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…rust implementation of salmon, added rammap as minimap alternative, alevin-fry/piscem and simpleaf as well as oarfish. salmon can nor quantify directly from spliced bam as intended by creators. optional dtu processing via terminus for more stable calling
… code into extra modules, removed dead code
…d param assignment to pass strict syntax parser. Fixed tests to brevent breaks after fixing bugs in kallisto/salmon nf runs
…ows based on CIRI2 template
…whenever a specific monsda version is released for exactly that version, keeps tooling clean and in direct line with conda envs
…dle gz can also handle bgz, no check if bgz and gz files have same content, is silently expected and irrelevant if projects are created with monsda_configure
…nakemake/nextflow, added versions.py to collect tool versions used in config and export to file, all of this can be picked up by multiqc now and used for report generation
…meing and wildcard fixes, new test template and golden update
…k drifts for newer version
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