run

#!/usr/bin/env bash
#$ -t 1
#$ -V
#$ -j y
#$ -cwd
#$ -o /dev/null
#$ -e /dev/null

# An example bash script demonstrating how to run the entire snakemake pipeline
# This script creates two separate log files:
# 	1) log - the basic snakemake log of completed rules
# 	2) qlog - a more detailed log of the progress of each rule and any errors

# Before running this snakemake pipeline, remember to verify that the config
# file has been appropriately completed with the required input info. In
# particular, make sure that you have created a samples.tsv file specifying
# paths to the fastq files for each of your samples.
# Make sure that this script is executed from the directory that it lives in!

# you can specify a dir for all output here
# it will override whatever value you set for the output_dir in the config file
out_path="out"
mkdir -p "$out_path"

# clear leftover log files
if [ -f "$out_path/log" ]; then
	echo ""> "$out_path/log";
fi
if [ -f "$out_path/qlog" ]; then
	echo ""> "$out_path/qlog";
fi

# try to find and activate the snakemake conda env if we need it
if ! command -v 'snakemake' &>/dev/null && \
   command -v 'conda' &>/dev/null && \
   [ "$CONDA_DEFAULT_ENV" != "snakemake" ] && \
   conda info --envs | grep "$CONDA_ROOT/snakemake" &>/dev/null; then
	echo "Snakemake not detected. Attempting to switch to snakemake environment." >> "$out_path/log"
	eval "$(conda shell.bash hook)"
	conda activate snakemake
fi

# check: are we being executed from within qsub?
if [ "$ENVIRONMENT" = "BATCH" ] || [[ $* == *--sge-cluster* ]]; then
	snakemake \
	--cluster "qsub -t 1 -V -j y -cwd -o $out_path/qlog" \
	--config output_dir="$out_path" \
	--latency-wait 60 \
	--use-conda \
	-k \
	-j 24 \
	--restart-times 2 \
	"$@" &>>"$out_path/log"
else
	snakemake \
	--config ouput_dir="$out_path" \
	--latency-wait 60 \
	--use-conda \
	-k \
	-j 24 \
	"$@" 2>>"$out_path/log" >>"$out_path/qlog"
fi

# message the user on slack if possible
exit_code="$?"
if command -v 'slack' &>/dev/null; then
	if [ "$exit_code" -eq 0 ]; then
		slack "snakemake finished successfully" &>/dev/null
	else
		slack "$(tail -n4 "$out_path/log")" &>/dev/null
	fi
fi
exit "$exit_code"