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autoDLML.sh
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#!/bin/bash
###########################################################################
######### ###########
######### AutoDL ###########
######### @uthor : D Baux david.baux<at>inserm.fr ###########
######### Date : 28/10/2021 ###########
######### ###########
###########################################################################
###########################################################################
###########
########### Script to automate MobiDL pipelines
########### to treat NGS data
###########
###########################################################################
#### This script is meant to be croned
#### must check the runs directory, identify new runs
#### and launch the appropriate MobiDL pipeline when a new run is available
############## If any option is given, print help message ##################################
VERSION=1.0
USAGE="
Program: AutoDLML
Version: ${VERSION}
Contact: Baux David <[email protected]>
Usage: This script is meant to be croned
Should be executed once per 10 minutes
"
if [ $# -ne 0 ]; then
echo "${USAGE}"
echo "Error Message : Arguments provided"
echo ""
exit 1
fi
RED='\033[0;31m'
LIGHTRED='\033[1;31m'
YELLOW='\033[1;33m'
BLUE='\033[0;34m'
NC='\033[0m'
# -- Script log
VERBOSITY=3
# -- Log variables
ERROR=1
WARNING=2
INFO=3
DEBUG=4
# -- Log functions got from cww.sh -- simplified here
error() { log "${ERROR}" "[${RED}error${NC}]" "$1" ; }
warning() { log "${WARNING}" "[${YELLOW}warn${NC}]" "$1" ; }
info() { log "${INFO}" "[${BLUE}info${NC}]" "$1" ; }
debug() { log "${DEBUG}" "[${LIGHTRED}debug${NC}]" "$1" ; }
# -- Print log
echoerr() { echo -e "$@" 1>&2 ; }
log() {
if [ "${VERBOSITY}" -ge "$1" ]; then
echoerr "[`date +'%Y-%m-%d %H:%M:%S'`] $2 - autoDLML version : ${VERSION} - $3"
fi
}
############### Get options from conf file ##################################
# CONFIG_FILE='./autoDL.conf'
CONFIG_FILE='/RS_IURC/data/MobiDL/panelCapture/conf/autoDL.conf'
#we check params against regexp
UNKNOWN=$(cat ${CONFIG_FILE} | grep -Evi "^(#.*|[A-Z0-9_]*=[a-z0-9_ \"\.\/\$\{\}\*-]*)$")
if [ -n "${UNKNOWN}" ]; then
error "Error in config file. Offending lines:"
error ${UNKNOWN}
exit 1
fi
source ${CONFIG_FILE}
############### 1st check whether another instance of the script is running ##################
RESULT=$(ps x | grep -v grep | grep -c ${SERVICE})
debug "${SERVICE} pids: $(ps x | grep -v grep |grep -c ${SERVICE})"
if [ "${RESULT}" -gt 3 ]; then
exit 0
fi
debug "CONFIG FILE: ${CONFIG_FILE}"
############### Get run info file ##################################
# the file contains the run id and a code
# 0 => not treated => to do - used to retreat a run in case ex of error
# 1 => nenufaar is running -in case the security above does not work
# 2 => run treated - ignore directory
# the file is stored in an array and modified by the script
declare -A RUN_ARRAY #init array
while read LINE
do
if echo ${LINE} | grep -E -v '^(#|$)' &>/dev/null; then
if echo ${LINE} | grep -F '=' &>/dev/null; then
RUN_ID=$(echo "${LINE}" | cut -d '=' -f 1)
RUN_ARRAY[${RUN_ID}]=$(echo "${LINE}" | cut -d '=' -f 2-)
fi
fi
done < ${RUNS_FILE}
#choosePipeline() {
# return $(${GREP} -F "${SAMPLE_SHEET}" "${SAMPLE_SHEET_DB}" | cut -d '=' -f 2)
#}
MAX_DEPTH=''
TRIGGER_FILE=''
TRIGGER_EXPR=''
SAMPLESHEET=''
assignVariables() {
#${RUN_PATH}
if [[ "${1}" =~ "MiniSeq" ]];then
MAX_DEPTH="${MINISEQ_MAX_DEPTH}"
TRIGGER_FILE="${MINISEQ_TRIGGER_FILE}"
TRIGGER_EXPR="${MINISEQ_TRIGGER_EXPR}"
SAMPLESHEET="${MINISEQ_SAMPLESHEET_PATH}"
elif [[ "${1}" =~ "MISEQ" ]];then
MAX_DEPTH="${MISEQ_MAX_DEPTH}"
TRIGGER_FILE="${MISEQ_TRIGGER_FILE}"
TRIGGER_EXPR="${MISEQ_TRIGGER_EXPR}"
SAMPLESHEET="${MISEQ_SAMPLESHEET_PATH}"
elif [[ "${1}" =~ "NEXTSEQ" ]];then
MAX_DEPTH="${NEXTSEQ_MAX_DEPTH}"
TRIGGER_FILE="${NEXTSEQ_TRIGGER_FILE}"
#TRIGGER_EXPR="${2} ${NEXTSEQ_TRIGGER_EXPR}"
TRIGGER_EXPR="${NEXTSEQ_TRIGGER_EXPR}"
SAMPLESHEET="${NEXTSEQ_SAMPLESHEET_PATH}"
fi
TMP_OUTPUT_DIR2="${TMP_OUTPUT_DIR}${RUN}/"
}
dos2unixIfPossible() {
