Changelog¶

1.4.2 (2026-05-04)¶

Bug Fixes¶

rm duplicate tmb_umi (4a817bd)
update config to newest versions of cov and mut (c320a13)
update config to newest versions of cov and mut (c6068cb)
updated cov and mut files for GMSCRC and GMSVAS (82ff4e0)
updated cov and mut files for GMSCRC and GMSVAS (ba19da3)

1.4.0 (2026-04-14)¶

Features¶

rm Fragle that did not work (b47d0b8)

Bug Fixes¶

Cnv report filtering (f65576b)
filter out Jumble copy neutral (1b0cece)
filter out Jumble copy neutral (5994081)
update reports to v1.1.1 to fix plot missing bug in cnv-report (2ba1bd5)
update reports to v1.1.1 to fix plot missing bug in cnv-report (8cc66a8)

1.3.0 (2026-04-02)¶

Features¶

added phased vcfs (db31353)
coverage and mutations files in new folder (f3b440f)
coverage and mutations files in new folder (6fac2d3)
Oncogenes in cnv html report (1f552fc)
updated jumble with hg38 and HRD score (c792aac)
updated report with additional highlighting features (c02b149)

Bug Fixes¶

path updated in general report (50d4941)
report version update fixing error bar bug (6771096)
update report hash (eb53419)
Update singularity.schema.yaml (2cced7e)
updated cancer gene file with new annotations (4bc4ceb)

Documentation¶

added documentation (a841c28)

1.2.1 (2026-03-23)¶

Bug Fixes¶

add sample name env to handle missing RG group in RNA bam files (80ebae9)
add sample name env to handle missing RG group in RNA bam files (cba17d5)

1.2.0 (2026-03-19)¶

Features¶

added fragle ctDNA fraction estimation (7d94be6)
added Fragle for ctDNA fraction estimation (02c2260)
added matching cutoff (d4feb93)
added reporting script for Somalier mixup test (c3a505b)
Added Somalier dna-dna match report (6cd9fcd)
Added Somalier dna-dna match report (6a02429)
added somalier output (2d23a4d)
new version of biomarker for fragle (7c5d680)
Somalier for mixup tests (d78f384)
update qc module with somalier (d496071)

Bug Fixes¶

adapt to new versions of report and cnv_sv (233bfd4)
adapt to new versions of report and cnv_sv (b62745a)
added missing fasta 2bit for hg38 (b100259)
added missing fasta 2bit for hg38 (7c87710)
added somalier site files (6788c63)
adjusted match_cutoff to dna dna comparison (6fcd803)
config.yaml: somalier docker (bb8ed53)
config.yaml: somalier docker (278a3fc)
correct docker for Somalier (30ed679)
new annotation module to fix MNV bug (3b3a079)
new annotation module to fix MNV bug (0e17e4f)
result files (e9f51f3)
somalier container version (d7707ac)
Update design_files.hg19.yaml (dc92daa)
Update design_files.hg38.yaml (ea2f3b8)
update report module to fix data point rendering issue (3fccc50)
update to new jumble container (7cff118)
updated cov and mut files for KIT and PDGFRA (bc4b2e4)
updated cov and mut files for KIT and PDGFRA (cef4101)

Documentation¶

added missing schema definitions (755054b)
update documentation (30718e1)

1.1.2 (2026-03-03)¶

Bug Fixes¶

corrected report and results for analyskod GMS560 (4f41ee4)
corrected report and results for analyskod GMS560 (9649eb0)

1.1.1 (2026-03-02)¶

Bug Fixes¶

config.data.hg19.yaml: correct cov and mutations files (0b73c95)
new cov and mut hg38 and TP53 fix (7c019b9)
new cov and mut hg38 and TP53 fix (e7450f9)
test_input_develop.tsv: fixed cov and mut files (eb55e1e)
test_input_develop.tsv: fixed cov and mut files (186b926)
test_input_main.tsv (300d94a)

1.1.0 (2026-02-26)¶

Features¶

add hg38 cov_and_mut files (e96ae39)
add the two new cov_and_mut files (b40f323)
added config files and PoN files for ctDNA and NovaseqX (06702a8)
added config files and PoN files for ctDNA and NovaseqX (4246d93)
added two new cov_and_mut files (PIK, VAS) (abf2234)
added two new cov_and_mut files (PIK, VAS) (00d3e86)
continued add new cov_and_mut files (d660699)
hotspot_report.yaml: add AA and CDS info till cov_and_mut file … (6768136)
hotspot_report.yaml: add AA and CDS info till cov_and_mut file for low coverage positions (8c51b7d)
New cov mut (7cd2877)
save cover_and_mut in diff folder based on analyskod (9c609b3)
save cover_and_mut in diff folder based on analyskod (fd8c969)
started add new cov_and_mut files (d1f3ec3)
strandbias filter more suitable for high coverage (3fbf0dc)
strandbias filter more suitable for high coverage (65bb46d)
strandbias filter more suitable for high coverage (0695d7f)
use the new cnv report (cde5dba)
use the new cnv report (e25898f)

