usage.txt

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USAGE
nextflow run metagenomics/MeRaGENE [OPTIONAL_ARGUMENTS] (--genome --ncbi --input --output --cov )

DESCRIPTION
MeRaGENE 0.1.0

--genome="/vol/genomeDat/test.faa"     Your faa to search in.

--ncbi="/vol/blastDat/blast.db"        Your blast-database to search in.

--input="/vol/project/hmmModels"       A folder containing hmm models. All hmm models in this folder are used for searching.

--output="/vol/project/output"         A folder path that the pipeline should produce.

--cov="/vol/cov1.txt,/vol/cov2.txt"    List your coverage files, link them here.


OPTIONAL ARGUMENTS

--blast_cpu=8                          Numbers of cores to be used executing blast.
    
--blastp="blastp"
--hmm_search="hmmsearch"
--hmm_scan="hmmscan"
--hmm_press="hmmpress"                 If you want to use a special version, change the name with its absolute path.
                                       E.g. blastp="blastp" -> blastp="/vol/tools/blast/blastp"
    
--hmm_cpu=16                           Numbers of cores to be used executing hmmsearch.

--hmm_evalue="1e-15"                   E-value threshold to be used executing hmmsearch.

--search="/vol/project/search.yaml"    If you want your results grouped, group them using a first level .yaml file.
                                       If you have downloaded MeRaGENE, you can look at the example file features/data/search.yaml
    
--keywords="/vol/project/keywords.txt" A text file, filled with one word per line.
                                       Publications associated with your blast hits will be scanned for these keywords.