if [[ "${RUN_PATH}" =~ "MiniSeq" || "${RUN_PATH}" =~ "MiSeq" ]];then
#if [ -w ${RUN_PATH}${RUN}/${SAMPLESHEET} ];then >/dev/null 2>&1
debug "dos2unix for ${RUN_PATH}${RUN}/${SAMPLESHEET}"
"${DOS2UNIX}" -q "${RUN_PATH}${RUN}/${SAMPLESHEET}"
debug "dos2unix for ${SAMPLESHEET_PATH}"
"${DOS2UNIX}" -q "${SAMPLESHEET_PATH}"
fi
}
#moveRunIfNecessary() {
# if [[ "${RUN_PATH}" =~ "NEXTSEQ" ]];then
#if [ !-w "${RUN_PATH}${RUN}/${SAMPLESHEET}" ];then
# ${RSYNC} -avq "${RUN_PATH}${RUN}" "${NEXTSEQ_RUNS_DEST_DIR}"
# if [ $? -eq 0 ];then
# RUN_PATH="${NEXTSEQ_RUNS_DEST_DIR}"
# else
# error "Error while syncing ${RUN_PATH}${RUN} to ${NEXTSEQ_RUNS_DEST_DIR}"
# fi
# fi
#}
modifyJsonAndLaunch() {
# debug "WDL:${WDL} - SAMPLE:${SAMPLE} - BED:${BED} - RUN:${RUN_PATH}${RUN}"
if [ ! -d "${AUTODL_DIR}/${RUN}" ];then
mkdir "${AUTODL_DIR}/${RUN}"
fi
if [[ ${BED} =~ (hg[0-9]{2}).+\.bed$ ]];then
GENOME=${BASH_REMATCH[1]}
else
GENOME=hg19
fi
debug "WDL:${WDL} - SAMPLE:${SAMPLE} - BED:${BED} - RUN:${RUN_PATH}${RUN} - GENOME:${GENOME}"
MOBIDL_JSON_TEMPLATE="${MOBIDL_JSON_DIR}${WDL}_inputs.json"
if [ "${GENOME}" != "hg19" ];then
MOBIDL_JSON_TEMPLATE="${MOBIDL_JSON_DIR}${WDL}_inputs_${GENOME}.json"
fi
debug "MOBIDL_JSON_TEMPLATE: ${MOBIDL_JSON_TEMPLATE}"
if [ ! -e "${MOBIDL_JSON_TEMPLATE}" ];then
error "No json file for ${WDL}: ${MOBIDL_JSON_DIR}${WDL}_inputs.json"
# if [ ! -e "${MOBIDL_JSON_DIR}${WDL}_inputs.json" ];then
# error "No json file for ${WDL}: ${MOBIDL_JSON_DIR}${WDL}_inputs.json"
else
cp "${MOBIDL_JSON_TEMPLATE}" "${AUTODL_DIR}${RUN}/${WDL}_${SAMPLE}_inputs.json"
# cp "${MOBIDL_JSON_DIR}${WDL}_inputs.json" "${AUTODL_DIR}${RUN}/${WDL}_${SAMPLE}_inputs.json"
JSON="${AUTODL_DIR}${RUN}/${WDL}_${SAMPLE}_inputs.json"
SUFFIX1=$(echo "${SAMPLES[${SAMPLE}]}" | cut -d ';' -f 1)
SUFFIX2=$(echo "${SAMPLES[${SAMPLE}]}" | cut -d ';' -f 2)
FASTQ_DIR=$(echo "${SAMPLES[${SAMPLE}]}" | cut -d ';' -f 3)
#https://stackoverflow.com/questions/6744006/can-i-use-sed-to-manipulate-a-variable-in-bash
#bash native character replacement
FASTQ_SED=${FASTQ_DIR////\\/}
ROI_SED=${ROI_DIR////\\/}
#RUN_SED=${RUN_PATH////\\/}
if [ ! -d "${TMP_OUTPUT_DIR2}" ];then
mkdir "${TMP_OUTPUT_DIR2}"
fi
TMP_OUTPUT_SED=${TMP_OUTPUT_DIR2////\\/}
sed -i.bak -e "s/\( \"${WDL}.sampleID\": \"\).*/\1${SAMPLE}\",/" \
-e "s/\( \"${WDL}\.suffix1\": \"\).*/\1_${SUFFIX1}\",/" \
-e "s/\( \"${WDL}\.suffix2\": \"\).*/\1_${SUFFIX2}\",/" \
-e "s/\( \"${WDL}\.fastqR1\": \"\).*/\1${FASTQ_SED}\/${SAMPLE}_${SUFFIX1}\.fastq\.gz\",/" \
-e "s/\( \"${WDL}\.fastqR2\": \"\).*/\1${FASTQ_SED}\/${SAMPLE}_${SUFFIX2}\.fastq\.gz\",/" \
-e "s/\( \"${WDL}\.workflowType\": \"\).*/\1${WDL}\",/" \
-e "s/\( \"${WDL}\.intervalBedFile\": \"\).*/\1${ROI_SED}${BED}\",/" \
-e "s/\( \"${WDL}\.bedFile\": \"\).*/\1\/dv2\/refData\/intervals\/${BED}\",/" \
-e "s/\( \"${WDL}\.outDir\": \"\).*/\1${TMP_OUTPUT_SED}\",/" \
-e "s/\( \"${WDL}\.dvOut\": \"\).*/\1\/dv2\/tmp_output\/${RUN}\"/" "${JSON}"
# if [ "${GENOME}" != "hg19" ];then # need more than just that - changed template see above
# sed "s/hg19/${GENOME}/g" "${JSON}"
# fi
rm "${JSON}.bak"
debug "$(cat ${JSON})"
info "${RUN} - ${SAMPLE} ready for ${WDL}"
info "Launching:"
info "sh ${CWW} -e ${CROMWELL} -o ${CROMWELL_OPTIONS} -c ${CROMWELL_CONF} -w ${WDL}.wdl -i ${JSON}"
if [ ! -d "${TMP_OUTPUT_DIR2}Logs" ];then
mkdir "${TMP_OUTPUT_DIR2}Logs"
fi
touch "${TMP_OUTPUT_DIR2}Logs/${SAMPLE}_${WDL}.log"
info "MobiDL ${WDL} log for ${SAMPLE} in ${TMP_OUTPUT_DIR2}Logs/${SAMPLE}_${WDL}.log"
# actual launch and copy in the end
sh "${CWW}" -e "${CROMWELL}" -o "${CROMWELL_OPTIONS}" -c "${CROMWELL_CONF}" -w "${WDL}.wdl" -i "${JSON}" >> "${TMP_OUTPUT_DIR2}Logs/${SAMPLE}_${WDL}.log"
if [ $? -eq 0 ];then
workflowPostTreatment "${WDL}"
else
# GATK_LEFT_ALIGN_INDEL_ERROR=$(grep 'the range cannot contain negative indices' "${TMP_OUTPUT_DIR2}Logs/${SAMPLE}_${WDL}.log")
# david 20210215 replace with below because of cromwell change does not report errors in main logs anymore
GATK_LEFT_ALIGN_INDEL_ERROR=$(egrep 'Job panelCapture.gatkLeftAlignIndels:....? exited with return code 3' "${TMP_OUTPUT_DIR2}Logs/${SAMPLE}_${WDL}.log")
