Test configuration bug fix

A bug fix to resolve #95 causing the pipeline to fail when running on anything but the test dataset (or .test was included in input file paths).

v1.7

• 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.

What's Changed

• QuaC is published!! by @ManavalanG in #93

Full Changelog: 1.6...1.7

v1.6

• Refactors to use a sample config file to provide filepaths of input files (bam, vcf, etc.) instead of relying on a very specific directory structure (#86)
• Updates documentation on editing quac watch config file (#85)

v1.5

• Improves documentation based on user feeback
• Adds FAQ section
• Clarifies required args to the wrapper script

v1.4

This release results from several PRs:

• #67
• #70
• #72
• #73
• #75
• #80
• #81

Please see the changelog for more details.

Adds license and modifies readthedocs setup slightly

2023-03-01 Manavalan Gajapathy

• Decouples readme.md from readthedocs setup

2023-02-28 Manavalan Gajapathy

• Adds license
• Bugfix: Changes github PR template filepath

What's Changed

• Add license and fix PR template bug by @ManavalanG in #63
• Decouples github readme from readthedocs by @ManavalanG in #64

Full Changelog: 1.2...1.3

Makes QuaC useable to non-Cheaha users

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)

Made resources configurable

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

v1.0

• 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