updated README

LOG.md

@@ -0,0 +1,8 @@
+### Version Updates
+
+#### v1.1.0
+* Conversion to YAML standard
+* Added components to prioritize driver mutations
+
+#### v1.0.0
+* Initial release

README.md

@@ -1 +1,14 @@
-# cgap-pipeline-SV-somatic
+<img src="https://github.com/dbmi-bgm/cgap-pipeline/blob/master/docs/images/cgap_logo.png" width="200" align="right">
+
+# CGAP Pipeline for Somatic Structural Variants
+
+This repository contains components for the CGAP pipeline for Structural Variants (SVs) in somatic data:
+
+  * CWL workflow descriptions
+  * CGAP Portal *Workflow* and *MetaWorkflow* objects
+  * CGAP Portal *Software*, *FileFormat*, and *FileReference* objects
+  * ECR (Docker) source files, which allow for creation of public Docker images (using `docker build`) or private dynamically-generated ECR images (using [*cgap pipeline utils*](https://github.com/dbmi-bgm/cgap-pipeline-utils/) `pipeline_deploy`)
+
+The pipeline starts from analysis-ready `bam` files and produces `vcf` files containing calls for SVs as output.
+Documentation for all CGAP Pipelines can now be found here:
+https://cgap-pipeline-main.readthedocs.io/en/latest/

portal_objects/software.yaml

@@ -6,13 +6,11 @@ name: ascat
 version: 3.0.0
 source_url: https://github.com/VanLoo-lab/ascat
 
---- 
+---
 
 ################################################################
 # cancerit-allelecount, 4.3.0
 ################################################################
 name: cancerit-allelecount
 version: 4.3.0
 source_url: https://anaconda.org/bioconda/cancerit-allelecount
-
-

portal_objects/workflows/ascat.yaml

@@ -62,4 +62,4 @@ output:
     argument_type: file.tsv_gz
 
   ascat_objects:
-    argument_type: file.Rdata
+    argument_type: file.Rdata

portal_objects/workflows/putative_drivers_cnv.yaml

@@ -32,4 +32,3 @@ output:
 
   putative_drivers_tsv:
     argument_type: file.tsv_gz
-