Changelog

0.6.0 (2025-11-19)

Features

  • add mosaic calling (91d792b)
  • changes to be able to run on miarka (9f3a817)
  • preparing for miarka (e58615d)
  • update build script (4ae13c5)
  • update hydra-genetics version (242dac8)
  • update snv_indels for mosaicforecast changes (3a426ca)
  • update snv_indels v2.0.0 and cnv_sv to v2.0.0 (9f18e1b)
  • update vep version to 110 (1040530)

Bug Fixes

  • cnv_sv version (80ffd77)
  • how to get modules (8fedb98)
  • move fmelt files for wp3 data (458407b)
  • new snv_indels tag, bam path from input in mosaicforecast (f36324a)
  • new version of VEP, comment about melt, more resources for deepsomatic (3273025)
  • no folder config in marvin analysis dir (37daa5b)
  • not change ref yet (0b8bdb4)
  • not hard coded path to melt (b74eca0)
  • not hardcoded pipeline version in miraka config (f71156a)
  • remove the get_input_bam function (67f9aed)
  • rm hardcodeed in MELT rule and efficientnet.pth in path (02d9e31)
  • sample_prep (9bc4266)
  • small changes to make it work on miarka (4f1809a)
  • specify resources for deepsomatic (c5d0f7c)
  • to make snakemake dry-run work (b1c74cd)
  • Update singularity and wrapper prefixes in profile (2bbb717)

Performance Improvements

  • newer versions of release-please and modules (c91c98e)

Documentation

  • updating README.md and ReadTheDocs (d71c019)

0.5.0 (2025-09-09)

Features

  • add exomedepth vcf for seqone and rename vcfs (f158a02)

Documentation

  • update docs and dag images (eaee15a)

0.4.0 (2025-03-11)

Features

  • add config with novaseqX exomedepth reference (34d0941)
  • copy the exomedepth config to the results (a2c8552)

0.3.1 (2024-06-04)

Bug Fixes

0.3.0 (2024-04-24)

Features

  • adding PATH_TO_REPO parameter in config (efad76a)
  • remove SampleSheet.csv for sample order (3aa4b74)

Bug Fixes

  • remove Snakefile in profile (5dac5ef)

0.2.0 (2024-04-04)

Features

  • switch gpu deepvariant to cpu version (a2a65b0)

Bug Fixes

Documentation

  • remove gpu from doc add cpu (3e8e72a)

0.1.4 (2024-03-14)

Bug Fixes

  • add missing bai to exomedepth, fix typo in start script (1c58ea7)

0.1.3 (2024-02-13)

Bug Fixes

  • pin pulp to 2.8 or less (5182cca)
  • replace total seq (samtools) with total reads (picard) in multiqc (81eb4a2)
  • run samtools stats without bed, use value in multiqc (ae637c9)

Performance Improvements

  • use correct num for common docker (3a2f797)

Documentation

  • update samtools stats info (4ef515f)

0.1.2 (2023-09-27)

Bug Fixes

  • add config to Results folder (5b00887)
  • update snakemakeprofile and normal panel for exomedepthversion (f49efe9)

Documentation

  • add config to resultsfiles.md (300fa5b)
  • update mkdocs.yaml (fa6f819)
  • update parabricks and links to main branch of marple (adf752e)
  • update README.md (51bf321)
  • update running.md with some hardware specs (635e60c)
  • update some links (60b4e7a)

0.1.1 (2023-09-14)

Bug Fixes

  • remove workflow/rules from mkdocs.yaml (65c1308)

0.1.0 (2023-09-14)

Features

  • add deepvariant instead of haplotypecaller (9d8dc06)
  • add g.vcf.gz (0c2e7e0)
  • add pgrs to xlsx file (9d462d6)
  • add referece pipeline for exomedepth normal pool (783fef1)
  • first draft pipeline (f3b3350)

Bug Fixes

  • add bedfile to deepvariant (70fd874)
  • add exon bedfile to mosdepth and hsmetrics (d203fbd)
  • add missing containers (31439c5)
  • add reference line to vcf for alissa (ea01741)
  • make pycodestyle happy (22de945)
  • more conda removed (bc6c0ef)
  • picard hsmetrics on full bed instead of exon only (4d0b017)
  • remove conda (d37b9ad)
  • remove duplicate rows in low_cov sheet (179aa49)
  • remove exomdepth output =1 (8556e33)
  • set coverage as number so table sort works (2745a78)
  • spelling misstake pgrs_bed (9f1bf5e)
  • spelling on requirements file (8170bdc)
  • update hydra version and update bedtools intersect schema (00ca936)
  • update parabricks version in config.yaml (23fc3df)
  • update path to repo (c1dd22c)

Documentation

  • add changelog to doc hooks.py (e62441a)
  • add link to github on readthedocs (db1197e)
  • add readthedocs (eeac5f1)
  • add reference workflow to readthedocs (739362a)
  • add rulegraph to hook to cp on build docs (dadf705)
  • readthedocs add step-by-step (2913bd3)
  • small docs updates (d2181b8)
  • structure changes (704c743)
  • update CODEOWNERS (ce8b0a7)
  • update hydra readthedocs links (cc9931f)
  • update paths to git repo (7fa888e)
  • update readme (d8d333c)
  • update readme with link to readthedocs (e2a749c)
  • update readthedocs (ac74ba2)
  • update readthedocs to include deepvariant (ea2f0eb)
  • update rulegraph (5ee4577)
  • update running ref (8f99ae7)
  • update schemas (fc25b81)