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CHANGELOG

Changelog format to use:

YYYY-MM-DD  John Doe

* Big Change 1:
    <reasoning here>
* Another Change 2:
    <reasoning here>

2024-07-08 Brandon Wilk

  • Makes minor bug fix for issue #95 found in the test run detection logging function

2023-10-09 Manavalan Gajapathy

  • Makes minor documentation updates - updating citation info, adding JOSS badge and updating zenodo badge to use generic DOI
  • Merges joss_manuscript to the master branch to bring it up to date.

2023-10-06 Manavalan Gajapathy

  • Adds documentation on providing sample filepaths via user-provided sample config file due to recent PRs #87, #88, #89 and #90 (closes #86).
  • Adds documentation on editing thresholds in the QuaC-Watch config file (closes #85)

2023-10-05 Manavalan Gajapathy

  • Refactors to accept sample filepaths via user-provided sample config file, when --allow_sample_renaming is used (#86)

2023-10-05 Manavalan Gajapathy

  • Refactors to accept sample filepaths via user-provided sample config file, when --include_prior_qc is used (#86)
  • Adds a test sample config file that includes priorQC filepaths

2023-10-05 Manavalan Gajapathy

  • Refactors to accept sample filepaths via user-provided sample config file. Only for exome mode in minimal manner (w/o --include_prior_qc, --allow_sample_renaming) (#86)
  • Adds a test sample config file
  • Refactors to get capture bed file as input from the sample configfile

2023-10-05 Manavalan Gajapathy

  • Refactors to accept sample filepaths via user-provided sample config file. Only for WGS mode in minimal manner (w/o --include_prior_qc, --allow_sample_renaming) (#86)
  • Adds sample config file to use with system testing datasets - .test/configs/no_priorQC/sample_config/project_2samples.tsv. This provides map of sample name to their VCF and BAM filepaths.
  • Refactors use of --sample_config arg to work with this config file as input
  • Deprecates args --project_name and --projects_path
  • Modifies workflow to use the new input setup
  • Updates README concerning the changes made

2023-07-17 Manavalan Gajapathy

  • Minor updates to documentation.

2023-07-16 Manavalan Gajapathy

  • Updates doc based on users feedback.

2023-06-30 Manavalan Gajapathy

  • Merges joss_manuscript to the master branch to bring it up to date.

2023-06-22 Manavalan Gajapathy

  • Refactors CLI script to accounting for user's environment specific slurm args requirements when submitting job to slurm (#76)
  • Removes CLI option --rerun_failed and instead configures it via snakemake-slurm profile (src/slurm/slurm_profile/config.yaml)
  • Removes --subtasks_slurm option and --snakemake_slurm as they were redundant
  • Checks if tool dependencies are available in user environment.
  • Adds time resource to configs/snakemake_cluster_config.json
  • Removes PR trigger from system testing github actions.
  • Tests if singularity is working as expected in user machine

2023-05-31 Manavalan Gajapathy

  • Adds system testing as github actions workflow

2023-05-18 Manavalan Gajapathy

  • Constructs snakemake's sbatch command using args and values from cluster config file supplied via --cluster_config.
  • Updates doc to include cluster config as a requirement

2023-05-09 Manavalan Gajapathy

  • Adds a verification step in the CLI wrapper script to check if the file/dirpaths to be mounted to singularity already exist as expected (#71)
  • Resolves dirpaths of datasets in the workflow config file to obtain their full path

2023-04-10 Manavalan Gajapathy

  • Refactors snakemake pipeline to fully run jobs in direct singularity containers. No more creation of conda environment using singularity containers! (#69)

2023-04-04 Manavalan Gajapathy

  • Retires use of cheaha-specific env variable $USER_SCRATCH
  • Auto-creates user-provided dir structures for --outdir, --tmp_dir, and --log_dir

2023-03-01 Manavalan Gajapathy

  • Decouples readme.md from readthedocs setup

2023-02-28 Manavalan Gajapathy

  • Adds license
  • Bugfix: Changes github PR template filepath

2023-01-31 Manavalan Gajapathy

Restructures the docs to make it clearer to non-Cheaha users, updates documentation to reflect recent CLI option changes, and hosts docs publicly using readthedocs.

  • Readme.md has grown bigger and became difficult to navigate. Especially for non-Cheaha users. So documentation in readme.md is now restructured to break into multiple files and is now easier to consume.
    • Makes the doc generic to non-Cheaha users
    • Identifies parts of the docs that are specific to Cheaha or CGDS users
  • Updates doc to reflect changes made in #59
  • Now hosts doc for "Sample QC review system".
  • Uses mkdocs to create static site for documentation.
  • Hosts QuaC docs using ReadTheDocs
  • Migrates Gitlab MR template to Github PR template
  • Adds github action to identify broken links in markdown files

2023-01-27 Manavalan Gajapathy

In efforts to make the repo generic to non-cheaha users, following changes were made:

  • Removes default quac_watch_config as it can lead to errors (#39)
  • Makes slurm schedule as dependency; now quac can be run locally. Local run is the default and --use_slurm allows running snakemake-triggered jobs in slurm. (#57)
  • Allows users to define custom slurm partitions and time limits via workflow configs (#58)
  • Updates median insert size threshold in quac-watch config (#54)

2023-01-20 Manavalan Gajapathy

As part of making QuaC publicly available, following updates were made to make it more generic to the environment and user friendly:

  • Removes prerun QC from small variant caller pipeline as requirement to QuaC (closes #45)
  • Explicitly defines conda environments (closes #49)
  • Uses container solution for covviz installation instead of conda to avoid pip based installation (closes #52)
  • Removes git submodules and instead saves their local copy to repo (closes #53)
  • Loads singularity module loading prior to executing the runner script
  • Uses minimal snakemake instead of full-featured snakemake (closes #56)

2022-04-07 Manavalan Gajapathy

  • Previously hardcoded hardware resources for snakemake rules can now be supplied via configs/workflow.yaml (closes #48)
  • Modified multiqc conda env config to use explicit dependencies to get around installation issues (closes #47)

2021-06-08 Manavalan Gajapathy

  • Bugfix: Fixes error when there is only one sample in input ped file (#34)
  • Adds system-testing for such only-one-sample-in-input setup (#35).

2021-05-28 Manavalan Gajapathy

  • QuaC is heavily reworked to be a companion pipeline to small variant caller pipeline and will now perform most of the QC analyses for WGS/WES data. While the small caller pipeline will still run few QC tools (for pragmatic reasons), QuaC will now take over the heavylifting of QC, including the QC-checkup, which is now called as QuaC-Watch.
  • Runs in containerized environment using Singularity.
  • QuaC can perform both sample-level and project-level QC. This is the major reason why it was decided to separate QC from small-variant caller pipeline, as it could only perform single-sample QC.
  • More QC tools were added
  • For QC checkup (ie. QuaC-Watch), QuaC now heavily expands to vcf metrics and adds significant amount of QC thresholds for bam metrics.
  • QuaC's input are output from the small variant caller pipeline, and former's output will fit seemlessly with the latter's output.
  • QuaC accepts pedigree file as input. A dummy pedigree file creator script is provided, which will be handy until phenotips is made available to us.
  • System-level testing is added

2021-03-16 Manavalan Gajapathy

  • Creates QuaC workflow, which can run somalier, mosdepth, indexcov, covviz and verifybamid2
  • Uses pedigree file as input
  • Makes it production ready.