Merge branch 'release/3.3.0'

Author: gregoryleeman

.circleci/config.yml

@@ -0,0 +1,71 @@
+version: 2.1
+jobs:
+  build-test-push-job:
+    docker:
+      - image: circleci/buildpack-deps:stretch
+    environment:
+      IMAGE_NAME: quay.io/wtsicgp/dockstore-cgpmap
+    steps:
+      - checkout
+      - setup_remote_docker
+      - run:
+          name: Build Docker image
+          command: |
+            set -e
+            echo "Building Docker image"
+            docker build -t test .
+      - run:
+          name: Validate CWL files
+          command: |
+            set -e
+            echo "Validating CWL files"
+            sudo apt-get -y install python3-pip
+            pip3 install cwltool
+            cwltool --validate Dockstore.cwl
+            cwltool --validate cwls/cgpmap-bamBaiOut.cwl
+            cwltool --validate cwls/cgpmap-bamCsiOut.cwl
+            cwltool --validate cwls/cgpmap-cramOut.cwl
+      - run:
+          name: Verify inherited programs
+          command: |
+            set -e
+            echo 'Verifying programs inherited from cgpbigwig'
+            docker run --rm -t test bwjoin --version
+            echo 'Verifying programs inherited from pcap-core'
+            docker run --rm -t test bwa_mem.pl -version
+            docker run --rm -t test bammarkduplicates2 --version
+            docker run --rm -t test samtools --version
+            docker run --rm -t test bash -c 'bwa 2>&1 | grep Version'
+      - run:
+          name: Verify programs
+          command: |
+            set -e
+            echo 'Verify programs from dockstore-cgpmap'
+            docker run --rm -t test ds-cgpmap.pl -h
+      - run:
+          name: Push image to quay.io
+          command: |
+            set -e
+            BRANCH_OR_TAG="${CIRCLE_TAG:-$CIRCLE_BRANCH}"
+            if [ "$CIRCLE_TAG" = "$BRANCH_OR_TAG" ]; then
+              echo 'Pushing image'
+              echo "$DOCKERHUB_PASSWORD" | docker login -u "$DOCKERHUB_USER" --password-stdin
+              echo "$QUAYIO_PASSWORD" | docker login -u "$QUAYIO_USER" --password-stdin quay.io
+              CLEAN_BRANCH=$(echo $BRANCH_OR_TAG | tr / -)
+              docker tag test ${IMAGE_NAME}:${CLEAN_BRANCH}
+              docker push ${IMAGE_NAME}:${CLEAN_BRANCH}
+            else
+              echo "I am not a tag so not pushing image"
+            fi
+
+workflows:
+  version: 2.1
+  build-test-push-workflow:
+    jobs:
+      - build-test-push-job:
+          context:
+            - dockerhub-casmservice
+            - quayio-casmservice
+          filters:
+            tags:
+              only: /.+/ 

.travis.yml

@@ -1,5 +1,9 @@
 # CHANGES
 
+## 3.3.0
+
+* Update PCAP-core to 5.7.0, which includes bwakit post processing
+
 ## 3.2.0
 
 * Update PCAP-core to 5.4.0, new ubuntu htslib/samtools 1.11.

CHANGES.md

@@ -1,9 +1,9 @@
-FROM  quay.io/wtsicgp/pcap-core:5.4.0
+FROM  quay.io/wtsicgp/pcap-core:5.7.0
 
 LABEL vendor="Cancer, Ageing and Somatic Mutation, Wellcome Trust Sanger Institute"
 LABEL maintainer="[email protected]"
 LABEL uk.ac.sanger.cgp.description="PCAP-core for dockstore.org"
-LABEL uk.ac.sanger.cgp.version="3.2.0"
+LABEL uk.ac.sanger.cgp.version="3.3.0"
 
 USER root
 

Dockerfile

@@ -7,19 +7,18 @@ packaged specifically for use with the [Dockstore.org](https://dockstore.org/) f
 
 [![Quay Badge][quay-status]][quay-repo]
 
-| Master                                        | Develop                                         |
-| --------------------------------------------- | ----------------------------------------------- |
-| [![Master Badge][travis-master]][travis-base] | [![Develop Badge][travis-develop]][travis-base] |
+| Master | Develop |
+| --- | --- |
+| [![Master Badge][circleci-master-badge]][circleci-master] | [![Develop Badge][circleci-develop-badge]][circleci-develop] |
 