Bug Fixes¶

config name (37d770f)
config.yaml: new fusion module to handle ctat_splicing empty files (7e5593f)
config.yaml: new fusion module to handle ctat_splicing empty files (f8111c3)
corrected MSI grey zone (7c14419)
corrected MSI grey zone (f26fcd5)
general_report.umi.yaml: missing umi prefix on vcf (6eceba8)
general_report.umi.yaml: missing umi prefix on vcf (069bd68)
msi grey zone (828647d)
msi grey zone (3605456)
requirements.txt: setuptools (ebdd606)
requirements.txt: setuptools (0bec6c8)
requirements.txt: setuptools version max v70.0.0 (9f4b511)
requirements.txt: setuptools version max v70.0.0 (329eb02)
requirements.txt: update hydra version for correct figshare down… (c0c335b)
requirements.txt: update hydra version for correct figshare download (a511f41)
rm Juli from general_report.prio.yaml (e781f1e)
rm Juli from general_report.prio.yaml (426a351)
use updated cov_and_mut files (363ec01)
use updated cov_and_mut files (5c0ff60)

Documentation¶

AI-assisted update of the pipeline documentation (bc8720f)

1.0.1 (2025-12-03)¶

Bug Fixes¶

rm JuLI from prio analysis (188bbf6)
rm JuLI from prio analysis (50cab1c)

1.0.0 (2025-11-28)¶

⚠ BREAKING CHANGES¶

use config and profile to start ctDNA instead of samples.tsv

### feat\

use config and profile to start ctDNA instead of samples.tsv (89ed27c)

Features¶

add CTAT-splicing (b95dc9e)
added ctat-splicing (db4f3e4)
added miarka build and ref files (b9a2e6e)
added updated CTAT references files (d2003f9)
handle tc in percent instead of fractions (d1caa63)
handle tc in percent instead of fractions (c9b7148)
use new fusion module version with ctat (80a265e)

Bug Fixes¶

build_conda.sh: Set pipeline version in path (05b0f06)
build: Optional to re-build ref. and apptain. (23192a5)
correct output file (16d8759)
correct output file (7631485)
make prio analysis work dynamically (d8dac01)
make prio analysis work dynamically (d53441d)
Miarka purecn (aa25b54)
remove old files (bb2f7e0)
resources.yaml: Resources optitype (92dba5a)
resources.yaml: Resources optitype (3cdd3e2)
rm hla optiype analysis (13d5b82)
rm hla optiype analysis (b934e16)
rm large unfiltered ITD results (7689af4)
rm large unfiltered ITD results (cbe9143)
Update build_conda.sh (426f182)
Update build_conda.sh (654fefb)
Update build_conda.sh (296e01c)
Update build_conda.sh (3ec795b)
Update build_conda.sh (eb51270)
Update design_files.hg19.yaml (30e663b)
Update design_files.hg19.yaml (eadb33e)
Update resources.yaml (da925df)
Update singularity.schema.yaml (ee6ae08)

Documentation¶

README: Updated build instructions. (86e66f0)
Update README.md (97aeb16)

0.24.0 (2025-10-17)¶

Features¶

cov_and_mut based on umi when umi is used (bf59619)
cov_and_mut file with aa one letter code (0b15bb1)
cov_and_mut file with aa one letter code (b88f617)
Coverage_and_mutations files for haloplex (568ab9e)
updated coverage and mutations files (3dda8c9)
updated coverage and mutations files (c392599)

Bug Fixes¶

adjust GRCh37 VEP cache download location (#667) (a1eaecb)
fix broken annotation in Mutation_Lung (09d01c4)
fix broken annotation in Mutation_Lung (9f43a82)
Gist cov and mut file (3794e29)
output file variable name (164050e)
reference files (7c1c2d8)
reference files (8aea148)
Update general_report.yaml (d295f16)
Update general_report.yaml (7ce88b9)
update mod cov and mut files (3db8110)
update mod cov and mut files (1fdc09e)
Update output_files.yaml (bde39b8)
Update output_files.yaml (aab581c)
Update Snakefile (8db0fd0)

Documentation¶

added clarifying info (e997a71)