Merge branch 'release/1.4.0'

.dockerignore

@@ -5,3 +5,5 @@
 /CHANGES.md
 /.gitignore
 /.git
+/cwls/
+/examples/

CHANGES.md

@@ -1,5 +1,9 @@
 # CHANGES
 
+## 1.4.0
+
+* Move cwl and examples into core cgpBigWig respository
+
 ## 1.3.0
 
 * Update to htslib 1.10.2

Dockerfile

@@ -45,7 +45,7 @@ FROM  ubuntu:20.04
 
 LABEL maintainer="[email protected]"\
       uk.ac.sanger.cgp="Cancer, Ageing and Somatic Mutation, Wellcome Sanger Institute" \
-      version="1.3.0" \
+      version="1.4.0" \
       description="cgpBigWig"
 
 ENV OPT /opt/wtsi-cgp

README.md

@@ -42,9 +42,7 @@ To install this package run:
 
 A docker image for this tool can be found at [quay.io][quay-repo] (this may be more current than the dockstore version).
 
-There are [docker][quay.io] and [dockstore.org][dockstore] wrappers for this project at [dockstore-cgpbigwig] including CWL bindings.
-
-See the [dockstore-cgpbigwig] documentation for more detail.
+There are [docker][quay.io] and [dockstore.org][dockstore] containers for this project (including CWL bindings).
 
 ## Programs
 
@@ -167,6 +165,11 @@ Other:
 -v --version   Prints the version number.
 ```
 
+## Contributors
+
+Thanks to the following contributors on `dockstore-cgpbigwig` which is now retired
+[Michael R. Crusoe](https://github.com/mr-c)
+
 ## License
 ```
 Copyright (c) 2017-2018 Genome Research Ltd.
@@ -204,8 +207,8 @@ identical to a statement that reads ‘Copyright (c) 2005, 2006, 2007, 2008,
 [BigWig]: https://genome.ucsc.edu/goldenpath/help/bigWig.html
 [htslib]: https://github.com/samtools/htslib
 [dockstore]: https://dockstore.org/tools
-[quay.io]: https://quay.io/repository/wtsicgp/dockstore-cgpbigwig
-[dockstore-cgpbigwig]: https://github.com/cancerit/dockstore-cgpbigwig/
+[quay.io]: https://quay.io/repository/wtsicgp/cgpbigwig
+[dockstore-cgpbigwig]: https://github.com/cancerit/cgpbigwig/
 
 <!-- Travis links -->
 [travis-master]: https://travis-ci.org/cancerit/cgpBigWig.svg?branch=master

VERSION.txt

@@ -1 +1 @@
-1.3.0
+1.4.0

cwls/bam2bedgraph.cwl

@@ -0,0 +1,71 @@
+#!/usr/bin/env cwl-runner
+
+doc: |
+  ![build_status](https://quay.io/repository/wtsicgp/cgpbigwig/status)
+
+  A wrapper for the cgpBigWig bam2bedgraph tool.
+
+  bam2bedgraph documentation can be found [here](https://github.com/cancerit/cgpBigWig#bam2bedgraph)
+
+  In order to run the example found in `example/bam2bedgraph.json` please download the relevant reference files
+  listed in the [`README`](https://github.com/cancerit/cgpcgpBigWig/README.md#Example_reference_files)
+
+  See the [cgpBigWig](https://github.com/cancerit/cgpBigWig)
+  website for more information about this wrapper.
+
+  For queries relating to the underlying software see [cgpBigWig](https://github.com/cancerit/cgpBigWig).
+
+cwlVersion: v1.0
+
+class: CommandLineTool
+
+id: "cgpbigwig-bam2bedgraph"
+label: "cgpbigwig-bam2bedgraph"
+
+baseCommand: bam2bedgraph
+
+requirements:
+  - class: DockerRequirement
+    dockerPull: "quay.io/wtsicgp/cgpbigwig:1.4.0"
+
+inputs:
+  input_path:
+    type: File
+    doc: "Path to bam/cram input file"
+    inputBinding:
+      prefix: --input
+      position: 1
+  region:
+    type: string?
+    doc: "Region in bam to access"
+    inputBinding:
+      prefix: --region
+  filter:
+    type: int
+    doc: "Ignore reads with the filter flags"
+    inputBinding:
+      prefix: --filter
+  overlap:
+    type: boolean
+    doc: "Flag to check for overlapping reads"
+    inputBinding:
+      prefix: --overlap
+
+outputs:
+  output:
+    type: stdout
+
+$namespaces:
+  s: http://schema.org/
+
+$schemas:
+  - https://schema.org/version/latest/schema.rdf
+
+s:codeRepository: https://github.com/cancerit/cgpBigWig
+s:license: https://spdx.org/licenses/GPL-3.0
+
+s:author:
+  - class: s:Person
+    s:identifier: https://orcid.org/0000-0002-0407-0386
+    s:email: mailto:[email protected]
+    s:name: David Jones

