From 10bd78c230be4e8a515f1385eaf0c25cc38b57f6 Mon Sep 17 00:00:00 2001 From: Geraldine Van der Auwera Date: Thu, 20 Apr 2017 23:37:01 -0400 Subject: [PATCH] Update README.md --- scripts/broad_dsde_workflows/README.md | 11 +++++++++++ scripts/broad_pipelines/README.md | 17 ++++++++++++++++- 2 files changed, 27 insertions(+), 1 deletion(-) diff --git a/scripts/broad_dsde_workflows/README.md b/scripts/broad_dsde_workflows/README.md index 6222eb6..b0e04d7 100644 --- a/scripts/broad_dsde_workflows/README.md +++ b/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. diff --git a/scripts/broad_pipelines/README.md b/scripts/broad_pipelines/README.md index 02a8783..acbc226 100644 --- a/scripts/broad_pipelines/README.md +++ b/scripts/broad_pipelines/README.md @@ -1,3 +1,5 @@ +### 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 @@ -5,7 +7,20 @@ 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-.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-.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)