OxoG-Dockstore-Tools

A set of CWL tools that are based on scripts used in the OxoGWrapperWorkflow.

Tools contained within:

check_minibams.sh - Checks that minibams are OK
clean_vcf.sh - Cleans VCFS so that they are ready to be processed by the OxoGWrapperWorkflow
normalize.sh - Normalizes INDEL files by calling bcf-tools norm.
pass_filter.sh - Performs pass-filtering on VCFs.
vcf_merge_by_type.pl - Merges VCFs.

To get the submodules, use a command like this:

$ git submodule update --init --recursive

Reference Files.

You will need to run the workflow with the cwltool flags --relax-path-checks and --non-strict.

Name		Name	Last commit message	Last commit date
Latest commit History 181 Commits
Variantbam-for-dockstore @ 1d8dcc0		Variantbam-for-dockstore @ 1d8dcc0
oxog_tool_dockerfile		oxog_tool_dockerfile
scripts		scripts
sga-annotate-docker @ ed84685		sga-annotate-docker @ ed84685
.dockerignore		.dockerignore
.gitignore		.gitignore
.gitmodules		.gitmodules
Dockerfile		Dockerfile
PreprocessedFilesType.yaml		PreprocessedFilesType.yaml
README.md		README.md
TumourType.yaml		TumourType.yaml
annotator_sub_wf.cwl		annotator_sub_wf.cwl
clean_vcf.cwl		clean_vcf.cwl
example_input.json		example_input.json
extract_snv.cwl		extract_snv.cwl
minibam_sub_wf.cwl		minibam_sub_wf.cwl
normalize.cwl		normalize.cwl
oxog.cwl		oxog.cwl
oxog_sub_wf.cwl		oxog_sub_wf.cwl
oxog_varbam_annotate_util.js		oxog_varbam_annotate_util.js
oxog_varbam_annotate_wf.cwl		oxog_varbam_annotate_wf.cwl
pass-filter.cwl		pass-filter.cwl
preprocess_util.js		preprocess_util.js
preprocess_vcf.cwl		preprocess_vcf.cwl
qa_check_subwf.cwl		qa_check_subwf.cwl
vcf_merge.cwl		vcf_merge.cwl
vcf_merge_util.js		vcf_merge_util.js
zip_and_index_vcf.cwl		zip_and_index_vcf.cwl