# search for an error with gatk LAI - if found relaunch without this step
# cannot explain this error - maybe a gatk bug?
if [ "${GATK_LEFT_ALIGN_INDEL_ERROR}" != '' ];then
sh "${CWW}" -e "${CROMWELL}" -o "${CROMWELL_OPTIONS}" -c "${CROMWELL_CONF}" -w "${WDL}_noGatkLai.wdl" -i "${JSON}" >> "${TMP_OUTPUT_DIR2}Logs/${SAMPLE}_${WDL}_noGatkLai.log"
if [ $? -eq 0 ];then
info "GATK LeftAlignIndel Error occured - relaunching MobiDL without this step"
workflowPostTreatment "${WDL}_noGatkLai"
else
error "Error while executing ${WDL}_noGatkLai for ${SAMPLE} in run ${RUN_PATH}${RUN}"
fi
else
error "Error while executing ${WDL} for ${SAMPLE} in run ${RUN_PATH}${RUN}"
fi
fi
fi
}
workflowPostTreatment() {
# if [[ "${RUN_PATH}" =~ "NEXTSEQ" ]];then
# RUN_PATH="${NEXTSEQ_RUNS_DEST_DIR}"
# elif [[ "${RUN_PATH}" =~ "MISEQ" ]];then
# RUN_PATH="${MISEQ_RUNS_DEST_DIR}"
# fi
# copy to final destination
${RSYNC} -aq --no-g --chmod=ugo=rwX -remove-source-files "${TMP_OUTPUT_DIR2}Logs/${SAMPLE}_${1}.log" "${TMP_OUTPUT_DIR2}${SAMPLE}"
info "Moving MobiDL sample ${SAMPLE} to ${OUTPUT_PATH}${RUN}/MobiDL/"
# ${RSYNC} -avq --no-g --chmod=ugo=rwX "${TMP_OUTPUT_DIR2}${SAMPLE}" "${OUTPUT_PATH}${RUN}/MobiDL/"
${RSYNC} -aqz --no-g --chmod=ugo=rwX "${TMP_OUTPUT_DIR2}${SAMPLE}" "${OUTPUT_PATH}${RUN}/MobiDL/"
if [ $? -eq 0 ];then
rm -r "${TMP_OUTPUT_DIR2}${SAMPLE}"
else
error "Error while syncing ${1} for ${SAMPLE} in run ${OUTPUT_PATH}${RUN}"
fi
# remove cromwell data
WORKFLOW_ID=$(grep "${CROMWELL_ID_EXP}" "${TMP_OUTPUT_DIR2}Logs/${SAMPLE}_${1}.log" | rev | cut -d ' ' -f 1 | rev)
if [[ -n "${WORKFLOW_ID}" ]]; then
# test récupérer le path courant
rm -r "./cromwell-executions/panelCapture/${WORKFLOW_ID}"
info "removed cromwell data for ${WORKFLOW_ID}"
fi
}
setvariables() {
ACHAB=captainAchab
ACHAB_TODO_DIR_SED=${ACHAB_TODO_DIR////\\/}
GENE_FILE_SED=${GENE_FILE////\\/}
RUN_PATH_SED=${RUN_PATH////\\/}
OUTPUT_PATH_SED=${OUTPUT_PATH////\\/}
ROI_DIR_SED=${ROI_DIR////\\/}
}
setjsonvariables() {
sed -i -e "s/\( \"${ACHAB}\.sampleID\": \"\).*/\1${SAMPLE}\",/" \
-e "s/\( \"${ACHAB}\.affected\": \"\).*/\1${SAMPLE}\",/" \
-e "s/\( \"${ACHAB}\.inputVcf\": \"\).*/\1${ACHAB_TODO_DIR_SED}${SAMPLE}\/${SAMPLE}\.vcf\",/" \
-e "s/\( \"${ACHAB}\.diseaseFile\": \"\).*/\1${ACHAB_TODO_DIR_SED}${SAMPLE}\/disease.txt\",/" \
-e "s/\( \"${ACHAB}\.genesOfInterest\": \"\).*/\1${GENE_FILE_SED}\",/" \
-e "s/\( \"${ACHAB}\.outDir\": \"\).*/\1${OUTPUT_PATH_SED}${RUN}\/MobiDL\/${SAMPLE}\/${ACHAB_DIR}\/\",/" \
"${1}"
}
modifyAchabJson() {
ACHAB_DIR=CaptainAchab
if [ "${MANIFEST}" != "GenerateFastQWorkflow" ] && [ "${MANIFEST}" != "GenerateFASTQ" ] && [ "${JSON_SUFFIX}" == "CFScreening" ]; then
ACHAB_DIR=CaptainAchabCFScreening
fi
setjsonvariables "${OUTPUT_PATH}${RUN}/MobiDL/${SAMPLE}/${SAMPLE}/captainAchab_inputs.json"
# move achab input folder in todo folder for autoachab
cp -R "${OUTPUT_PATH}${RUN}/MobiDL/${SAMPLE}/${SAMPLE}/" "${ACHAB_TODO_DIR}"
ACHAB_DIR=CaptainAchab
}
prepareAchab() {
# function to prepare dirs for autoachab execution
if [ ! -d "${OUTPUT_PATH}${RUN}/MobiDL/${SAMPLE}/${SAMPLE}/" ];then
