Changelog

0.3.1 (2024-02-28)

Bug Fixes

  • handle incomplete trios (35e7e5a)

0.3.0 (2024-01-03)

Features

  • add verifybamid2 to the QC (540b6d6)
  • handle when the coverage bed file that has mitochondria genes (75d6296)

0.2.0 (2023-12-07)

Features

  • add constraint to the rule resources (bc7fd42)
  • add singularity download and reference files compression (af55a2a)
  • add snakemake wrapper prefix path to bianca profile (ed90e49)
  • change deeptrio to deepvariant in the upd analysis (10d93a7)
  • support running the pipeline on bianca cluster (1691c4d)

Bug Fixes

  • point to the WGS model for deepvariant CPU (18c4966)
  • use updated qc module so that samtools stats avoids using design_bed (c970216)

0.1.0 (2023-10-20)

Features

  • add conversion from stranger vcf to bed file (c0e8c79)
  • add deeptrio and upd (38ddc8f)
  • Add ExpansionHunter (43b0c50)
  • add functions to generate cp rules (fdd4ce9)
  • add logging to coverage script (80d5244)
  • Add options to run the bwa mapping and deepvariant calling on CPU (6493c85)
  • add reference to VCF header of tiddit and svdb merge VCF files (d301d04)
  • add scripts for sample info extraction and running the pipeline (8a0530c)
  • add SMNcopynumbercaller (7fcdc94)
  • add stranger rule (af4e15a)
  • add vcf to aed for cnvpytor vcf files (75e7970)
  • change how the reference is added in the header of the vcfs (32ab5b1)
  • change to samtools cram (65dd919)
  • handle cases in the sample sheet where the sex is unknown (ad0c5b1)
  • handle update gres requirements (8807e2c)
  • increase the runtime for cnvpytor (e571362)
  • look for sample order and replacement files in config folder (a0b67de)
  • make deepvariant vcf compressed to work with script (d00ab67)
  • order samples in multiqc based on sample sheet (a8d5ac1)
  • remove rule and script for sample ordering (5117352)
  • update cnvpytor version (4574806)
  • update create_peddy_fam.py to use sample.tsv (c48f52d)
  • update GPU partition info (11e7eb8)
  • update marvin start script to process only WP3 samples in the sample sheet (7d1ea28)
  • update parabricks steps for parabricks 4 (02eda9b)
  • update reference file (622f296)
  • Update start_HG_marvin.sh (67571f6)
  • update the config files (3003d01)
  • update to latest versioned hydra-genetics modules (3074822)

Bug Fixes

  • _cp_reviewer: set directory on output of rule (3b69884)
  • add /projects,/scratch,/data to --bind in profile (16e90df)
  • add bam index a input for CNVpytor (444bbb3)
  • add bam index for child in deeptrio make_examples (7303275)
  • add configfile to multiqc (ef7d36a)
  • Change how gene panel files paths are constructed (e0a84f7)
  • change to uncompressed bed file (246415e)
  • change wildcard constraints to get the _copy_spring rule working (df216c9)
  • correctly name family id column (c2c838e)
  • directory and vep vonfig (2ec1563)
  • fix multiqc params.extra (0ab3279)
  • fix path for log and benchmark rules (93e60d6)
  • fix pbrun deepvariant command for v1.0.0 module (c76146a)
  • handle cases when all members of a trio are not in the samples.tsv (1394fdc)
  • Handle cases where the rel_df is empty due to lack of trios or peddy errors (08187a8)
  • handle overlapping genes by sorting by gene name (dd7497d)
  • handle overlapping genes in create_excel.py (91f09e7)
  • Include all peddy files as inputs for multiqc (76113ab)
  • keep the gVCF, useful when runs crash (955dc8d)
  • list all input files in create_cov_excel rile (53171aa)
  • make output_file for _copy_reviewer a directory (07f1e94)
  • peddy: point to the samples in config for input (bd217f6)
  • point to the correct module versions (5b124ba)
  • remove snakemke module and update snakemake version in requirements (56f3c05)
  • remove unneeded lines (080a86b)
  • Snakefile: set gvcf_records output and remove unused chr wildcard (9cabdf6)
  • throw error if no samples found in samplesheet (30dc3fc)
  • update and rename start_Poirot_marvin.sh to start_HG_marvin.sh (154e140)
  • update cnv_sv module (1bc9357)
  • update coverage file (9b654a6)
  • Update create_excel.py (ed8bd36)
  • Update input files for multiqc report (84550c3)
  • update multiqc_config_DNA.yaml (66cdd5f)
  • update random_stuff (6c73a97)
  • WGS genepanel in config.yaml (d1018a9)

Performance Improvements

  • fix sample order so it works for up to 999 samples (d9344d3)

Documentation

  • add a rulegraph for the pipeline (4f9ac0e)