Merge pull request #105 from broadinstitute/vdauwera-readme_tweaks

Trivial updates to note limitations of the scripts we provide.

scripts/broad_dsde_workflows/README.md

@@ -1,6 +1,17 @@
+### Content overview
+
 This directory contains WDL scripts developed at the Broad Institute and supported by the DSDE group (which develops GATK, Picard and Cromwell/WDL among other things). These scripts are NOT run in production at Broad; for production pipeline scripts, see the `broad_pipelines` directory. 
 
 When these scripts get updated, old versions are stored in the `archive` directory. Versions are distinguished with a datestamp (format: YYMMDD). Each WDL  script is accompanied by a JSON file of example inputs bearing the same  name, with the `.inputs.json` extension instead of `.wdl`. Unless otherwise specified, all WDL scripts can be run with the generic options file `generic.options.json`. 
 
+### Important limitations
+
+These scripts are provided "as-is", without any guarantees as to performance 
+or results. It is the responsibility of the user to test these scripts 
+fully before running them in production.
+
+Many parameters and implementation decisions are optimized for our use of 
+the Google Cloud Platform. In some cases (such as dynamic filename modifications and extension swapping using the sub() function) the scripts may need to be 
+modified in order to be run successfully on a different platform. 
 
 

scripts/broad_pipelines/README.md

@@ -1,11 +1,26 @@
+### Content overview
+
 This directory contains the following WDL scripts used in production at
 the Broad Institute. Old versions are stored in the `archive` directory.
 Versions are distinguished with a datestamp (format: YYMMDD). Each WDL 
 script is accompanied by a JSON file of example inputs bearing the same 
 name, with the `.inputs.json` extension instead of `.wdl`, as well as a 
 JSON file of example options with the `.options.json` extension. 
 
-####`PublicPairedSingleSampleWf-<datestamp>.wdl`
+### Important limitations
+
+These scripts are provided "as-is", without any guarantees as to performance 
+or results. It is the responsibility of the user to test these scripts 
+fully before running them in production.
+
+Many parameters and implementation decisions are optimized for our use of 
+the Google Cloud Platform. In some cases (such as dynamic filename modifications 
+and extension swapping using the sub() function) the scripts may need to be 
+modified in order to be run successfully on a different platform. 
+
+### Inventory of scripts
+
+#### `PublicPairedSingleSampleWf-<datestamp>.wdl`
 This WDL pipeline implements data pre-processing and initial variant
 calling (GVCF generation) according to the GATK Best Practices for 
 germline SNP and Indel discovery in human whole-genome sequencing (WGS)