mkdir "${OUTPUT_PATH}${RUN}/MobiDL/${SAMPLE}/${SAMPLE}/"
fi
# disease and genes of interest files
debug "Manifest file: ${MANIFEST}"
debug "BED file: ${BED}"
unset DISEASE_FILE
unset GENE_FILE
unset JSON_SUFFIX
if [ "${MANIFEST}" != "GenerateFastQWorkflow" ] && [ "${MANIFEST}" != "GenerateFASTQ" ]; then
DISEASE_FILE=$(grep "${MANIFEST%?}" "${ROI_FILE}" | cut -d '=' -f 2 | cut -d ',' -f 4)
GENE_FILE=$(grep "${MANIFEST%?}" "${ROI_FILE}" | cut -d '=' -f 2 | cut -d ',' -f 3)
JSON_SUFFIX=$(grep "${MANIFEST%?}" "${ROI_FILE}" | cut -d '=' -f 2 | cut -d ',' -f 5)
else
debug "FASTQ workflows file: ${FASTQ_WORKFLOWS_FILE}"
DISEASE_FILE=$(grep "${BED}" "${FASTQ_WORKFLOWS_FILE}" | cut -d ',' -f 3)
GENE_FILE=$(grep "${BED}" "${FASTQ_WORKFLOWS_FILE}" | cut -d ',' -f 2)
JSON_SUFFIX=$(grep "${BED}" "${FASTQ_WORKFLOWS_FILE}" | cut -d ',' -f 4)
fi
# do it only once
# we keep on filling the example conf file for merge_multisample
# if [ -z "${FAMILY_FILE_CREATED}" ];then
if [ "${FAMILY_FILE_CREATED}" -eq 0 ];then
if [ -z "${FAMILY_FILE_CONFIG}" ];then
# we need to redefine the file path - can happen with MiniSeq when the fastqs are imported manually (thks LRM2)
FAMILY_FILE_CONFIG="${BASE_DIR}Families/${RUN}/Example_file_config.txt"
fi
debug "Family config file: ${FAMILY_FILE_CONFIG}"
echo "BASE_JSON=${MOBIDL_JSON_DIR}captainAchab_inputs_${JSON_SUFFIX}.json" >> "${FAMILY_FILE_CONFIG}"
echo "DISEASE_FILE=${DISEASE_ACHAB_DIR}${DISEASE_FILE}" >> "${FAMILY_FILE_CONFIG}"
echo "GENES_OF_INTEREST=${GENE_FILE}" >> "${FAMILY_FILE_CONFIG}"
echo "ACHAB_TODO=/RS_IURC/data/MobiDL/captainAchab/Todo/" >> "${FAMILY_FILE_CONFIG}"
echo "##### FIN ne pas modifier si analyse auto" >> "${FAMILY_FILE_CONFIG}"
echo "NUM_FAM=" >> "${FAMILY_FILE_CONFIG}"
echo "TRIO=" >> "${FAMILY_FILE_CONFIG}"
echo "# si oui" >> "${FAMILY_FILE_CONFIG}"
echo "CI=" >> "${FAMILY_FILE_CONFIG}"
echo "FATHER=" >> "${FAMILY_FILE_CONFIG}"
echo "MOTHER=" >> "${FAMILY_FILE_CONFIG}"
echo "AFFECTED=" >> "${FAMILY_FILE_CONFIG}"
echo "# si non" >> "${FAMILY_FILE_CONFIG}"
echo "HEALTHY=" >> "${FAMILY_FILE_CONFIG}"
FAMILY_FILE_CREATED=1
fi
# treat VCF for CF screening => restrain to given regions
if [ "${MANIFEST}" != "GenerateFastQWorkflow" ] && [ "${MANIFEST}" != "GenerateFASTQ" ] && [ "${JSON_SUFFIX}" == "CFScreening" ]; then
# https://www.biostars.org/p/69124/
# bedtools intersect -a myfile.vcf.gz -b myref.bed -header > output.vcf
"${BEDTOOLS}" intersect -a "${OUTPUT_PATH}${RUN}/MobiDL/${SAMPLE}/panelCapture/${SAMPLE}.vcf.gz" -b "${ROI_DIR}CF_screening_v2.bed" -header > "${OUTPUT_PATH}${RUN}/MobiDL/${SAMPLE}/${SAMPLE}/${SAMPLE}.vcf"
fi
if [ ! -f "${OUTPUT_PATH}${RUN}/MobiDL/${SAMPLE}/${SAMPLE}/${SAMPLE}.vcf" ];then
# if not CF then just copy the VCF
cp "${OUTPUT_PATH}${RUN}/MobiDL/${SAMPLE}/panelCapture/${SAMPLE}.vcf" "${OUTPUT_PATH}${RUN}/MobiDL/${SAMPLE}/${SAMPLE}/"
fi
debug "Disease file: ${DISEASE_FILE}"
debug "Genes file: ${GENE_FILE}"
if [ -n "${DISEASE_FILE}" ] && [ -n "${GENE_FILE}" ] && [ -n "${JSON_SUFFIX}" ]; then
