Please add a clear description of what the PR is about:
This PR deals with stage 4 of the planned changes (ie. Refactor to allow --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.
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? Yes
[x] Updated Changelog.md file with change logs in recommended format? Yes
Anything else reviewer should know?
Please review #88 before reviewing this PR.
Documentation was modified to reflect just the most important changes. More complete doc updates will be dealt in later PRs.
Pull request
Please add a clear description of what the PR is about:
This PR deals with stage 4 of the planned changes (ie. Refactor to allow --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.
Please 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? YesChangelog.mdfile with change logs in recommended format? YesAnything else reviewer should know?