/ccs-bam-to-fastq-qc-crate

Workflow Testing RO-Crate setup for CCS.BAM to FASTQ + QC

GNU General Public License v3.0GPL-3.0

ccs-bam-to-fastq-qc-crate

Workflow Testing RO-Crate setup for CCS.BAM to FASTQ + QC.

Steps followed

  • Installed Python prerequisites with pip install planemo repo2rocrate.
  • Clicked on the "Run on usegalaxy.eu" on the workflow's page in WorkflowHub to import the workflow in Galaxy Europe.
  • Uploaded ce#unmap2.bam to Galaxy to be used as an input file.
  • Ran the workflow on Galaxy and retrieved the invocation id from the Workflow Invocations page (User > Workflow Invocations).
  • Ran planemo workflow_test_init --galaxy_url https://usegalaxy.eu --from_invocation <INVOCATION_ID> --galaxy_user_key <GALAXY_API_KEY> (User > Preferences > Manage API Key). This generates an first version of the test setup including: the workflow file; a test-data directory containing the input and all outputs; the Planemo configuration file. The latter specifies an exact comparison of all output files with the expected ones (i.e., the ones under test-data, taken from the specified invocation).
  • Edited the test setup, changing some file names (note that if the workflow is named xyz.ga, the Planemo configuration file must be called xyz-tests.yml) and the configured checks (some outputs are in a free text format that may easily change between releases or even invocations, so an exact comparison would not be appropriate).
  • Added a simple GitHub Action workflow to run the test under .github/workflows/wftest.yml.
  • Generated the crate with repo2rocrate:
repo2rocrate \
  --repo-url https://github.com/simleo/ccs-bam-to-fastq-qc-crate \
  -o ccs-bam-to-fastq-qc.crate.zip

Copyright info

The Galaxy workflow bam-to-fastq-qc.ga has been copied from CCS.BAM to FASTQ + QC at version 1, created by Gareth Price and licensed under the GNU General Public License v3.0 or later.

The input data file test-data/ce#unmap2.bam has been copied from samtools@1224ffb, distributed under the following license:

The MIT/Expat License

Copyright (C) 2008-2022 Genome Research Ltd.

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