Wrapper tool of RaGOO by CWL and Docker
- cwl-runner such as cwltool
- Docker
- If you cannot use docker, this tool runs with
--no-container
options. - However, you have to install dependent tools of RaGOO, such as python3, intervaltree, numpy, and minimap2
- If you cannot use docker, this tool runs with
With the CWL reference implementation (cwltool
), toil-cwl-runner
, or arvados-cwl-runner
as your cwl-runner
:
cwl-runner --outdir ${PATH_TO_OUTPUT_DIR} \
ragoo.cwl \
--contigs_fasta ${PATH_TO_CONTIG_FILE} \
--reference_fasta ${PATH_TO_REFERENCE_FILE} \
For other runners an input object is required:
inputs.yml
contigs_fasta:
class: File
path: path/to/file
reference_fasta:
class: File
path: path/to/other/file
cwl-runner --outdir ${PATH_TO_OUTPUT_DIR} \
ragoo.cwl \
inputs.yml
As the original RaGOO implementation cannot handle with absolute file path, this tool uses modified version in the container.