diff --git a/CHANGES.md b/CHANGES.md index 10eab9c..518b191 100644 --- a/CHANGES.md +++ b/CHANGES.md @@ -1,3 +1,6 @@ +### 2.0.1 +* Test data in `examples/analysis_config.local.json` moved to a non-expiring location. + ### 2.0.0 * See [dockstore-cgp:2.0.0](https://github.com/cancerit/dockstore-cgpmap/releases/tag/2.0.0) * Streamlined install process to reduce build time and size of image. diff --git a/Dockerfile b/Dockerfile index d0db456..1776b03 100644 --- a/Dockerfile +++ b/Dockerfile @@ -1,9 +1,9 @@ -FROM quay.io/wtsicgp/dockstore-cgpmap:2.0.0 +FROM quay.io/wtsicgp/dockstore-cgpmap:2.0.1 MAINTAINER keiranmraine@gmail.com LABEL uk.ac.sanger.cgp="Cancer Genome Project, Wellcome Trust Sanger Institute" \ - version="2.0.0" \ + version="2.0.1" \ description="The CGP WXS pipeline for dockstore.org" USER root diff --git a/Dockstore.cwl b/Dockstore.cwl index 767852a..3e55973 100644 --- a/Dockstore.cwl +++ b/Dockstore.cwl @@ -19,7 +19,7 @@ dct:creator: requirements: - class: DockerRequirement - dockerPull: "quay.io/wtsicgp/dockstore-cgpwxs:2.0.0" + dockerPull: "quay.io/wtsicgp/dockstore-cgpwxs:2.0.1" hints: - class: ResourceRequirement diff --git a/build/opt-build.sh b/build/opt-build.sh index ef7046a..a93b860 100644 --- a/build/opt-build.sh +++ b/build/opt-build.sh @@ -17,6 +17,8 @@ VER_CGPPINDEL="v2.1.0" # cgpCaVEManPostProcessing VER_CGPCAVEPOSTPROC="1.6.8" +# Warning bedtools 2.24.0 and 2.25.0 have a swapped usage in coverageBed +# No upgrades until [this ticket](https://github.com/arq5x/bedtools2/issues/319) is resolved VER_BEDTOOLS="2.21.0" # cgpCaVEManWrapper diff --git a/examples/analysis_config.local.json b/examples/analysis_config.local.json index 847ce08..2795942 100644 --- a/examples/analysis_config.local.json +++ b/examples/analysis_config.local.json @@ -12,11 +12,11 @@ "class": "File" }, "tumour": { - "path": "ftp://ngs.sanger.ac.uk/scratch/project/cancer/cgpwxs/testdata/COLO-829_ex.bam", + "path": "ftp://ngs.sanger.ac.uk/production/cancer/dockstore/cgpwxs/COLO-829_ex.bam", "class": "File" }, "normal": { - "path": "ftp://ngs.sanger.ac.uk/scratch/project/cancer/cgpwxs/testdata/COLO-829-BL_ex.bam", + "path": "ftp://ngs.sanger.ac.uk/production/cancer/dockstore/cgpwxs/COLO-829-BL_ex.bam", "class": "File" }, "exclude": "NC_007605,hs37d5,GL%",