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))

configs/cluster_config.json

@@ -9,7 +9,7 @@
     },
     "qualimap_bamqc": {
         "partition": "short",
-        "mem-per-cpu": "24G"
+        "mem-per-cpu": "{params.java_mem}"
     },
     "picard_collect_multiple_metrics": {
         "partition": "short"
@@ -20,4 +20,4 @@
     "multiqc_aggregation_all_samples": {
         "mem-per-cpu": "24G"
     }
-}
+}
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