Changelog

1.1.0 (2026-01-26)

The main change in this version is a huge improvement to the documentation, mainly thanks to @CarolinaPB.

make pipeline usable on- and offline (#86) (b5d8452)
make the pipeline compatible with both online or offline HPC environments (#82) (9d9240f)

add background to reference pipeline and annotation to snvs vcfs (#70) (f5c1903)
add pindel artifact annotation and filter (#71) (8aaa171)
update hydra genetics version to include software version into multiqc (#63) (19b33d3)

add annotation and seq dict for pindel vcf (046d2a5)
add artifafct annotation (25c43a7)
add CNV HTML report (#40) (373c012)
add cnvkit rules (2cce492)
add cnvkit vcf to output (fd40472)
add GATK CNVs to SVDB output (1698966)
add GATK interval list to output files (6829ca0)
add GATK panel of normals to output (c93d77e)
add lower ad filter for myd88 and cxcr4 (gbg) (c0c8e62)
add pindelfilter (6b5d320)
add purecn (#50) (71bda05)
add somatic soft filter vcf (0dda471)
add svdb output (11e9398)
add vep annotation to pindel if not empty (1d540ee)
added pindel and individual vcf (e0c7452)
adding softwareversion files, and updating multiqc to latest to include said version log (2cb422a)
allow comments using "#" in samples and units (6beeea8)
annotated snv vcf (7f4b3d9)
better copy-number thresholds for hematology (#53) (c507302)
generate svdb database (e0b545d)
integration test dataset (186749a)
make tumor content optional (#54) (b50a63c)
more wildcard constraints (58a3101)
normalize, decompose and add af and dp to pindel vcf (38eda80)
reference pipeline improvements (#43) (407e1db)
specific freebayes filter for low qual (0594e95)
specify pipeline output in yaml file (59e94e9)
supply config file on command line (3c42289)
Update prealignment module to v0.1.0, as well as hydra-genetics to v0.9.1 (8fa9003)
update reports module to v0.3.1 (#45) (43350b3)
update vepto 109 and hg38 (2f65f7a)

add minimum hydra version (59ae8ad)
add missing lines and chars in configs (c89ea4c)
add missing mapping bias to purecn and update cnvkit_batch inputname for normal pool (8c4027e)
add softfilter flag (428d4a2)
bug where files w/o wildcards were missing (89f9e5f)
bump cnv_sv version (87aae77)
check that fastq files exist (7120a2b)
config: correct fastqc path (418d109)
containers and rules in config (0accab4)
ensemble vcf config (a2b6ae1)
fix container definition for pindel_update_vcf (b50a63c)
flesh out config validation schema (9a76b67)
incorrect type for copy number thresholds (#55) (97cc0c7)
indentation error in validation schema (4ed18f3)
make sure pindel if statement works on all files (baeb542)
make the db_string config parameter mandatory (39c314b)
more concise validation error message (1073900)
pin pulp version for snakemake <8.1.2 (#47) (c07beb7)
reference: allow for sample to be split over several lines in units_references.tsv (e269995)
set default reference name (2981a9b)
spelling on softfilter filename (9381cbb)
update minimum snakemake version (4e90b8a)
update module versions (eea7afe)
use repo config (8492bd7)
validation: add cnvkit rules to schema (f65b824)