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Samantha edited this page Nov 22, 2021 · 2 revisions

Welcome to the iCLIP Pipeline Dev Notes

Pipeline Maintenance

In progress dev work is stored on the activeDev branch. To work on the pipeline, users should run a Git clone on the latest version, then perform changes, push to branch, and commit.

Once changes are stable, and ready for production, two things should be completed:

  1. snakemake_config.yaml file should be updated to include a new version number: minor changes +0.1, significant, non-backwards compatible changes +1.

  2. All changes should be pushed to the main branch. Once merged, they should be tagged with the appropriate version number.The main branch should then be cloned directly to the RBL_NCI dir for public use.

cd /data/RBL_NCI/Pipelines/iCLIP/[version number]

Utilizing test data

Two tests were created for development use only. Test A will include a larger sample, to ensure peak calls while test B includes a smaller sample to ensure functionality of updates performed.

  1. Full test (multiplex_flag="Y", splice_aware="Y", DE_method="none")

    test_a: one sample, hg38

  2. Small test (multiplex_flag="Y", splice_aware="Y", DE_method="none")

    test_b: one sample, hg38

These tests can be called from the initialization script, as done with production-level tests For example, to run test_b:

sh /data/CCBR_Pipeliner/iCLIP/test/run_test.sh -t test_b -o /path/to/output/dir

Troubleshooting

Utilize the error script by running the script in the output folder.

cd /output/dir/log/timestamp/

sh 00_create_error_report.sh

If there are errors, you'll see a message to review the log.

cd /output/dir/log/timestamp/

cat error_log.txt
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