QuaC - First major review

QuaC pipeline has been modified to make it user-friendly and share interface similar to other pipelines at CGDS.

Note that one major deviation compared to our other pipeline is that QuaC uses recent snakemake version (6.0.5), and they are made available via conda environment. That is, we don't use snakemake module from cheaha.

The following may need review at some level. Note: This list is not exhaustive.

• Snakemake pipeline
• Documentation. I kept it simple; let me know if it needs more info.

workflow/rules/coverage_analysis.smk

@@ -52,7+52,7 @@
         in_dir = lambda wildcards, input: Path(input[0]).parent,
         workflow_dir = Path(workflow.basedir).parent
     shell:
         r"""
         echo "Heads up: Mosdepth-plotting is run on all samples in "{params.in_dir}"; Not just the files mentioned in the rule's input."
 
         cd {params.in_dir}  # if not in directory, mosdepth uses filepath as sample name :(
@@ -73,7+73,7 @@
     output:
         html = OUT_DIR / "indexcov" / "index.html",
         bed = OUT_DIR / "indexcov" / f"indexcov-indexcov.bed.gz",
-        log = OUT_DIR / "indexcov" / "stdout.log",
     message:
         "Running indexcov"
+    log:
+        OUT_DIR / "indexcov" / "stdout.log",
     params:
         outdir = lambda wildcards, output: Path(output[0]).parent,
         project_dir = lambda wildcards, input: str(Path(input['bam'][0]).parents[2]),
@@ -86,7 +87,7 @@ rule indexcov:
         {input.goleft_tool} indexcov \
             --directory {params.outdir} \
             {params.project_dir}/[LU][WD]*/bam/*.bam \
-            > {output.log} 2>&1
+            > {log} 2>&1
         """
 
 
@@ -97,9 +98,10 @@ rule covviz:
         ped = PEDIGREE_FPATH,
     output:
         html = OUT_DIR / "covviz" / "covviz_report.html",
-        log = OUT_DIR / "covviz" / "stdout.log",
     message:
         "Running covviz"
+    log:
+        OUT_DIR / "covviz" / "stdout.log",
     conda:
         str(WORKFLOW_PATH / "configs/env/covviz.yaml")
     shell:
@@ -108,5 +110,5 @@ rule covviz:
             --ped {input.ped} \
             --output {output.html} \
             {input.bed} \
-            > {output.log} 2>&1
+            > {log} 2>&1
         """