Configuration file - AndreaRP/METAGENOMICS GitHub Wiki

Before starting the analysis you must create a configuration file with the following information and save it as pikaVirus.config inside the directory where you are executing the workflow.

Full path to the directory where the whole analysis will take place. It is optional and not used in the workflow, but it can make the config file cleaner.

Full path to your analysis directory. The analysis directory must contain a directory named 00-reads with all the raw reads you want to analyse. The raw reads can be gzipped or not, but must be paired end and with a file name with the following structure:

sampleName_*_R1__*.fastq.gz or sampleName_*_R1__*.fastq sampleName_*_R2__*.fastq.gz or sampleName_*_R2__*.fastq All the analysis directories will be automatically generated by pikaVirus inside this one. ### resultsDir="/absolute/path/to/your/results/directory/" Full path to the directory where you want your results to be generated. ### virDB="/absolute/path/to/your/virus/reference/directory/" Full path to the directory containg all the references for virus. The directory must contain already processed databases for blast and bowtie mapping. ### bacDB="/absolute/path/to/your/bacteria/reference/directory/" Full path to the directory containg all the references for bacteria. The directory must contain already processed databases for blast and bowtie mapping. ### fungiDB="/absolute/path/to/your/fungi/reference/directory/" Full path to the directory containg all the references for fungi. The directory must contain already processed databases for blast and bowtie mapping. ### invertebrateDB="/absolute/path/to/your/invertebarte/reference/directory/" Full path to the directory containg all the references for invertebrate. The directory must contain already processed databases for blast and bowtie mapping. ### protozoaDB="/absolute/path/to/your/protozoa/reference/directory/" Full path to the directory containg all the references for virus. The directory must contain already processed databases for blast and bowtie mapping. ### hostDB="/absolute/path/to/your/host/reference/directory/" Full path to the directory containg all the references for the host. The directory must contain already processed databases for blast and bowtie mapping.

All the information to generate the references can be found here