 * [Supported input formats](#supported-input-formats)
 * [Options for customisation:](#options-for-customisation)
 * [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)
+* [Run instructions](#run-instructions)
+* [Development](#development)
+	* [Verifying your deployment](#verifying-your-deployment)
+	* [Development environment](#development-environment)
+	* [Release process](#release-process)
 * [LICENCE](#licence)
 
 ## Supported input formats
@@ -31,73 +30,23 @@ packaged specifically for use with the [Dockstore.org](https://dockstore.org/) f
 
 ## Options for customisation:
 
-* BWA specific mapping parameters (defaults are based on attempts at a global standard).
-* Optionally output CRAM (scramble parameters can be modified)
+* BWA specific mapping parameters (defaults are based on attempts at a global standard)
+* Optionally output CRAM (see `seqslice` to for faster access, recommend 1000)
+    * applied to `seqs_per_slice` option of htslib/samtools.
+* Optionally run with BWA-MEM2
+* Optionally run with bwa-kit post-processing (for calling on alternative contigs)
 
-## Usable Cores
+## Run instructions
 
-When running outside of a docker container you can set the number of CPUs via:
+The full documentation covering input files, optional parameters, and methods of running dockstore-cgpmap can be found in the [github wiki][github-wiki].
 
-* `export CPU=N`
-* `-threads|-t` option of `ds-cgpmap.pl`
+## Development
 
-If not set detects available cores on system.
+### Verifying your deployment
 
-## Other uses
+The `examples/` tree contains test json files populated with data that can be used to verify the tool. More details on running Dockstore locally for testing purposes can be found in the [github wiki][github-wiki].
 
-### Native docker
-
-All of the tools installed as part of [PCAP-core][pcap-core] are available for direct use.
-
-```
-export CGPMAP_VER=X.X.X
-docker pull quay.io/wtsicgp/dockstore-cgpmap:$CGPMAP_VER
-# interactive session
-docker --rm -ti [--volume ...] quay.io/wtsicgp/dockstore-cgpmap:$CGPMAP_VER bash
-```
-
-### Singularity
-
-The resulting docker container has been tested with Singularity.  The command to exec is:
-
-```
-ds-cgpmap.pl -h
-```
-
-Expected use would be along the lines of:
-
-```
-export CGPMAP_VER=X.X.X
-singularity pull docker://quay.io/wtsicgp/dockstore-cgpmap:$CGPMAP_VER
-
-singularity exec\
- --workdir /.../workspace  \
- --home /.../workspace:/home  \
- --bind /.../ref/human:/var/spool/ref:ro  \
- --bind /.../example_data/cgpmap/insilico_21:/var/spool/data:ro  \
- dockstore-cgpmap-${CGPMAP_VER}.simg  \
- ds-cgpmap.pl  \
- -r /var/spool/ref/core_ref_GRCh37d5.tar.gz  \
- -i /var/spool/ref/bwa_idx_GRCh37d5.tar.gz  \
- -s SOMENAME  \
- -t 6 \
- /var/spool/data/\*.bam
-```
-
-For a system automatically attaching _all local mount points_ (not default singularity behaviour)
-you need not specify any `exec` params (workdir, home, bind) but you should specify the `-outdir`
-option for `ds-cgpmap.pl` to prevent data being written to your home directory.
-
-By default results are written to the home directory of the container so ensure you bind
-a large volume and set the `-home` variable.  As indicated above the location can be overridden
-via the options of `ds-cgpmap.pl`
-
-## Verifying your deployment
-
-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).
-
-## Development environment
+### Development environment
 
