Merge branch 'release/3.1.0'

CHANGES.md

@@ -1,5 +1,16 @@
 # CHANGES
 
+## 3.1.0
+
+* Update to dockstore-cgpmap:3.1.0 for base image
+* Update dependencies to support fragment based read counts (and other fixes):
+  * cancerit/cgpPindel - v3.1.2
+  * cancerit/cgpCaVEManPostProcessing - 1.8.6
+  * cancerit/cgpCaVEManWrapper - 1.13.12
+  * cancerit/CaVEMan - 1.13.14
+  * cancerit/VAGrENT - v3.3.3
+* Drop `expected` tree, will be revising how verification of container is achieved.
+
 ## 3.0.3
 
 Bumps dockstore-cgpmap to include new version of dockstore-cgpbigwig for GRCh38

Dockerfile

@@ -1,4 +1,4 @@
-FROM  quay.io/wtsicgp/dockstore-cgpmap:3.0.4 as builder
+FROM  quay.io/wtsicgp/dockstore-cgpmap:3.1.0 as builder
 
 USER  root
 
@@ -33,7 +33,7 @@ MAINTAINER  cgphelp@sanger.ac.uk
 
 LABEL vendor="CASM/Cancer IT, Wellcome Sanger Institute"
 LABEL uk.ac.sanger.cgp.description="CGP WXS pipeline for dockstore.org"
-LABEL uk.ac.sanger.cgp.version="3.0.3"
+LABEL uk.ac.sanger.cgp.version="3.1.0"
 
 RUN apt-get -yq update
 RUN apt-get install -yq --no-install-recommends\

README.md

@@ -14,15 +14,15 @@ associated annotation of VCF files.  This has been packaged specifically for use
 
 <!-- TOC depthFrom:2 depthTo:6 withLinks:1 updateOnSave:1 orderedList:0 -->
 
-- [Supported input formats](#supported-input-formats)
-- [Usable Cores](#usable-cores)
-- [Other uses](#other-uses)
-	- [Native docker](#native-docker)
-	- [Singularity](#singularity)
-- [Verifying your deployment](#verifying-your-deployment)
-- [Development environment](#development-environment)
-- [Release process](#release-process)
-- [LICENCE](#licence)
+* [Supported input formats](#supported-input-formats)
+* [Usable Cores](#usable-cores)
+* [Other uses](#other-uses)
+  * [Native docker](#native-docker)
+  * [Singularity](#singularity)
+* [Verifying your deployment](#verifying-your-deployment)
+* [Development environment](#development-environment)
+* [Release process](#release-process)
+* [LICENCE](#licence)
 
 <!-- /TOC -->
 
@@ -118,8 +118,6 @@ via the options of `ds-cgpwxs.pl`
 The `examples/` tree contains test json files populated with data that can be used to verify the
 tool.  More details can be found [here](examples/README.md).
 
-The `expected/` tree contains the expected output for each tool.  More details can be found [here](expected/README.md).
-
 ## Development environment
 
 This project uses git pre-commit hooks.  Please enable them to prevent inappropriate large files
@@ -137,15 +135,15 @@ git config core.hooksPath git-hooks
 This project is maintained using HubFlow.
 
 1. Make appropriate changes
-1. Build image locally
-1. Run all example inputs and verify any changes are acceptable
-1. Update `expected/` tree with output of last step
-1. Bump version in `Dockerfile` and `Dockstore.cwl`
-1. Push changes
-1. Check state on Travis
-1. Generate the release (add notes to GitHub)
-1. Confirm that image has been built on [quay.io][quay-builds]
-1. Update the [dockstore][dockstore-cgpwgs] entry, see [their docs][dockstore-get-started].
+2. Build image locally
+3. Run all example inputs and verify any changes are acceptable
+4. Update `expected/` tree with output of last step
+5. Bump version in `Dockerfile` and `Dockstore.cwl`
+6. Push changes
+7. Check state on Travis
+8. Generate the release (add notes to GitHub)
+9. Confirm that image has been built on [quay.io][quay-builds]
+10. Update the [dockstore][dockstore-cgpwgs] entry, see [their docs][dockstore-get-started].
 
 ## LICENCE
 

build/opt-build.sh

@@ -13,19 +13,19 @@ VER_CGPVCF="v2.2.1"
 VER_VCFTOOLS="0.1.15"
 
 # cgpPindel
-VER_CGPPINDEL="v3.0.1"
+VER_CGPPINDEL="v3.1.2"
 
 # cgpCaVEManPostProcessing
-VER_CGPCAVEPOSTPROC="1.8.2"
+VER_CGPCAVEPOSTPROC="1.8.6"
 # if issues found downgrade to 2.23.0 but can't find any use of bedtools coverage
 VER_BEDTOOLS="2.27.1"
 
 # cgpCaVEManWrapper
-VER_CGPCAVEWRAP="1.13.2"
-VER_CAVEMAN="1.13.2"
+VER_CGPCAVEWRAP="1.13.12"
+VER_CAVEMAN="1.13.14"
 
 # VAGrENT
-VER_VAGRENT="v3.3.2"
+VER_VAGRENT="v3.3.3"
 
 if [ "$#" -lt "1" ] ; then
   echo "Please provide an installation path such as /opt/ICGC"

cwls/cgpwxs.cwl

@@ -24,7 +24,7 @@ doc: |
 
 requirements:
   - class: DockerRequirement
-    dockerPull: "quay.io/wtsicgp/dockstore-cgpwxs:3.0.3"
+    dockerPull: "quay.io/wtsicgp/dockstore-cgpwxs:3.1.0"
 
 hints:
   - class: ResourceRequirement

examples/README.md

@@ -1,14 +1,3 @@
 # Example parameters
 
 An example json file exists for the various combinations of sequence input file (and index).
-
-For each `examples/<tool>/<params>.json` file there is a corresponding folder named
-`expected/<tool>/<params>/` containing the expected file listing for the result archive.
-
-e.g.
-
-* JSON: `examples/cgpwxs/bam_bai.json`
-  * Generates archive: `result_WXS_bam_bai.tar.gz`
-* Unpacked archive can be compared to: `expected/cgpwxs/bam_bai`
-
-See [`expected/README.md`](../expected/README.md) for content of that area.