debug ci tests dev #254
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debug ci tests dev #254
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* Adds --cleanup option to clean work directory * Adds explanatory comment to config for cleanup option * Adds "Workdir cleanup" param to pipeline summary * Adds --cleanup option description to help message * Adds --cleanup option description to usage.md * Adds singularity check in ci.yml (#240) * Adds local singularity profile (#239) * Adds profile to run with singularity locally * Adds docks on how to run the pipeline locally * Adds link to new docs to README.md * Renames profile to singularity * Adds singularity check in ci.yml (#240) * Renames singularity_local -> singularity everywhere Co-authored-by: cgpu <38183826+cgpu@users.noreply.github.com> * Adds workflow.onComplete notifications * Reduces ci tests (#241) * Reduces ci tests to only run on pull_request, not push * Reduces ci tests to only run with max_retries: 1 * Updates ci test nextflow version 19.04.0 -> 20.01.0 * Removes max_retries matrix option from ci tests Co-authored-by: cgpu <38183826+cgpu@users.noreply.github.com>
* Adds trimmomatic logs to multiqc report * Puts Trimmomatic above STAR in MultiQC report
Best solution to #246 is to update documentation.
Adding some clarification to address #247
Adding the description to run pipeline with bams.csv to documentation
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