# cp disease file in achab input dir
cp "${DISEASE_ACHAB_DIR}${DISEASE_FILE}" "${OUTPUT_PATH}${RUN}/MobiDL/${SAMPLE}/${SAMPLE}/disease.txt"
# cp json file in achab input dir and modify it
cp "${MOBIDL_JSON_DIR}captainAchab_inputs_${JSON_SUFFIX}.json" "${OUTPUT_PATH}${RUN}/MobiDL/${SAMPLE}/${SAMPLE}/captainAchab_inputs.json"
setvariables
modifyAchabJson
# If CF then copy original VCF from CF_panel bed file to Achab ready dir for future analysis
if [ "${MANIFEST}" != "GenerateFastQWorkflow" ] && [ "${MANIFEST}" != "GenerateFASTQ" ] && [ "${JSON_SUFFIX}" == "CFScreening" ]; then
cp "${OUTPUT_PATH}${RUN}/MobiDL/${SAMPLE}/panelCapture/${SAMPLE}.vcf" "${OUTPUT_PATH}${RUN}/MobiDL/${SAMPLE}/${SAMPLE}/"
cp "${MOBIDL_JSON_DIR}captainAchab_inputs_CFPanel.json" "${OUTPUT_PATH}${RUN}/MobiDL/${SAMPLE}/${SAMPLE}/captainAchab_inputs.json"
ACHAB_DIR_OLD="${ACHAB_DIR}"
ACHAB_DIR=CaptainAchabCFPanel
setjsonvariables "${OUTPUT_PATH}${RUN}/MobiDL/${SAMPLE}/${SAMPLE}/captainAchab_inputs.json"
ACHAB_DIR="${ACHAB_DIR_OLD}"
fi
fi
}
prepareGatkCnv() {
cp "${AUTODL_DIR}gatk_cnv.yaml" "${1}"
# sed -i -e "s/OUTPUT_DIR:/OUTPUT_DIR:${OUTPUT_PATH_SED}${RUN}\/MobiDL\/alignment_files\/gatk_cnv/" \
# -e "s/SAMPLES_PATH:/SAMPLES_PATH:${OUTPUT_PATH_SED}${RUN}\/MobiDL\/alignment_files/" \
# -e "s/BED_PATH:/BED_PATH:${ROI_DIR_SED}${BED}/" \
# "${OUTPUT_PATH}${RUN}/MobiDL/alignment_files/gatk_cnv.yaml"
sed -i -e "s/OUTPUT_DIR:/OUTPUT_DIR: ${OUTPUT_PATH_SED}${RUN}\/MobiDL\/alignment_files\/${2}gatk_cnv/" \
-e "s/SAMPLES_PATH:/SAMPLES_PATH: ${OUTPUT_PATH_SED}${RUN}\/MobiDL\/alignment_files\/${2}/" \
-e "s/BED_PATH:/BED_PATH: ${ROI_DIR_SED}${BED}/" \
-e "s/VCF_path:/VCF_path: ${OUTPUT_PATH_SED}${RUN}\/MobiDL\/MobiCNVvcfs/" \
"${1}gatk_cnv.yaml"
}
############### Now we'll have a look at the content of the directories ###############################
# http://moinne.com/blog/ronald/bash/list-directory-names-in-bash-shell
# --time-style is used here to ensure awk $8 will return the right thing (dir name)
RUN_PATHS="${MINISEQ_RUNS_DIR} ${MISEQ_RUNS_DIR} ${NEXTSEQ_RUNS_DIR}"
for RUN_PATH in ${RUN_PATHS}
do
debug "RUN_PATH:${RUN_PATH}"
# assignVariables "${RUN_PATH}"
OUTPUT_PATH=${RUN_PATH}
RUNS=$(ls -l --time-style="long-iso" ${RUN_PATH} | egrep '^d' | awk '{print $8}' | egrep '^[0-9]{6}_')
for RUN in ${RUNS}
do
###### do not look at runs set to 2 in the runs.txt file
if [ -z "${RUN_ARRAY[${RUN}]}" ] || [ "${RUN_ARRAY[${RUN}]}" -eq 0 ]; then
assignVariables "${RUN_PATH}"
debug "SAMPLESHEET:${SAMPLESHEET},MAX_DEPTH:${MAX_DEPTH},TRIGGER_FILE:${TRIGGER_FILE},TRIGGER_EXPR:${TRIGGER_EXPR}"
# now we must look for the AnalysisLog.txt file
# get finished run
if [[ -n $(find "${RUN_PATH}${RUN}" -mindepth 1 -maxdepth ${MAX_DEPTH} -type f -name "${TRIGGER_FILE}" -exec egrep "${TRIGGER_EXPR}" "{}" \; -quit) ]]; then
# need to determine BED ROI from samplesheet
SAMPLESHEET_PATH="${RUN_PATH}${RUN}/${SAMPLESHEET}"
# if [ -e ${RUN_PATH}${RUN}/${SAMPLESHEET} ];then
debug "SAMPLESHEET PATH TESTED:${SAMPLESHEET_PATH}"
