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@github-actions github-actions released this 13 Feb 09:01
v0.18.3
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Release notes v0.18.1, v0.18.2 and v0.18.3

Fixes

v0.18.3 fixes a bug in the cnv html report where some calls could be missing. The logic in the reported variants was updated to handle three callers correctly.
v0.18.3 also removes the extra line in the MultiQC report.

Three notemp fixes: general report input file that were missing as it is only specified in a config and optitype temp directory that removed all output. Also, all temporary files from purecn was removed to avoid checkpoint issues that came up in the v0.18.1.

Features

v0.18.3 introduces the possibility to change the tumor content in the cnv html report.

Release notes v0.18.0

Features

MSI site filtering

Now calculates both filtered and unfiltered MSI scores. The filtered sites are approximately 400 sites chosen to be informative MSI sites reducing noise and enabling us to better differenciate MSI from MSS in Endometrial cancer (ENC)

New fusion caller (JuLI)

Performs similar or better than FuseqWES. Good complement as it finds some new true fusions. Also has a shorter wall-time.

General result report

A general result report for each samples is added where results are collected and links are supplied to various results files in addition to smaple specific QC data.

HLA typing

Added HLA typing of HLA-A, HLA-B, and HLA-C with 4 digit resolution (ie HLA-A*02:01).

Save germline vcf

The germilne vaf could be useful to save in case of for example contamination

Fixes

Correct NA handling of Jumble calls

Jumble does not report BAF values which caused problems in the filtering used in the reports of CNVs. This caused lots of neutral copy variant to pass the filtering. Now missing values return True and the filtering works as expected.

MultiQC DNA

The general table had several lines per sample. This will be fixed in next release.

Reference pipeline: MSI Panel of normal

Corrected the generation of the MSI PoN so that all the steps are run and not only the scan for MSI sites.

Changes in config.yaml

general_report: "config/reports/general_report.yaml"

general_html_report:
  final_directory_depth: 4
  multiqc_config: "config/reports/multiqc_config_dna.yaml"

juli_annotate:
  container: "docker://hydragenetics/juli:0.1.6.2"

juli_call:
  container: "docker://hydragenetics/juli:0.1.6.2"

optitype:
  container: "docker://fred2/optitype:release-v1.3.1"

Changes in config/config.data.hg19.yaml

juli_annotate:
  cosmic: "{{PROJECT_REF_DATA}}/ref_data/juli/CosmicFusionExport_V76.tsv"
  pfam: "{{PROJECT_REF_DATA}}/ref_data/juli/Pfam-A.full.human"
  ref_genes: "{{PROJECT_REF_DATA}}/ref_data/juli/refGene_hg19.txt"
  uniprot: "{{PROJECT_REF_DATA}}/ref_data/juli/HGNC_GeneName_UniProtID_160524.txt"

juli_call:
  gap_file: "{{PROJECT_REF_DATA}}/ref_data/juli/gap_hg19.txt"
  ref_genes: "{{PROJECT_REF_DATA}}/ref_data/juli/refGene_hg19.txt"
  
msisensor_pro: 
=>
msisensor_pro_filter_sites:
  PoN: "{{PROJECT_PON_DATA}}/GMS560/PoN/Msisensor_pro_reference_nextseq_36.list_baseline"
  msi_sites_bed: "{{PROJECT_PON_DATA}}/GMS560/design/SelectedMSIloci2019Sorted.bed"

Hydra modules with releases

  • prealignment: v1.0.0 (No change)
  • alignment: v0.5.0 (No change)
  • snv_indels: v1.1.0 (No change)
  • annotation: v1.1.0 (No change)
  • filtering: v0.3.0 (No change)
  • qc: v0.5.0 (No change)
  • biomarker: v0.5.0 (MSI filtering)
  • fusions: v0.2.2 (JuLI fusion calling)
  • cnv_sv: v0.7.0 (No change)
  • reports: v0.7.0 (Adds General results report and TC in cnv_html_report)

Snakemake min version

7.18.0 (no change)

Hydra genetics min version

3.0.0 (no change)

Hydra genetics common singularity version

3.0.0 (no change)

Bug Fixes

  • broken links (34d15fe)
  • Snakefile: Fix linting (97f4acf)
  • Snakefile: Linting (d36806e)
  • Snakefile: Linting again... (a2ddc3c)
  • Snakefile: Linting... (b7b3954)
  • Snakefile: No temporary files in purecn out (a4f662c)
  • hla: Correct results folder structure for HLA calling files (ad73f94)
  • one row per sample in MultiQC report (9feab74)
  • rm fp from html report (1265f46)
  • update html-report to latest merge-cnv with table bugfix (5e89b41)
  • update style to latest report version (66bfad2)
  • update to latest report module (9afee9c)
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