Nf phage finder #9
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Multistage docker builds + charliecloud for modules currently in main.
Nf run assembly
Nf reads taxonomy
aw-watson
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Oct 30, 2024
* initial commit * Prokka and RATT running * generating plots and KEGG pathway views * Full workflow, with explicit outputs and TODOs resolved. * Containerized * comments * Nf phage finder (#9) Merging two workflows with related functionality. * Image version bump and documentation for phageFinder
aw-watson
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Dec 23, 2024
* initial commit * Prokka and RATT running * generating plots and KEGG pathway views * Full workflow, with explicit outputs and TODOs resolved. * Containerized * comments * Nf phage finder (#9) Merging two workflows with related functionality. * proof of concept: linked runAnnotation and phageFinder, with phageFinder able to be turned on or off * restructured early pipeline. added nf-test infrastructure * testing added for sra2fastq * Testing for the first few modules * integrated hostRemoval * runAssembly in pipeline * host removal testing + cleanup * tests for runAssembly * reads to contig restructured as subworkflow. adding nf-test CI * fixing JDK version for CI * testing Apptainer for CI * cleanup * updated snapshots for JDK 17 * adding debugging output * more testing output for GH actions * added Git LFS to testing yml * adding sharding to tests - checking to see if this resolves space issues with the runner * removing files from LFS * basic testing for runReadsToContig * adding nf-test file * attempting optimized testing requirements * reverting testing strategy * host removal testing accounts for inconsistent file naming
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Merging annotation and phageFinder