cwls/bam2bw.cwl

@@ -0,0 +1,88 @@
+#!/usr/bin/env cwl-runner
+cwlVersion: v1.0
+
+class: CommandLineTool
+
+id: "cgpbigwig-bam2bw"
+label: "cgpBigWig bam2bw flow"
+
+doc: |
+  ![build_status](https://quay.io/repository/wtsicgp/cgpbigwig/status)
+
+  A wrapper for the cgpBigWig bam2bw tool.
+
+  bam2bw documentation can be found [here](https://github.com/cancerit/cgpBigWig#bam2bw)
+
+  In order to run the example found in `example/bam2bw.json` please download the relevant reference files
+  listed in the [`README`](https://github.com/cancerit/cgpcgpBigWig/README.md#Example_reference_files)
+  and change the reference path in bam2bw.json
+
+  See the [cgpBigWig](https://github.com/cancerit/cgpBigWig)
+  website for more information about this wrapper.
+
+  For queries relating to the underlying software see [cgpBigWig](https://github.com/cancerit/cgpBigWig).
+
+baseCommand: bam2bw
+
+requirements:
+  - class: DockerRequirement
+    dockerPull: "quay.io/wtsicgp/cgpbigwig:1.4.0"
+  - class: InlineJavascriptRequirement
+
+inputs:
+  input_path:
+    type: File
+    doc: "Path to the input [b|cr]am file"
+    secondaryFiles: $(self.basename + self.nameext.replace('m','i'))
+    inputBinding:
+      prefix: --input
+      position: 1
+  filter:
+    type: int?
+    doc: "SAM flags to filter"
+    inputBinding:
+      prefix: --filter
+  region:
+    type: File?
+    doc: "A bed file of regions over which to produce the bigwig file"
+    inputBinding:
+      prefix: --region
+  include_zeros:
+    type: boolean?
+    doc: "Include zero coverage regions as additional entries to the bw file"
+    inputBinding:
+      prefix: --include-zeroes
+  reference:
+    type: File?
+    doc: "Core reference genome.fa file (required for cram if ref_path cannot be resolved)"
+    secondaryFiles:
+    - .fai
+    inputBinding:
+      prefix: --reference
+  overlap:
+    type: boolean
+    doc: "Flag to check for overlapping reads"
+    inputBinding:
+      prefix: --overlap
+
+outputs:
+  output:
+    type: File
+    outputBinding:
+      glob: output.bam.bw
+
+$schemas:
+  - https://schema.org/version/latest/schema.rdf
+
+$namespaces:
+  s: http://schema.org/
+
+
+s:codeRepository: https://github.com/cancerit/cgpBigWig
+s:license: https://spdx.org/licenses/AGPL-3.0-only
+
+s:author:
+  - class: s:Person
+    s:identifier: https://orcid.org/0000-0002-0407-0386
+    s:email: mailto:[email protected]
+    s:name: David Jones

