• 1. Usage
  • 1.1. Step 1: Obtain a copy of this workflow
  • 1.2. Step 2: Configure workflow
  • 1.3. Step 3: Install Snakemake
  • 1.4. Step 4: Execute workflow
• 2. check output dir
• 3. Acknowledgements

# Snakemake workflow: Analysis of cfRNA signals captured by fragmentation patterns of cell-free RNA

1. Usage

1.1. Step 1: Obtain a copy of this workflow

#Clone the repository to the place to perform the data analysis
git clone https://github.com/hunnngry/tWPS.git

1.2. Step 2: Configure workflow

dst="GSE71008_NCpool"

#specify required parameters and file paths
vi config/$dst/config.yml

#specify your sample setup
vi config/$dst/samples.tsv

#specify target regions
vi config/$dst/regions.tsv

1.3. Step 3: Install Snakemake

Install Snakemake using conda:

conda create -c bioconda -c conda-forge -n tWPS snakemake

1.4. Step 4: Execute workflow

The workflows are executed from the repository root folder. The different analyses have to be executed separately. To specify the respective workflow use the -s switch followed by the path of the Snakefile (e.g.: ./snakemake/test.smk)

#Activate the conda environment
conda activate tWPS
mkdir -p log/${dst}

#Test your configuration by performing a dry-run via
snakemake \
    --snakefile snakemake/snakefile_WPS_RBP_tx.smk \
    --configfile config/${dst}/config.yml \
    -npr 

#op1: Run in local machine (PC/MAC)
snakemake --rerun-incomplete --keep-going --printshellcmds --reason --use-conda --nolock --latency-wait 20 --restart-times 1 --jobs 6  \
    --snakefile snakemake/snakefile_WPS_RBP_tx.smk \
    --configfile config/${dst}/config.yml \
    > log/${dst}/run-${dst}_local.log 2>&1

#op2: Run in cluster (bsub)
snakemake --rerun-incomplete --keep-going --printshellcmds --reason --use-conda --nolock --latency-wait 80 --restart-times 1 --jobs 100  \
    --snakefile snakemake/snakefile_WPS_RBP_tx.smk \
    --configfile config/${dst}/config.yml \
    --cluster-config snakemake/cluster/cluster-lsf.json \
    --cluster "bsub -n {cluster.threads} -J {cluster.jobname} -q {cluster.queue} -o {cluster.output} -e {cluster.error} " \
    > log/${dst}/run-${dst}_cluster.log 2>&1

2. check output dir

ls -hl results/intermediate/$dst

3. Acknowledgements

tWPS for cfRNA was adapted from WPS for cfDNA repository