Snakemake

#!/bin/bash

# This is a custom wrapper script for Snakemake EukBook pipeline.

# Wrapper features:
# 1. By default sets snakemake options always used in EukBook pipeline. 
#    The only option stil required is is the samples file (see example). 
# 2. Additionally specifies the path to conda packages of pipeline.
# 3. Measures computation time with "time". 
# 4. Saves the entire stdout, as well as timing and start/end time
#    to non-default log file of desired location.

# Example minimal usege:
# ./Snakemake --configfile sample_yamls/samples_small.yaml
# Example with more options (all the options are passed to snakemake command) :
# ./Snakemake --configfile sample_yamls/samples_small.yaml --config Quick_mode=True -n -R Download_fastq


source MinIO_secret.sh

LOGDIR="${HOME}/snakemake_logs"
mkdir -p $LOGDIR
START=$(date +"%y-%m-%d_%H-%M-%S")
LOGFILE=${LOGDIR}/snakemake_${START}_log.txt


echo "Pipeline started on" ${START} > ${LOGFILE}

( /usr/bin/time -v snakemake -p -j --use-conda --conda-prefix ${HOME}/conda_snakemake_EukBook ${@} ) |& tee -a ${LOGFILE}

END=$(date +"%y-%m-%d_%H-%M-%S")

echo "Pipeline started on: " ${START}  >> ${LOGFILE}
echo "Pipeline ended on:   " ${END}    >> ${LOGFILE}