cwls/bam2bwbases.cwl

@@ -0,0 +1,76 @@
+#!/usr/bin/env cwl-runner
+
+doc: |
+  ![build_status](https://quay.io/repository/wtsicgp/cgpbigwig/status)
+
+  A wrapper for the cgpBigWig bam2bwbases tool.
+
+  bam2bwbases documentation can be found [here](https://github.com/cancerit/cgpBigWig#bam2bwbases)
+
+  In order to run the example found in `example/bam2bwbases.json` please download the relevant reference files
+  listed in the [`README`](https://github.com/cancerit/cgpcgpBigWig/README.md#Example_reference_files)
+  and change the reference path in bam2bwbases.json
+
+  See the [cgpBigWig](https://github.com/cancerit/cgpBigWig)
+  website for more information about this wrapper.
+
+  For queries relating to the underlying software see [cgpBigWig](https://github.com/cancerit/cgpBigWig).
+
+cwlVersion: v1.0
+
+class: CommandLineTool
+
+id: "cgpbigwig-bam2bwbases"
+label: "cgpbigwig-bam2bwbases"
+
+baseCommand: bam2bwbases
+
+requirements:
+  - class: DockerRequirement
+    dockerPull: "quay.io/wtsicgp/cgpbigwig:1.4.0"
+inputs:
+  input_path:
+    type: File
+    inputBinding:
+      prefix: --input
+      position: 1
+    secondaryFiles: .bai
+  filter:
+    type: int?
+    inputBinding:
+      prefix: --filter
+  region:
+    type: string?
+    inputBinding:
+      prefix: --region
+  reference:
+    type: File?
+    inputBinding:
+      prefix: --reference
+  overlap:
+    type: boolean
+    doc: "Flag to check for overlapping reads"
+    inputBinding:
+      prefix: --overlap
+
+
+outputs:
+  output:
+    type: stdout
+
+stdout: bam2bwbases.out.bw
+
+$namespaces:
+    s: http://schema.org/
+
+$schemas:
+    - https://schema.org/version/latest/schema.rdf
+
+s:codeRepository: https://github.com/cancerit/cgpBigWig
+s:license: https://spdx.org/licenses/GPL-3.0
+
+s:author:
+  - class: s:Person
+    s:identifier: https://orcid.org/0000-0002-0407-0386
+    s:email: mailto:[email protected]
+    s:name: David Jones

cwls/bg2bw.cwl

@@ -0,0 +1,61 @@
+#!/usr/bin/env cwl-runner
+
+doc: |
+  ![build_status](https://quay.io/repository/wtsicgp/cgpbigwig/status)
+
+  A wrapper for the cgpBigWig bg2bw tool.
+
+  bg2bw documentation can be found [here](https://github.com/cancerit/cgpBigWig#bg2bw)
+
+  In order to run the example found in `example/bg2bw.json` please download the relevant reference files
+  listed in the [`README`](https://github.com/cancerit/cgpcgpBigWig/README.md#Example_reference_files)
+
+  See the [cgpBigWig](https://github.com/cancerit/cgpBigWig)
+  website for more information about this wrapper.
+
+  For queries relating to the underlying software see [cgpBigWig](https://github.com/cancerit/cgpBigWig).
+
+cwlVersion: v1.0
+
+class: CommandLineTool
+
+id: "cgpbigwig-bg2bw"
+label: "cgpbigwig-bg2bw"
+
+baseCommand: bg2bw
+
+requirements:
+  - class: DockerRequirement
+    dockerPull: "quay.io/wtsicgp/cgpbigwig:1.4.0"
+
+inputs:
+  input_path:
+    type: File
+    doc: "Path to the input [b|cr]am file"
+    inputBinding:
+      prefix: --input
+      position: 1
+  chrom_list:
+    type: File
+    doc: "Path to chrom.list a .tsv where first two columns are contig name and length (i.e. .fai file)"
+    inputBinding:
+      prefix: --chromList
+
+outputs:
+  output:
+    type: stdout
+
+$schemas:
+  - https://schema.org/version/latest/schema.rdf
+
+$namespaces:
+  s: http://schema.org/
+
+s:codeRepository: https://github.com/cancerit/cgpBigWig
+s:license: https://spdx.org/licenses/GPL-3.0
+
+s:author:
+  - class: s:Person
+    s:identifier: https://orcid.org/0000-0002-0407-0386
+    s:email: mailto:[email protected]
+    s:name: David Jones