facets annotation of somatic MAF #681
correct mafSize #682

1.0.0

Merge pull request #676 from mskcc/develop

Release 1.0.0

0.19.1

Changelog

#500 Adding accidentally-deleted book.json

0.19.0

Changelog

#482 Documentation updates
#483 Bugfix: Manta VCF
#409 Revise Dockerfile for facets-htstools
#420 Accept BAM as input for pipeline.nf
#486 Group QCs
#487 Bam output directory
#484 Add publishAll output flag
#490 Removed NetMHCPan resource
#491 Fixed bug in RecalibrateBam
#481 Merge VCFs (SomaticAggregate, GermlineAggregate)
#489 Bugfix: Concat SV VCFs
#488 Change FACETS suite version and container

0.16.2

Changelog

#436: Proper output channel in RunPolysolver

0.16.1

Changelog

#431: Fixed paths in SomaticVcf2Maf process.