Please add a clear description of what the PR is about:
This PR deals with stage 1 of the planned changes (ie. Refactor for WGS mode in minimal manner (w/o --include_prior_qc, --allow_sample_renaming) in order to allow user to provide sample filepaths via a config file, instead of relying on CGDS specific directory structure (as part of #86). Note that output directory structure will still be in line with that we use at CGDS.
Major changes made:
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
Please fill in the checklist below and comment as needed:
[x] Was code modified? Briefly describe. Yes. See description.
[x] Was documentation modified? Briefly describe. Minor updates to reflect major changes. More updates will come in later PRs
[x] Is this a bug-fix? Briefly describe. No.
[x] Is this a feature addition? Briefly describe. Yes. See description.
[x] Did you modify QuaC-Watch config file? If so, did you modify multiqc template
configs/multiqc_config_template.jinja2 and script src/quac_watch/create_mutliqc_configs.py as necessary? No
[x] Did you perform system-level testing manually, using ----cli_cluster_config and --snakemake_cluster_config
options, as described in the documentation? Did it pass
completely? If not why?
[x] Updated Changelog.md file with change logs in recommended format?
Documentation was modified to reflect just the most important changes. More complete doc updates will be dealt in later PRs.
Commented out rule aggregate_sample_rename_configs in workflow/rules/aggregate_results.smk, as it caused error due to a missing variable, which is now deprecated. This will be tackled in stage 4 changes, where --allow_sample_renaming will be refactored.
Pull request
Please add a clear description of what the PR is about:
This PR deals with stage 1 of the planned changes (ie. Refactor for WGS mode in minimal manner (w/o --include_prior_qc, --allow_sample_renaming) in order to allow user to provide sample filepaths via a config file, instead of relying on CGDS specific directory structure (as part of #86). Note that output directory structure will still be in line with that we use at CGDS.
Major changes made:
.test/configs/no_priorQC/sample_config/project_2samples.tsv. This provides map of sample name to their VCF and BAM filepaths.--sample_configarg to work with this config file as input--project_nameand--projects_pathPlease fill in the checklist below and comment as needed:
configs/multiqc_config_template.jinja2and scriptsrc/quac_watch/create_mutliqc_configs.pyas necessary? No----cli_cluster_configand--snakemake_cluster_configoptions, as described in the documentation? Did it pass completely? If not why?Changelog.mdfile with change logs in recommended format?Anything else reviewer should know?
rule aggregate_sample_rename_configsinworkflow/rules/aggregate_results.smk, as it caused error due to a missing variable, which is now deprecated. This will be tackled in stage 4 changes, where--allow_sample_renamingwill be refactored.