1.4.4

Hotfix includes merged PR #990

1.4.3

1. Updated oncokb base url from oncokb.org to https://legacy.oncokb.org/api/v1 to accommodate recent oncokb api change.

• SomaticAnnotateMaf and GermlineAnnotateMaf are affected.

2. Bugfix for BRCA Exchange Variants annotation for GermlineAnnotateMaf.
3. Change combine and pairing strategies for Qualimap channels for input to SomaticMultiQC to avoid memory leak issues.

1.4.2

1. #923 Bugfixes and enhancements for QC reporting
2. #919 Bugfix in maf filtering step
3. #925 Updated fastq paths in multiple test_inputs files as previous fastq paths are no longer valid.

1.4.1

Hotfix/1.4 official #914

1. Replaced Polysolver's hard-coded genome parameter with dynamically set parameter.
2. Bugfix in CreateScatteredInterval for genome mode.
3. Bugfix in check of input file targets.
4. Updates in documentation

1.4

1. Enhancement/multiqc format and plot improvements #844
2. bugfix/aggregate bam statistics #846
3. enhancement/write cache and memory management for Qualimap and Facets #857
4. enhancement: Use new neoantigen docker #869
5. Bugfix/parsealfred genome #871
6. bugfix/parsing read number in fastq file #865
7. Enhancement/improve watch detection #858
8. bugfix/aggregate_from_path #873
9. bugfix/lable_AggregateLOHHLA #872
10. bugfix: corrected reference files for knownIndels and knownIndelsIndex #878
11. Enhancement/combine MergeBams and MarkDuplicates #875
12. bugfix: changed checkParamReturnFile method #879
13. bugfix: handled absence of fastp results in multiqc processes #882
14. Enhancement: combine bqsr processes into one #877
15. Bugfix/filter strandbias #908
16. Enhancement/unfiltered vcf #907
17. Custom targets Custom targets #902

1.3.4

1. Fixed mapping files megatron list for samples to make them consistent with LIMS and IGO endpoint #810
2. Added facets qc and use a formal facets-preview container now. #822
3. Enhancements to multiqc report #823
4. Qualimap added to the QC module and multiqc report #824
5. Bugfixing #829 Double memory increase after second time failure for MsiSensor #830
6. Bugfixing in process SomaticCombineChannel #828
7. Bugfixing: for #658 llohhla error cathing #836
8. Bugfixing: modify SomaticCombineChannel and genome RunMsiSensor 4th try mem #839
9. Enhancement: rearrange facets dockers #835
10. Enhanbcement: tempoSig optional cosmic signature reference version #837

1.3.3

Bugfix/Fix multiple input channels in single process for aggregate #817

1.3.2

1. Bugfix/scrawny maf handling #809
2. Bugfix/lohhla output #803
3. Bugfix/tempoSig single-variant error handling #805
4. Bugfix/add TERM to catch #800
5. Bugfix/facetsSuite_2.0.8_update #793
6. Bugfix/scrawny maf handling in neoantigen #812
7. Bugfix/handling all homozygous or no suitable HLA and in lohhla #813
8. Feature/multiqc QC report #808
9. Bugfix/change columns for facetsSuite 2.x gene level aggregate #815

1.3.1

1. Add wall time tiers and more wall time exit code #795
2. Feature/qc result reorganize #796
3. parameterize LOHHLA minCoverageFilter #794
4. Feature/anonymize fastq #791
5. tempoSig #788
6. Feature/megatron list update #733

1.3

1. Move delly output from MergeDellyManta to DellyCall #753
2. Change --aggregate <tsv> format and logic to support aggregate of different cohorts in one run #755
3. Change maximum run time to 500 hours for 3rd and 4th time of task retry so that jobs won't fail because of run time on JUNO #759
4. Add hidden feature of supporting watch mode for --maping/--bamMapping <tsv>, --pairing <tsv> and --aggregate <tsv> #754 #755 . (No docs for how to use it. Only aiming for supporting routine operation in CCS. For questions please reach out to @gongyixiao @anoronh4 )
5. move RunNeoantigen before SomaticFacetsAnnotation #764
6. Feature/facets suite2.0 #762
7. Fixed Facets armlevel file path for aggregate and when aggregation from existing results folder, duplicated normal alfred files were input into QcBamAggregate process #766
8. Fixed SomaticCombineChannel process failure due to no read counts reporeted by Strelka2 when using it to call multiallelic #768
9. Supports for multiple part of fastq files for the same lane as SampleX_L001_R1_001.fastq.gz and SampleX_L001_R1_002.fastq.gz #770
10. Bugfix/use facets1 gene level amp filter #772
11. improve splitLanes #774 (Increased Nextflow version requirement to 20.01.0)
12. initialize pairingQc variable and set pairingQc to true when --QC par… #780
13. fix facets seed random error #782
14. fixed bam truncation bug by using beforeScript and catch_USR2 #767
15. PR #790. Temporary solution for #777 and #785. Explain in the doc for #781