Add basic docs

Dockstore.cwl

@@ -6,7 +6,7 @@ label: "CGP BWA-mem mapping flow"
 cwlVersion: v1.0
 doc: |
     ![build_status](https://quay.io/repository/cancerit/dockstore-cgpmap/status)
-    A Docker container for the CGP BWA-mem mapping flow. See the [cgpmap](https://github.com/cancerit/dockstore-cgpmap) website for more information.
+    A Docker container for the CGP BWA-mem mapping flow. See the [dockstore-cgpmap](https://github.com/cancerit/dockstore-cgpmap) website for more information.
 
 dct:creator:
   "@id": "http://orcid.org/0000-0002-5634-1539"

README.md

@@ -0,0 +1,46 @@
+dockstore-cgpmap
+======
+`dockstore-cgpmap` provides a complete multi threaded BWA mem mapping workflow.  This has been packaged specifically for use with the [Dockstore.org](https://dockstore.org/) framework.
+
+Supports input in following formats:
+* Multiple BAM
+* Multiple CRAM
+* Multiple fastq[.gz] (paired or interleaved)
+  * Please see [PCAP-core/bin/bwa_mem.pl](https://github.com/ICGC-TCGA-PanCancer/PCAP-core/blob/master/bin/bwa_mem.pl) for formatting of file names.
+
+Options for customisation:
+
+* BWA specific mapping parameters (defaults are based on attempts at a global standard).
+* Optionally ouput CRAM (scramble parameters can be modified)
+
+LICENCE
+=======
+
+Copyright (c) 2016 Genome Research Ltd.
+
+Author: Cancer Genome Project <[email protected]>
+
+This file is part of dockstore-cgpmap.
+
+dockstore-cgpmap is free software: you can redistribute it and/or modify it under
+the terms of the GNU Affero General Public License as published by the Free
+Software Foundation; either version 3 of the License, or (at your option) any
+later version.
+
+This program is distributed in the hope that it will be useful, but WITHOUT
+ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
+FOR A PARTICULAR PURPOSE. See the GNU Affero General Public License for more
+details.
+
+You should have received a copy of the GNU Affero General Public License
+along with this program. If not, see <http://www.gnu.org/licenses/>.
+
+1. The usage of a range of years within a copyright statement contained within
+this distribution should be interpreted as being equivalent to a list of years
+including the first and last year specified and all consecutive years between
+them. For example, a copyright statement that reads ‘Copyright (c) 2005, 2007-
+2009, 2011-2012’ should be interpreted as being identical to a statement that
+reads ‘Copyright (c) 2005, 2007, 2008, 2009, 2011, 2012’ and a copyright
+statement that reads ‘Copyright (c) 2005-2012’ should be interpreted as being
+identical to a statement that reads ‘Copyright (c) 2005, 2006, 2007, 2008,
+2009, 2010, 2011, 2012’."