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| Code Block |
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params {
blastlocaldb = true
spades = true
contamination_detection = true
} |
Preparing the data
Preparing
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an index.csv file
You need to create a TAB delimited text file that will be the input for the workflow. By default the pipeline will look for a file called “index.csv” in the base directory but you can specify any file name using the --indexfile [filename] in the nextflow run command. This text file requires the following columns (which needs to be included as a header): sampleid,samplepath,minlen,maxlen:
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