You need to place the dependent tool definition files in the same directory of the workflow definition file. Use the bundled shell script to copy the tool files for workflow steps.
$ cd /path/to/pitagora-cwl
$ sh ./test/bin/collect-steps.sh
This will copy the CWL tool definition files in tools directory to the directories of workflow definitions. This will copy the files for all the pitagora-cwl workflows, so you do not have to run for each workflow.
You can use any CWL implementation to run the CWL workflow. Below is the example command line to run the workflow by cwltool, the reference implementation of CWL runner.
For single-end reads:
$ cwltool single_end/kallisto_wf_se.cwl [-h] [--bootstrap_samples BOOTSTRAP_SAMPLES] [--fragment_length FRAGMENT_LENGTH] --index_file INDEX_FILE --nthreads NTHREADS [--out_dir_name OUT_DIR_NAME] [--repo REPO] --run_ids RUN_IDS [--standard_deviation STANDARD_DEVIATION]
For paired-end reads:
$ cwltool paired_end/kallisto_wf_pe.cwl [-h] [--bootstrap_samples BOOTSTRAP_SAMPLES] --index_file INDEX_FILE --nthreads NTHREADS [--out_dir_name OUT_DIR_NAME] [--repo REPO] --run_ids RUN_IDS
The test script is bundled in this repository. It requires you to install cwltool beforehand, and will download the reference data from AWS S3 and get sequence data from Sequence Read Archive to run the workflow.
Running the test script will download Kallisto index for GRCh38 Gencode transcripts (2.0GB, md5: 9953fa039e2b3d07f76f54a1ad13be17).
If you already cloned this repository, run run-cwl command in test/bin with the path to the repo and workflow name as below:
Single-end input version:
$ cd /path/to/pitagora-cwl
$ ./test/bin/run-cwl --cwl-repo . "kallisto_wf_se"
Paired-end input version:
$ cd /path/to/pitagora-cwl
$ ./test/bin/run-cwl --cwl-repo . "kallisto_wf_pe"
Or simply use curl command which clones this repository to $HOME/.pitagora-cwl and run the workflow.
Single-end input version:
$ curl https://raw.githubusercontent.com/pitagora-network/pitagora-cwl/master/test/bin/run-cwl | bash -s "kallisto_wf_se"
Paired-end input version:
$ curl https://raw.githubusercontent.com/pitagora-network/pitagora-cwl/master/test/bin/run-cwl | bash -s "kallisto_wf_pe"