###### if multiple sample sheets found in the run ,if [[ -f ${SAMPLESHEET_PATH} ]] does not work!!!!
###### we need to split get the latest - david 20210307
if [[ ! -f ${SAMPLESHEET_PATH} ]];then
debug "FAILED SAMPLESHEET:${SAMPLESHEET_PATH}"
SAMPLESHEET_LIST=$(ls ${SAMPLESHEET_PATH})
debug "SAMPLESHEET_LIST:${SAMPLESHEET_LIST}"
# https://linuxhint.com/bash_split_examples/
IFS=' '
readarray -t SAMPLESHEET_ARRAY <<< $(ls ${SAMPLESHEET_PATH})
debug "LAST SAMPLESHEET:${SAMPLESHEET_ARRAY[-1]}"
SAMPLESHEET_PATH="${SAMPLESHEET_ARRAY[-1]}"
IFS=$'\n'
fi
if [[ -r ${SAMPLESHEET_PATH} ]];then
debug "SAMPLESHEET TESTED:${SAMPLESHEET_PATH}"
info "RUN ${RUN} found for analysis"
dos2unixIfPossible
TREATED=0
unset MANIFEST
unset BED
unset WDL
MANIFEST=$(grep -F -e "`cat ${ROI_FILE} | cut -d '=' -f 1`" ${SAMPLESHEET_PATH} | cut -d ',' -f 2)
if [ -n "${MANIFEST}" ];then
BED=$(grep "${MANIFEST%?}" "${ROI_FILE}" | cut -d '=' -f 2 | cut -d ',' -f 1)
# Multiple library types in one single run
# Description,MultiLibraries,,,,,,,,,
MULTIPLE=$(grep "MultiLibraries" ${SAMPLESHEET_PATH} | cut -d ',' -f 2)
debug "MANIFEST: ${MANIFEST}"
debug "BED: ${BED}"
debug "MULTIPLE: ${MULTIPLE}"
if [ ${BED} == "FASTQ" ];then
MANIFEST="GenerateFASTQ"
fi
debug "MANIFEST: ${MANIFEST}"
if [[ ${BED} =~ (hg[0-9]{2}).+\.bed$ ]];then
GENOME=${BASH_REMATCH[1]}
else
GENOME=hg19
fi
debug "${MANIFEST%?}:${BED}"
debug "GENOME:${GENOME}"
info "BED file to be used for analysis of run ${RUN}:${BED}"
if [ "${BED}" = "FASTQ" ] && [ -z "${MULTIPLE}" ];then
# GenerateFASTQ modes
BED=$(grep -m1 'Description,' ${SAMPLESHEET_PATH} | cut -d ',' -f 2 | cut -d '#' -f 1)
debug "BED: ${BED} - WDL: ${WDL}"
debug "ROI_DIR: ${ROI_DIR}${BED}"
if [ ! -f "${ROI_DIR}${BED}" ];then
BED=''
fi
# WDL=$(grep -m1 'Description,' ${SAMPLESHEET_PATH} | cut -d ',' -f 2 | cut -d '#' -f 2)
# dos2unix fails on 140 for weird permission issue
WDL=$(cat ${SAMPLESHEET_PATH} | sed $'s/\r//' | grep -m1 'Description,' | cut -d ',' -f 2 | cut -d '#' -f 2)
debug "BED: ${BED} - WDL: ${WDL}"
# elif [ -n "${MULTIPLE}" ];then
# WDL=$(grep "${MANIFEST%?}" "${ROI_FILE}" | cut -d '=' -f 2 | cut -d ',' -f 2)
# BED="perSampleRoi"
# WDL="perSampleWorkflow"
# else
# WDL=$(grep "${MANIFEST%?}" "${ROI_FILE}" | cut -d '=' -f 2 | cut -d ',' -f 2)
# fi
else
WDL=$(grep "${MANIFEST%?}" "${ROI_FILE}" | cut -d '=' -f 2 | cut -d ',' -f 2)
if [ -n "${MULTIPLE}" ];then
BED="perSampleRoi"
WDL="perSampleWorkflow"
fi
fi
if [ -n "${MANIFEST}" ] && [ -n "${WDL}" ] && [ -n "${BED}" ];then
info "MobiDL workflow to be launched for run ${RUN}:${WDL}"
if [ -z "${RUN_ARRAY[${RUN}]}" ];then
echo ${RUN}=1 >> ${RUNS_FILE}
RUN_ARRAY[${RUN}]=1
elif [ "${RUN_ARRAY[${RUN}]}" -eq 0 ];then
#Change value on array and file to running
sed -i -e "s/${RUN}=0/${RUN}=1/g" "${RUNS_FILE}"
RUN_ARRAY[${RUN}]=1
fi
if [[ "${RUN_PATH}" =~ "NEXTSEQ" ]];then
OUTPUT_PATH=${NEXTSEQ_RUNS_DEST_DIR}
if [ ! -d "${OUTPUT_PATH}${RUN}" ];then
mkdir -p "${OUTPUT_PATH}${RUN}"
fi
elif [[ "${RUN_PATH}" =~ "MISEQ" ]];then
OUTPUT_PATH=${MISEQ_RUNS_DEST_DIR}
if [ ! -d "${OUTPUT_PATH}${RUN}" ];then
mkdir -p "${OUTPUT_PATH}${RUN}"
fi
fi
if [ ! -d "${BASE_DIR}Families/${RUN}" ];then
# create folder meant to put family files for afterwards merging
mkdir -p "${BASE_DIR}Families/${RUN}"
chmod -R 777 "${BASE_DIR}Families/${RUN}"
# create example config file for merge_multisample.sh
# RUN_PATH=/RS_IURC/data/NextSeq/nd/2021 # ou trouver le répertoire de base qui contient le run
# BASE_JSON=/usr/local/share/refData/mobidlJson/captainAchab_inputs_ND.json # json pour achab
# DISEASE_FILE=/usr/local/share/refData/disease_achab/disease_ND.txt # fichier disease contenant les codes HPO de la famille
# GENES_OF_INTEREST=/RS_IURC/data/MobiDL/captainAchab/Example/nd.txt # gènes à mettre en avant dans achab
# ACHAB_TODO=/RS_IURC/data/MobiDL/captainAchab/
# RUN_ID=210924_NB501631_0419_AH5LHNBGXK
# NUM_FAM=
# TRIO=
# # si oui
# CI=
# FATHER=
# MOTHER=
# AFFECTED=
# # si non
# HEALTHY=
FAMILY_FILE_CONFIG="${BASE_DIR}Families/${RUN}/Example_file_config.txt"
