User configurable hardware resources

Merge request

Please fill in the checklist below and comment as needed.

• Was code modified? Briefly describe. See below
• Was documentation modified? Briefly describe.
• Is this a bug-fix? Briefly describe. Yes. See below
• Is this a feature addition? Briefly describe. Yes. See below
• 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
• Did you perform system-level testing manually as described in master readme doc? Did it pass completely? If not why?
• Updated Changelog.md file with change logs in recommended format?

Anything else reviewer should know?

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

README.md

@@ -186,17 +186,18 @@ snakemake rules.
 ### Set up workflow config file
 
 QuaC requires a workflow config file in yaml format ([`configs/workflow.yaml`](./configs/workflow.yaml)), which provides filepaths to necessary
-dependencies required by certain QC tools. In addition, hardware resources can be configured (refer to [`configs/workflow.yaml`](./configs/workflow.y) for more info)  format should look like:
+dataset dependencies required by certain QC tools. In addition, hardware resources can be configured (refer to [`configs/workflow.yaml`](./configs/workflow.y) for more info). File format should look like:
 
 ```yaml
-ref: "path to ref genome path"
-somalier:
-    sites: "path to somalier's site file"
-    labels_1kg: "path to somalier's ancestry-labels-1kg file"
-    somalier_1kg: "dirpath to somalier's 1kg-somalier files"
-verifyBamID:
-    svd_dat_wgs: "path to WGS resources .dat files"
-    svd_dat_exome: "path to exome resources .dat files"
+datasets:
+    ref: "path to ref genome path"
+    somalier:
+        sites: "path to somalier's site file"
+        labels_1kg: "path to somalier's ancestry-labels-1kg file"
+        somalier_1kg: "dirpath to somalier's 1kg-somalier files"
+    verifyBamID:
+        svd_dat_wgs: "path to WGS resources .dat files"
+        svd_dat_exome: "path to exome resources .dat files"
 
 #### hardware resources ####
 resources: