From 37333ef2fc6f21e84dee776c7ca75bb12b5853bc Mon Sep 17 00:00:00 2001
From: Michele Berselli <berse@MacBook-Pro-2.local>
Date: Mon, 30 Jan 2023 11:28:32 -0500
Subject: [PATCH] updated README

---
 LOG.md                                            |  8 ++++++++
 README.md                                         | 15 ++++++++++++++-
 portal_objects/software.yaml                      |  4 +---
 portal_objects/workflows/ascat.yaml               |  2 +-
 .../workflows/putative_drivers_cnv.yaml           |  1 -
 5 files changed, 24 insertions(+), 6 deletions(-)
 create mode 100644 LOG.md

diff --git a/LOG.md b/LOG.md
new file mode 100644
index 0000000..7607283
--- /dev/null
+++ b/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
diff --git a/README.md b/README.md
index 9e34553..f88dd7e 100644
--- a/README.md
+++ b/README.md
@@ -1 +1,14 @@
-# cgap-pipeline-SV-somatic
\ No newline at end of file
+<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/
diff --git a/portal_objects/software.yaml b/portal_objects/software.yaml
index 8474a20..e0edf13 100644
--- a/portal_objects/software.yaml
+++ b/portal_objects/software.yaml
@@ -6,7 +6,7 @@ name: ascat
 version: 3.0.0
 source_url: https://github.com/VanLoo-lab/ascat
 
---- 
+---
 
 ################################################################
 # cancerit-allelecount, 4.3.0
@@ -14,5 +14,3 @@ source_url: https://github.com/VanLoo-lab/ascat
 name: cancerit-allelecount
 version: 4.3.0
 source_url: https://anaconda.org/bioconda/cancerit-allelecount
-
-
diff --git a/portal_objects/workflows/ascat.yaml b/portal_objects/workflows/ascat.yaml
index 0fe7154..59d4f53 100644
--- a/portal_objects/workflows/ascat.yaml
+++ b/portal_objects/workflows/ascat.yaml
@@ -62,4 +62,4 @@ output:
     argument_type: file.tsv_gz
 
   ascat_objects:
-    argument_type: file.Rdata
\ No newline at end of file
+    argument_type: file.Rdata
diff --git a/portal_objects/workflows/putative_drivers_cnv.yaml b/portal_objects/workflows/putative_drivers_cnv.yaml
index 6f3b663..15f38e0 100644
--- a/portal_objects/workflows/putative_drivers_cnv.yaml
+++ b/portal_objects/workflows/putative_drivers_cnv.yaml
@@ -32,4 +32,3 @@ output:
 
   putative_drivers_tsv:
     argument_type: file.tsv_gz
-  
\ No newline at end of file