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))

workflow/rules/aggregate_results.smk

@@ -51,7 +51,9 @@ rule multiqc_by_sample_initial_pass:
         # using custom rename config file
         extra=lambda wildcards, input: f"--config {input.multiqc_config} --sample-names {input.rename_config}",
     wrapper:
-        "0.64.0/bio/multiqc"
+        # "0.64.0/bio/multiqc"
+        ### see issue #47 on why local wrapper is used ###
+        "file:src/wrapper_edited/0.64.0_bio_multiqc/wrapper.py"
 
 
 rule quac_watch:
@@ -134,7 +136,10 @@ rule multiqc_by_sample_final_pass:
         # using custom rename config file
         extra=lambda wildcards, input: f"--config {input.multiqc_config} --sample-names {input.rename_config}",
     wrapper:
-        "0.64.0/bio/multiqc"
+        # "0.64.0/bio/multiqc"
+        ### see issue #47 on why local wrapper is used ###
+        "file:src/wrapper_edited/0.64.0_bio_multiqc/wrapper.py"
+
 
 
 ##########################   Multi-sample QC aggregation  ##########################
@@ -193,4 +198,7 @@ rule multiqc_aggregation_all_samples:
                                             --cl_config "max_table_rows: 2000"'
         ),
     wrapper:
-        "0.64.0/bio/multiqc"
+        # "0.64.0/bio/multiqc"
+        ### see issue #47 on why local wrapper is used ###
+        "file:src/wrapper_edited/0.64.0_bio_multiqc/wrapper.py"
+