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.

README.md

@@ -52,10 +52,25 @@ available for both these tools and they are hence easy to install.
 
 ### Setup config file
 
-Workflow config file `configs/workflow.yaml` provides path to certain tool installation path as well as other files that
-the tools require. Modify them as necessary. Refer to the QC tool's documentation for more information on files that
+Workflow config file `configs/workflow.yaml` provides path to path to necessary QC tools as well as other files that
+some QC tools require. Modify them as necessary. Refer to the QC tool's documentation for more information on files that
 they require.
 
+#### Prepare verifybamid datasets for exome analysis
+
+*This step is necessary only for exome samples.* verifybamid has provided auxiliary resource files, which are necessary
+for analysis. However, chromosome contigs do not include `chr` prefix in their exome resource files, which are expected for
+our analysis. Follow these steps to setup resource files with `chr` prefix in their contig names.
+
+```sh
+# cd into exome resources dir
+cd <path-to>/VerifyBamID-2.0.1/resource/exome/
+sed -e 's/^/chr/' 1000g.phase3.10k.b38.exome.vcf.gz.dat.bed > 1000g.phase3.10k.b38_chr.exome.vcf.gz.dat.bed
+sed -e 's/^/chr/' 1000g.phase3.10k.b38.exome.vcf.gz.dat.mu > 1000g.phase3.10k.b38_chr.exome.vcf.gz.dat.mu
+cp 1000g.phase3.10k.b38.exome.vcf.gz.dat.UD 1000g.phase3.10k.b38_chr.exome.vcf.gz.dat.UD
+cp 1000g.phase3.10k.b38.exome.vcf.gz.dat.V 1000g.phase3.10k.b38_chr.exome.vcf.gz.dat.V
+```
+
 ### Create conda environment
 
 ```sh
@@ -69,29 +84,5 @@ conda activate quac
 
 # if you need to update the existing environment
 conda env update --file configs/env/quac.yaml
-
 ```
 
-
-
-If the default path to `datasets_central` is going to be used (i.e. you'll be using the tool for testing and/or
-development), then you'll also need to initialize the default `datasets_central` directory. This can be done by running
-the following (must be done for each user):
-
-```sh
-mkdir -p $USER_SCRATCH/tmp/datasets_central_manager/datasets $USER_SCRATCH/tmp/datasets_central_manager/logs
-```
-
-
-### Prep VerifyBamID datasets for exome analysis
-
-Need to add `chr` prefix to contigs.
-
-```sh
-# cd into exome resources dir
-cd /path/to/VerifyBamID-2.0.1/resource/exome/
-sed -e 's/^/chr/' 1000g.phase3.10k.b38.exome.vcf.gz.dat.bed > 1000g.phase3.10k.b38_chr.exome.vcf.gz.dat.bed
-sed -e 's/^/chr/' 1000g.phase3.10k.b38.exome.vcf.gz.dat.mu > 1000g.phase3.10k.b38_chr.exome.vcf.gz.dat.mu
-cp 1000g.phase3.10k.b38.exome.vcf.gz.dat.UD 1000g.phase3.10k.b38_chr.exome.vcf.gz.dat.UD
-cp 1000g.phase3.10k.b38.exome.vcf.gz.dat.V 1000g.phase3.10k.b38_chr.exome.vcf.gz.dat.V
-```