Snakemake Workflow for miRNA detection

This is a snakemake pipeline to detect miRNA in samples.

Edit the configfile

You will need to edit your config file as described below:

The pipeline takes samples with a suffix 'r_1.fq.gz' and 'r_2.fq.gz' if the samples are paired. Or it takes samples with suffix 'fq.gz' if the samples is single-end reads.

Regardless your samples are paired, single-ended, samples names should be samples.tsv without the suffix.

The pipeline uses by default "mature.fa" from mirbase.

Run the pipeline

snakemake -jn

where n is the number of cores for example for 10 cores use:

snakemake -j10

Use conda

For less froodiness, use conda:

snakemake -jn --use-conda

For example, for 10 cores use:

snakemake -j10 --use-conda

This will pull automatically the same versiosn of tools we used. Conda has to be installed in the system, in addition to snakemake.

Dry Run

For a dry run use:

snakemake -j1 -n

and to print command in dry run use:

snakemake -j1 -n -p

Use Corresponding configfile:

Just update your config file to include all your sample names, edit your interval.list file to include your intervals of interest, your path, etc for example:

snakemake -j1 --configfile config-WES.yaml

or:

snakemake -j1 configfile config-WGS.yaml