touch "${FAMILY_FILE_CONFIG}"
chmod -R 777 "${BASE_DIR}Families/${RUN}"
echo "##### DEBUT ne pas modifier les champs ci-dessous si analyse auto" > "${FAMILY_FILE_CONFIG}"
echo "RUN_PATH=${OUTPUT_PATH}" >> "${FAMILY_FILE_CONFIG}"
echo "RUN_ID=${RUN}" >> "${FAMILY_FILE_CONFIG}"
FAMILY_FILE_CREATED=0
fi
if [ ! -d "${OUTPUT_PATH}${RUN}/MobiDL" ];then
mkdir "${OUTPUT_PATH}${RUN}/MobiDL"
fi
if [ ! -d "${OUTPUT_PATH}${RUN}/MobiDL/MobiCNVtsvs/" ];then
mkdir "${OUTPUT_PATH}${RUN}/MobiDL/MobiCNVtsvs/"
fi
if [ ! -d "${OUTPUT_PATH}${RUN}/MobiDL/MobiCNVvcfs/" ];then
mkdir "${OUTPUT_PATH}${RUN}/MobiDL/MobiCNVvcfs/"
fi
# now we have to identifiy samples in fastqdir (identify fastqdir,which may change depending on the Illumina workflow) then sed on json model, then launch wdl workflow
declare -A SAMPLES
FASTQS=$(find "${RUN_PATH}${RUN}" -mindepth 1 -maxdepth 4 -type f -name *.fastq.gz | grep -v 'Undetermined' | sort)
for FASTQ in ${FASTQS[@]};do
FILENAME=$(basename "${FASTQ}" ".fastq.gz")
# debug "SAMPLE FILENAME:${FILENAME}"
REGEXP='^([a-zA-Z0-9-]+)_(.+)$'
if [[ ${FILENAME} =~ ${REGEXP} ]];then
if [ ${SAMPLES["${BASH_REMATCH[1]}"]} ];then
SAMPLES["${BASH_REMATCH[1]}"]="${SAMPLES[${BASH_REMATCH[1]}]};${BASH_REMATCH[2]};${FASTQ%/*}"
# debug "SAMPLE:${SAMPLES[${BASH_REMATCH[1]}]};${BASH_REMATCH[2]};${FASTQ%/*}"
else
SAMPLES["${BASH_REMATCH[1]}"]=${BASH_REMATCH[2]}
fi
else
warning "SAMPLE DOES NOT MATCH REGEXP ${REGEXP}: ${FILENAME} ${RUN_PATH}${RUN}"
fi
done
# ifcnv/gatk_cnv specific feature: create a folder with symbolic links to the alignment files
mkdir -p "${OUTPUT_PATH}${RUN}/MobiDL/alignment_files/"
declare -A ROI_TYPES
for SAMPLE in ${!SAMPLES[@]};do
if [[ ${MULTIPLE} != '' ]];then
# Multiple library types in one single run
# returns ",roi1.bed#panelCapture" => bed#wdl...
# NEXTSEQ
DESCRIPTION_FIELD=11
if [[ "${RUN_PATH}" =~ "MISEQ" ]];then
DESCRIPTION_FIELD=10
elif [[ "${RUN_PATH}" =~ "MINISEQ" ]];then
DESCRIPTION_FIELD=3
fi
# if [[ "${RUN_PATH}" =~ "NEXTSEQ" ]];then
# BED=$(grep "${SAMPLE}," "${SAMPLESHEET_PATH}" | cut -d "," -f 11 | cut -d "#" -f 1)
# WDL=$(grep "${SAMPLE}," "${SAMPLESHEET_PATH}" | cut -d "," -f 11 | cut -d "#" -f 2)
# elsif [[ "${RUN_PATH}" =~ "MISEQ" ]];then
# BED=$(grep "${SAMPLE}," "${SAMPLESHEET_PATH}" | cut -d "," -f 10 | cut -d "#" -f 1)
# WDL=$(cat ${SAMPLESHEET_PATH} | sed $'s/\r//' | grep "${SAMPLE}," | cut -d "," -f 103 | cut -d "#" -f 2)
# fi
# elsif [[ "${RUN_PATH}" =~ "MINISEQ" ]];then
# BED=$(grep "${SAMPLE}," "${SAMPLESHEET_PATH}" | cut -d "," -f 3 | cut -d "#" -f 1)
# WDL=$(cat ${SAMPLESHEET_PATH} | sed $'s/\r//' | grep "${SAMPLE}," | cut -d "," -f 3 | cut -d "#" -f 2)
# fi
BED=$(grep "${SAMPLE}," "${SAMPLESHEET_PATH}" | cut -d "," -f ${DESCRIPTION_FIELD} | cut -d "#" -f 1)
WDL=$(cat ${SAMPLESHEET_PATH} | sed $'s/\r//' | grep "${SAMPLE}," | cut -d "," -f ${DESCRIPTION_FIELD} | cut -d "#" -f 2)
SAMPLE_ROI_TYPE=$(grep "${SAMPLE}," "${SAMPLESHEET_PATH}" | cut -d "," -f 11 | cut -d "#" -f 1 | cut -d "." -f 1)
info "MULTIPLE SAMPLE:${SAMPLE} - BED:${BED} - WDL:${WDL} - SAMPLE_ROI_TYPE:${SAMPLE_ROI_TYPE}"
# exit 0
# check custom output PATH
# info "MANIFEST: ${MANIFEST}"
# if [ "${MANIFEST}" = "GenerateFastQWorkflow" ] || [ "${MANIFEST}" = "GenerateFASTQ" ];then
# NEW_OUTPUT_PATH=$(grep "${BED}" "${FASTQ_WORKFLOWS_FILE}" | cut -d ',' -f 5)
# if [ -n "${NEW_OUTPUT_PATH}" ];then
# rm -rf "${OUTPUT_PATH}${RUN}"
# info "Defining new output path for run ${RUN}: ${NEW_OUTPUT_PATH}"
# OUTPUT_PATH=${NEW_OUTPUT_PATH}
# mkdir -p "${OUTPUT_PATH}${RUN}"
# else
# info "NEW_OUTPUT_PATH: ${NEW_OUTPUT_PATH} - MANIFEST: ${MANIFEST} - BED: ${BED} - FASTQ_WORKFLOWS_FILE: ${FASTQ_WORKFLOWS_FILE}"
# fi
# fi
# put ROI in a hash table with ROI as keys then loop on the hash and launch mobiCNV and multiqc
ROI_TYPES["${SAMPLE_ROI_TYPE}"]=1
