hydra-genetics v0.3.0

##Features
#Automatic testing
Automatic testing and comparison of the result with the previous version is now implemented

#Bedfile
reference:
design_bed: updated
design_intevals: updated
bcftools_filter_include_region:
nocnv: removed
exon: updated
gene_fuse:
genes: updated
report_gene_fuse:
filter_fusions: new

#CNV
1p19q is reported if more than 30% of both chromosome arms are under 1.4 copies (configurable).
New html CNV report!

#VCF filters

#Result files configuration
New simplified file for specifying output files: config/output_list.json

#DNA fusions
Added genepartners. New gene file.
Report is configurable regarding read support limits.

#QC
Added contamination estimation

#HRD
New implementation of HRD: CNVkit + scarHRD using only backbone regions. Still under development!

##Bugfix
RNA pipeline is now generating fusioncatcher output.
RNA exonskipping is now working
RNA report with correted gene names

##Local git
It is now possible to use a local git

##Hydra modules with releases
prealignment: v0.5.0
alignment: v0.3.0
snv_indels: v0.3.0
annotation: v0.2.0
filtering: v0.1.0
qc: v0.2.0
biomarker: v0.1.0
cnv_sv: v0.2.0

##Containers
All containers are now availiable on hydra-genetics dockerhub
Common container updated to 0.1.9 (only added features)
Hydra-genetics updated to 0.15.0

Features

• add cnvkit html report to final output (4384b81)
• add GATK data to visualisation (4407006)
• add gene annotations (3f5986e)
• add gene label background (2352864)
• add report template to schema (5b46741)
• add resource to generate rules (9593690)
• add table to CNV report (87cabe3)
• add three fusion partners to gene_fuse (fb1f4af)
• add VAF to chromosome view (6a96631)
• add VAF to JSON (c0aa776)
• added contamination check to pipeline (aedb308)
• added fp filtering of one fusion gene (9322c6d)
• added gatk_cnv scarHRD score (f7df157)
• added merged mutect2 bam files and bai. Also put cnv output in one folder per sample. (1fab0b7)
• added scarhrd calculations (f729310)
• animate dataset transition (857feec)
• big data validation for develop and master (8829aa2)
• bump up cnv_sv version to v0.2.0 (6c58d5c)
• config: better ranges and coloring (c4fa71e)
• config: decreased limit for 1p19q (3ad9cde)
• config: even better ranges and coloring (f2abf75)
• d3.js visualisation of all chromosomes (7fef05f)
• enable exclusion of chromosomes (e2052b8)
• gene_fuse: gene_fuse fusion filtering is now configurable (6f7171a)
• genome view before chromosome view (e892aef)
• indicate selected chromosome (8d74eed)
• limit log ratio y-axis to [-2, 2] (c814fce)
• make gene annotations optional (5ff402c)
• manta: run targeted manta (d38d22e)
• multiqc: added contamination as custom data to qc-stats table (5c5f407)
• multiqc: added contamination to multiqc (4f7a5cc)
• navigate to chromosomal region from table (6e5bb5f)
• new cnv_sv realease (d7d1e83)
• new configs for running the pipeline with hg38 (d4c6fce)
• plot all VAF data in genome view (86e92ee)
• plot selected chromosome (7f6cff1)
• plot single chromosomes (9d59b84)
• rename files to better reflect functionality (2200805)
• rm inhouse HRD output (58c970b)
• rm scarHRD based on GATK_cnv (ed8d8ea)
• scarHRD + CNVkit only on cnv backbone (f1fa85c)
• schema: set which version of default container that must be used (633b98f)
• script: update and correct fusion filtering (e73dbee)
• set version for misc (2468043)
• update list of output files (f47375c)
• update test_input_ALL.tsv (2468043)
• update test_input_VAL2022.tsv (2468043)
• updated tag to cnv_sv release (46f037e)
• updated tools requirements. (2f0f629)
• use filtered CNV data (94a004d)
• use svdb vcfs for results table (fa121d6)
• write cnvkit data as json (009319e)
• zoom in chromosome view (a6e554c)

Bug Fixes

• add conda and container to copy rules (21da2e1)
• add key functions (66aa201)
• add missing (new) output files (9593690)
• added folder to activate generic samtools rule (1e1a59b)
• apply clip path to gene annotations (b28ec6e)
• avoid duplicated genes in JSON (6d6d433)
• better hover-effect (5202a82)
• better transitions (5e281d8)
• better y scaling (3d052ec)
• bgzip and tabix input vcf files (cce76f6)
• bug in new snakemake release (3a40227)
• bug where animations were interrupted (499aaaa)
• bug where gene annotation got negative width (af3daa0)
• config: bed files that include all hotspots (7619819)
• config: interval files that include all hotspots (7725130)
• config: rm % in table and corrected column name (d0598ea)
• config: update common container to work with cnv visualization (302f091)
• config: update config to match new cnv_sv release for manta config (96b2f3b)
• config: updated cnv caller name according to new module release (6e92714)
• correct output file name (5bb11af)
• do not overwrite all output files! (6413ab9)
• flexible sizing of svg elements (fd74250)
• jenkins: keep files on failure (1be36b9)
• less cramped x-axis (e409bfd)
• match new hrd values (4bcaaad)
• match new region filtered manta results (c224e19)
• multiqc config (a236093)
• new qc tag (9b28d84)
• new tag for qc (32ac232)
• nicer fonts (999e78a)
• output file names and updated qc tag (45fc55a)
• prevent zooming outside chromosome boundaries (2063f7f)
• problem with empty CNV table (1a0af92)
• remember chromosome selection (511c99f)
• remember zoom range (4f18777)
• req: added cyvcf2 to requirement to fix cnv report (cc4a6aa)
• rm mgc tag on files (a1f35ab)
• sample name (478ced7)
• schema: update required field in singularity (eb48289)
• schema: update to match new config (b60083f)
• script: rm extra chr in chromosomes in exon skipping (c33a0aa)
• set data for chromosome view (dfb88ed)
• table styling (962158a)
• test fixes (34fc26d)
• test run errors (3fcc9f4)
• test run fixes (a64502d)
• update checksum (7f2708c)
• update config/output_list.json (2468043)
• update tag (7e5b548)
• update tag (152fcf3)
• x label alignment (5a6c797)