run_pipeline.sh

#!/bin/bash

set -euo pipefail

#----------------------------------------------#
# User parameters
if [ ! -z "${1}" ] || [ ! -z "${2}" ] || [ ! -z "${irods_input_projectID}" ]
then
    input_dir="${1}"
    output_dir="${2}"
    PROJECT_NAME="${irods_input_projectID}"
else
    echo "One of the parameters is missing, make sure there is an input directory, output directory and project name(param 1, 2 or irods_input_projectID)."
    exit 1
fi

if [ ! -d "${input_dir}" ] || [ ! -d "${output_dir}" ]
then
    echo "The input directory $input_dir, output directory $output_dir or fastq dir ${input_dir}/clean_fastq does not exist"
    exit 1
else
    input_fastq="${input_dir}/clean_fastq"
fi

case $PROJECT_NAME in

    rvp_spn)
        SPECIES="streptococcus_pneumoniae";;
    *)
        SPECIES="other";;
      
esac

#----------------------------------------------#
# Create/update necessary environments
PATH_MAMBA_YAML="envs/mamba.yaml"
PATH_MASTER_YAML="envs/population_master.yaml"
MAMBA_NAME=$(head -n 1 ${PATH_MAMBA_YAML} | cut -f2 -d ' ')
MASTER_NAME=$(head -n 1 ${PATH_MASTER_YAML} | cut -f2 -d ' ')

echo -e "\nUpdating necessary environments to run the pipeline..."

# Removing strict mode because it sometimes breaks the code for 
# activating an environment and for testing whether some variables
# are set or not
set +euo pipefail 

conda env update -f "${PATH_MAMBA_YAML}"
source activate "${MAMBA_NAME}"

mamba env update -f "${PATH_MASTER_YAML}"

source activate "${MASTER_NAME}"

#----------------------------------------------#
# Run the pipeline

echo -e "\nRun pipeline..."

if [ ! -z ${irods_runsheet_sys__runsheet__lsf_queue} ]; then
    QUEUE="${irods_runsheet_sys__runsheet__lsf_queue}"
else
    QUEUE="bio"
fi

set -euo pipefail

if [ ${SPECIES} == "streptococcus_pneumoniae" ]; then
    python population.py --queue "${QUEUE}" -i "${input_dir}" -o "${output_dir}" -s "${SPECIES}" --external-clustering
else
    python population.py --queue "${QUEUE}" -i "${input_dir}" -o "${output_dir}" -s "${SPECIES}"
fi

result=$?

# Propagate metadata

set +euo pipefail

SEQ_KEYS=
SEQ_ENV=`env | grep irods_input_sequencing`
for SEQ_AVU in ${SEQ_ENV}
do
    SEQ_KEYS="${SEQ_KEYS} ${SEQ_AVU%%=*}"
done

for key in $SEQ_KEYS irods_input_illumina__Flowcell irods_input_illumina__Instrument \
    irods_input_illumina__Date irods_input_illumina__Run_number irods_input_illumina__Run_Id
do
    if [ ! -z ${!key} ] ; then
        attrname=${key:12}
        attrname=${attrname/__/::}
        echo "${attrname}: '${!key}'" >> ${OUTPUTDIR}/metadata.yml
    fi
done

set -euo pipefail

exit ${result}