Nf composition #15
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Nf composition #15
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…ues with the runner
aw-watson
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Jan 7, 2025
* 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 * Edits to match EDGE v3 UI * Nf composition (#15) This merge will change some workflow inputs, so it'll require additional commits to fix, but this is necessary for the repository restructuring happening. * 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 * updated tests for EDGEv3 inputs * fixed host removal for edgev3 settings * checking if testing issues related to ubuntu version * Actions testing uses compatible Apptainer version for ubuntu 24.04 * fixed badly merged snapshot for sra2fastq * continued snapshot fix
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Updating EDGEv3 branch with new subworkflows