- 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)
- remove freebayes caller (0217502)