 This project uses git pre-commit hooks.  Please enable them to prevent inappropriate large files
 being included.  Any pull request found not to have adhered to this will be rejected and the branch
@@ -109,14 +58,14 @@ Activate the hooks with
 git config core.hooksPath git-hooks
 ```
 
-## Release process
+### Release process
 
 This project is maintained using HubFlow.
 
 1. Make appropriate changes
 2. Bump version in `Dockerfile` and `cwls/mixins/requirements.yml`
 3. Push changes
-4. Check state on Travis
+4. Check state on CircleCi
 5. Generate the release (add notes to GitHub)
 6. Confirm that image has been built on [quay.io][quay-builds]
 7. Update the [dockstore][dockstore-cgpmap] entry, see [their docs][dockstore-get-started].
@@ -158,11 +107,13 @@ identical to a statement that reads ‘Copyright (c) 2005, 2006, 2007, 2008,
 [bwa-mem.pl]: https://github.com/cancerit/PCAP-core/blob/master/bin/bwa_mem.pl
 [cgpmap-expected]: ftp://ftp.sanger.ac.uk/pub/cancer/dockstore/expected
 [pcap-core]: https://github.com/cancerit/PCAP-core
+[github-wiki]: https://github.com/cancerit/dockstore-cgpmap/wiki
 
-<!-- Travis -->
-[travis-base]: https://travis-ci.org/cancerit/dockstore-cgpmap
-[travis-master]: https://travis-ci.org/cancerit/dockstore-cgpmap.svg?branch=master
-[travis-develop]: https://travis-ci.org/cancerit/dockstore-cgpmap.svg?branch=develop
+<!-- CircleCi -->
+[circleci-master-badge]: https://circleci.com/gh/cancerit/dockstore-cgpmap/tree/master.svg?style=svg
+[circleci-master]: https://circleci.com/gh/cancerit/dockstore-cgpmap/tree/master
+[circleci-develop-badge]: https://circleci.com/gh/cancerit/dockstore-cgpmap/tree/develop.svg?style=svg
+[circleci-develop]: https://circleci.com/gh/cancerit/dockstore-cgpmap/tree/master
 
 <!-- Gitter -->
 [gitter-svg]: https://badges.gitter.im/dockstore-cgp/Lobby.svg

README.md

@@ -91,28 +91,35 @@ inputs:
       prefix: -bwamem2
       position: 9
 
+  bwakit:
+    type: boolean
+    doc: "Use bwakit post-processing"
+    inputBinding:
+      prefix: -bwakit
+      position: 10
+
   nomarkdup:
     type: boolean
     doc: "Do not mark duplicates"
     inputBinding:
       prefix: -nomarkdup
-      position: 10
+      position: 11
 
   dupmode:
     type: string?
     doc: "Duplicate mode as defined by 'samtools markdup' (t)emplate or (s)equence"
     default: 't'
     inputBinding:
       prefix: -dupmode
-      position: 11
+      position: 12
       separate: true
 
   legacy:
     type: boolean
     doc: "Use legacy merge/dupmark from biobambam2 tools, slower, more memory"
     inputBinding:
       prefix: -legacy
-      position: 12
+      position: 13
 
   seq_in:
     type:
@@ -121,7 +128,7 @@ inputs:
       items: File
     doc: "Can be BAM, CRAM, fastq (paired or interleaved), BAM/CRAM can be mixed together but not FASTQ."
     inputBinding:
-      position: 13
+      position: 14
 
 outputs:
   out_bam:

cwls/cgpmap-bamBaiOut.cwl

@@ -91,28 +91,35 @@ inputs:
       prefix: -bwamem2
       position: 9
 
+  bwakit:
+    type: boolean
+    doc: "Use bwakit post-processing"
+    inputBinding:
+      prefix: -bwakit
+      position: 10
+
   nomarkdup:
     type: boolean
     doc: "Do not mark duplicates"
     inputBinding:
       prefix: -nomarkdup
-      position: 10
+      position: 11
 
   dupmode:
     type: string?
     doc: "Duplicate mode as defined by 'samtools markdup' (t)emplate or (s)equence"
     default: 't'
     inputBinding:
       prefix: -dupmode
-      position: 11
+      position: 12
       separate: true
 
   legacy:
     type: boolean
     doc: "Use legacy merge/dupmark from biobambam2 tools, slower, more memory"
     inputBinding:
       prefix: -legacy
-      position: 12
+      position: 13
 
   seq_in:
     type:
@@ -121,7 +128,7 @@ inputs:
       items: File
     doc: "Can be BAM, CRAM, fastq (paired or interleaved), BAM/CRAM can be mixed together but not FASTQ."
     inputBinding:
-      position: 13
+      position: 14
 
 outputs:
   out_bam: