Commit 7deecaa1 authored by Deepti Mittal's avatar Deepti Mittal

Update README.md

parent e1c30f21
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* **Default run to the end of the workflow**
~~~
MG= <input/"MG.R1.fq"> <input/"MG.R2.fq"> MT=<input/"MT.R1.fq"> <input/"MT.R2.fq"> -o <output directory> CONDAPATH="/Path/to//IMP/conda" IMP_ASSEMBLER="megahit" snakemake -s /Path/to/IMP/Snakefile --use-conda -p;
MG= <input/"MG.R1.fq"> <input/"MG.R2.fq"> MT=<input/"MT.R1.fq"> <input/"MT.R2.fq"> -o <output directory> CONDAPATH="/Path/to//IMP/conda" DBPATH= "/Path/to/db" FILTER="hg38" IMP_ASSEMBLER="megahit" snakemake -s /Path/to/IMP/Snakefile --use-conda -p;
~~~
`<output directory>` is the directory where output files will be located.
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