fix absolute / relative path issue in fastqc results parsing

Addressing the issue: https://git.scicore.unibas.ch/zavolan_group/pipelines/rhea/issues/106
Additionally, fixed a few log variables in MultiQC-related rules.

Snakefile

@@ -1108,5+1108,5 @@
                 params.results_dir,
                 "samples",
                 "*",
                 "*_fastqc",
                 "*_fastqc.zip"))
         for zipfile in fastq_zip_list:
             sample_name = zipfile.split("/")[-3]
             zipfile_path_chunks = zipfile.split("/")
-            new_path = os.path.join(*(zipfile_path_chunks[:-1]))
-            if params.results_dir.startswith("/"): new_path = "/" + new_path
+            new_path = os.path.abspath(
+                os.path.join(
+                    *(zipfile_path_chunks[:-1])))
             with ZipFile(zipfile, 'r') as zip_f:
                 zip_f.extractall(new_path)
             fastqc_data_f = os.path.join(
@@ -1204,7+1205,7 @@
         stdout = os.path.join(
             config["log_dir"],
             "prepare_MultiQC_config.stdout.log")
     run:
         with open(output.multiqc_config, "w") as YAML:
             YAML.write("---\n\n")
             YAML.write("title: \"Rhea\"\n")
@@ -1245,7+1246,7 @@
             YAML.write("  - TIN_scores:\n")
             YAML.write("      path_filters:\n")
             YAML.write("      - \"*/TIN scores_mqc.png\"\n")
             YAML.write("\n")  
             YAML.write("  - salmon:\n")
             YAML.write("      path_filters:\n")
             YAML.write("      - \"*/salmon_quant/*\"\n")