launch_pipeline.sh

#! /bin/sh

### ASDP PIPELINE ###
## Version: 0.0.1
## Licence: AGPLV3
## Author: Anne-Sophie Denommé-Pichon
## Description: script to launch the pipeline for STR detection. Receive multiple samples: one sample per line

# $1 : first argument in the command line : a list containing one sample per line, for exemple samples.list
SAMPLES="$1"

# Check if sample is specified
if [ -z "$SAMPLES" ]
then
    echo "List of samples is not specified"
    echo "$(date +"%F_%H-%M-%S"): END"
    exit 1
fi

# Source configuration file
. "$(dirname "$0")/config.sh"

# Parallel allow to parallelize the processing of multiple samples
"$PARALLEL" \
    --jobs "$PARALLEL_JOB_COUNT" \
    --line-buffer \
    "$(dirname "$0")/pipeline.sh" \
    < "$SAMPLES"