Quickstart Guide¶

Summary¶

To translate a tool / workflow, we use the translate functionality of janis.

If we have a local CWL tool, tools/samtools_flagstat.cwl, we can translate it to Nextflow with the following command:

janis translate --from cwl --to nextflow tools/samtools_flagstat.cwl

Translating a workflow has the same syntax:

janis translate --from cwl --to nextflow workflows/align_sort_markdup.cwl

Note that we only need to point janis to the main workflow file we wish to translate. All supplementary files are detected and translated automatically.

Sample Translations¶

Try out the translation functionality by following the instructions below.

(Go to the bottom to see the full usage of the translate command)

Install Janis

python -m venv venv
source venv/bin/activate
pip install janis-pipelines

Obtain Sample Files

git clone https://github.com/GraceAHall/sample_translation_files

Sample Tool Translations

# From CWL
janis translate --from cwl --to nextflow sample_translation_files/cwl_tool/samtools_flagstat.cwl
janis translate --from cwl --to wdl sample_translation_files/cwl_tool/samtools_flagstat.cwl

# From Galaxy
janis translate --from galaxy --to cwl sample_translation_files/galaxy_tool/samtools_flagstat.xml
janis translate --from galaxy --to nextflow sample_translation_files/galaxy_tool/samtools_flagstat.xml
janis translate --from galaxy --to wdl sample_translation_files/galaxy_tool/samtools_flagstat.xml

# From WDL
janis translate --from wdl --to cwl sample_translation_files/wdl_tool/cutadapt.wdl
janis translate --from wdl --to nextflow sample_translation_files/wdl_tool/cutadapt.wdl

Sample Workflow Translations

# From CWL
janis translate --from cwl --to nextflow sample_translation_files/cwl_workflow/align_sort_markdup.cwl
janis translate --from cwl --to wdl sample_translation_files/cwl_workflow/align_sort_markdup.cwl

# From Galaxy
janis translate --from galaxy --to cwl sample_translation_files/galaxy_workflow/rna-seq-reads-to-counts.ga
janis translate --from galaxy --to nextflow sample_translation_files/galaxy_workflow/rna-seq-reads-to-counts.ga
janis translate --from galaxy --to wdl sample_translation_files/galaxy_workflow/rna-seq-reads-to-counts.ga

# From WDL
janis translate --from wdl --to cwl sample_translation_files/wdl_workflow/linear.wdl
janis translate --from wdl --to nextflow sample_translation_files/wdl_workflow/linear.wdl

Full Usage¶

NAME
    janis translate - generate translation from a source tool / workflow

SYNOPSIS
    janis translate --from src --to dest [OPTION] infile

DESCRIPTION
    Ingests a source tool / workflow to generate a translation in the destination language.

    infile
        Path to the source tool / main workflow file.
        For workflow translation, all supplementary files are detected and translated.

    --from STRING
        Source language of infile.  Options: cwl | wdl | galaxy

    --to STRING
        Destination language to translate to.  Options: cwl | wdl | nextflow

    --mode STRING
        Translation flavour.  Options: skeleton | regular | extended.  Default: extended
            extended: full translation as close to original as possible.
            regular:  only "required" tool inputs / outputs appear during workflow translation.
                      inferred based on workflow connections & optionality.
            skeleton: as regular mode, except command blocks are not templated.
                      for CWL, InputBindings are not templated for tool inputs.

    --output-dir STRING
        Path to the output directory for the translated files.  Default: "./translated"