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A lot of restructuring and cleanup has been made, to facilitate a meaningful wrapper. This commit includes: * A conceptual wrapper script * Removal of unused variables * A deployment_dir which are used to store databases and conda environments, as created by snakemake. * Reorganisation of files. * Metadata renamed to target_screening for now * Analysis relevant files are moved into config/analysis (e.g. species_configs) * reads/ and assemblies/ folder now located in data folder * samplesheet now located in data folder * examples/ folder removed * Added Test and Deploy to .gitignore, I suggest to use Test/Results for output_folder, and Deploy for deployment_dir * MLST-db-update rule removed completely, as MLST has removed the update script
* Illumina and Assembly paths removed from config and snakefile, now it must be specified directly in the samplesheet * Samplesheet changes: * Adeded Illumina_mate1 and _mate2 * Removed Nanopore path * Renamed Assembly path variable * Removed sample_to_illumina, _to_nanopore, & _assembly vars and replaced with samplesheet * Samples can be accessed as samplesheet.index * Updated rules to acces samplesheet directory Replaced lambda wildcards with lambda wc, to avoid confusion with snakemake.wildcards object
This was referenced Jan 13, 2026
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Maybe the config.yaml can be further streamlined of the illumina and nanopore reads path since they are specified in the samplesheet, the path is taken from there and not from the config.yaml, same as the assembly path and configuration file for the species. It is a bit redundant. |
Launcher has been added. Now config files are automatically created and executed FROM the launcher. A bit of polishing has been provided for all downstream files for supporting new launcher. Symbolic links of assembly files has NOT YET been added!
* If assemblies specified in samplesheet exists, it will be symlinked (unless allready exists as file and not link in results) * Tool versioning removed from assemblies, as this would disrupt the circumvension of assembly linking - Think about alternatives see #112 * Migrated contents of config/analysis into config/ for simplicity
KasperThystrup
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Should be working now |
Collaborator
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Closed for now, since it's already been merged into pkging branch (#110) |
KasperThystrup
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Adding a wrangler requires a lot of restructuring. Thus this PR wil drastically change the software architecture. I suggest to merge everything prior to this branch, and then to re-clone repo once this has been merged.