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[Juke34]

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[Juke34]

• add csv input + test
• add AlineUtils to add functions (e.g. for name cleaning)
• params added by AliNe are now handled by sample (not globally. So ait was in main.nf header now it is a process) => All is saved in a new output file
• warn for best aligner according to data type is now a dedicated process
• remove skip-strandedness parameters (now strandedness empty is equivalent )
• new route for guessing strandedness and read length to avoid to redo the subsampling.
• now AliNe can handle several types of data_type in a single run (via csv)