dnaseq_slurm_api.sh

#!/usr/bin/env bash
# ANALYSIS_ID, FAMILY, and DATA are provided by STAGER

set -euo pipefail

# set environment variables
export ANNOTSV=/srv/shared/data/dccdipg/crg2-non-conda-tools/AnnotSV_2.1

# set pipeline variables
SF="/srv/shared/pipelines/crg2/Snakefile"; 
CP="/srv/shared/conda_envs/crg2-conda/";
SLURM="/srv/shared/pipelines/crg2/slurm_profile";
ANALYSIS_ID="$1"
FAMILY="$2"
# DATA is a json string in the format { participant1: [linked files], participant2: ['linked files']...}
DATA="$3"
FILEPATH="/srv/shared/analyses/exomes"
ANALYSIS_DIR="${FILEPATH}/${FAMILY}/${ANALYSIS_ID}"
CONFIG="${ANALYSIS_DIR}/config_cheo_ri.yaml"

source /storage/modules/anaconda/2020.11/etc/profile.d/conda.sh
conda activate /srv/shared/conda_envs/snakemake_5.10.0/

umask 0002
if [ ! -d "$ANALYSIS_DIR" ];then
    mkdir  -p "$ANALYSIS_DIR"
    python3 /srv/shared/pipelines/crg2/exome_setup_stager.py \
        -a "$ANALYSIS_DIR" \
        -f "$FAMILY" \
        -d "$DATA"
fi

cd "$ANALYSIS_DIR"

snakemake --use-conda -s "$SF" --conda-prefix "$CP" --configfile "$CONFIG" --profile "$SLURM" -p