if [ ! -d "${OUTPUT_PATH}${RUN}/MobiDL/MobiCNVtsvs/${SAMPLE_ROI_TYPE}/" ];then
mkdir -p "${OUTPUT_PATH}${RUN}/MobiDL/MobiCNVtsvs/${SAMPLE_ROI_TYPE}/"
fi
if [ ! -d "${OUTPUT_PATH}${RUN}/MobiDL/MobiCNVvcfs/${SAMPLE_ROI_TYPE}/" ];then
mkdir -p "${OUTPUT_PATH}${RUN}/MobiDL/MobiCNVvcfs/${SAMPLE_ROI_TYPE}/"
fi
fi
modifyJsonAndLaunch
prepareAchab
TREATED=1
# ifcnv/gatk_cnv specific feature: create a folder with symbolic links to the alignment files
if [[ ${MULTIPLE} != '' ]];then
if [ ! -d "${OUTPUT_PATH}${RUN}/MobiDL/alignment_files/${SAMPLE_ROI_TYPE}/" ];then
mkdir -p "${OUTPUT_PATH}${RUN}/MobiDL/alignment_files/${SAMPLE_ROI_TYPE}/"
fi
ln -s "${OUTPUT_PATH}${RUN}/MobiDL/${SAMPLE}/${WDL}/${SAMPLE}.crumble.cram" "${OUTPUT_PATH}${RUN}/MobiDL/alignment_files/${SAMPLE_ROI_TYPE}/${SAMPLE}.crumble.cram"
ln -s "${OUTPUT_PATH}${RUN}/MobiDL/${SAMPLE}/${WDL}/${SAMPLE}.crumble.cram.crai" "${OUTPUT_PATH}${RUN}/MobiDL/alignment_files/${SAMPLE_ROI_TYPE}/${SAMPLE}.crumble.cram.crai"
else
ln -s "${OUTPUT_PATH}${RUN}/MobiDL/${SAMPLE}/${WDL}/${SAMPLE}.crumble.cram" "${OUTPUT_PATH}${RUN}/MobiDL/alignment_files/${SAMPLE}.crumble.cram"
ln -s "${OUTPUT_PATH}${RUN}/MobiDL/${SAMPLE}/${WDL}/${SAMPLE}.crumble.cram.crai" "${OUTPUT_PATH}${RUN}/MobiDL/alignment_files/${SAMPLE}.crumble.cram.crai"
fi
# LED specific block
LED_FILE="${OUTPUT_PATH}${RUN}/MobiDL/MobiCNVvcfs/${SAMPLE_ROI_TYPE}/${SAMPLE}.txt"
DISEASE=''
TEAM=''
EXPERIMENT=''
if [[ "${SAMPLE}" =~ ^[Aa][0-9]+$ ]];then
DISEASE="ATAXIA"
TEAM="ATAXIA"
EXPERIMENT="trusight_one_exp"
elif [[ "${SAMPLE}" =~ ^[Hh][Oo][Rr]-[0-9]+$ ]];then
DISEASE="DSD"
TEAM="DSD"
EXPERIMENT="nimblegen_custom"
elif [[ "${SAMPLE}" =~ ^[Cc][SsAa][GgDd][0-9]+$ ]];then
DISEASE="CF"
TEAM="MUCO"
EXPERIMENT="agilent_custom"
elif [[ "${SAMPLE}" =~ ^[DdIi][0-9]+-.*$ ]];then
DISEASE="MYOPATHY"
TEAM="NEUROMUSCULAR"
EXPERIMENT="nimblegen_custom"
elif [[ "${SAMPLE}" =~ ^[Ss][Uu][0-9]+$ ]];then
DISEASE="DFNB"
TEAM="SENSORINEURAL"
EXPERIMENT="nimblegen_custom"
elif [[ "${SAMPLE}" =~ ^[Rr][0-9]+$ ]];then
DISEASE="RP"
TEAM="SENSORINEURAL"
EXPERIMENT="nimblegen_custom"
fi
touch "${LED_FILE}"
echo "#patient_id less than 10 chars" >> "${LED_FILE}"
echo "#family_id less than 10 chars" >> "${LED_FILE}"
echo "#gender m/f" >> "${LED_FILE}"
echo "#disease_name RP,DFNB,DFNA,USH,ATAXIA,MYOPATHY,HEALTHY,CF,CF-RD,CBAVD,OTHER,AUTISM,DSD" >> "${LED_FILE}"
echo "#team_name SENSORINEURAL,NEUROMUSCULAR,ATAXIA,MUCO,DSD" >> "${LED_FILE}"
echo "#visibility 0/1" >> "${LED_FILE}"
echo "#experiment trusight_one,exome_ss_v6,exome_ss_v5,truseq_rapid_exome,cftr_complete,medexome,nimblegen_inherited_disease,trusight_one_exp,nimblegen_custom,agilent_custom", >> "${LED_FILE}"
echo "patient_id:${SAMPLE}" >> "${LED_FILE}"
echo "family_id:" >> "${LED_FILE}"
echo "gender:" >> "${LED_FILE}"
echo "disease_name:${DISEASE}" >> "${LED_FILE}"
echo "team_name:${TEAM}" >> "${LED_FILE}"
echo "visibility:1" >> "${LED_FILE}"
echo "experiment_type:${EXPERIMENT}" >> "${LED_FILE}"
# end led specific block
cp "${OUTPUT_PATH}${RUN}/MobiDL/${SAMPLE}/${WDL}/${SAMPLE}.vcf" "${OUTPUT_PATH}${RUN}/MobiDL/MobiCNVvcfs/${SAMPLE_ROI_TYPE}"
cp "${OUTPUT_PATH}${RUN}/MobiDL/${SAMPLE}/${WDL}/coverage/${SAMPLE}_coverage.tsv" "${OUTPUT_PATH}${RUN}/MobiDL/MobiCNVtsvs/${SAMPLE_ROI_TYPE}"
debug "SAMPLE(SUFFIXES):${SAMPLE}(${SAMPLES[${SAMPLE}]})"
done
unset SAMPLES
fi
if [ "${TREATED}" -eq 1 ];then
# MobiCNV && multiqc
# no VCF anymore fo mobicnv: -v ${OUTPUT_PATH}${RUN}/MobiDL/MobiCNVvcfs/
if [ -n "${MULTIPLE}" ];then
# get folders in ${OUTPUT_PATH}${RUN}/MobiDL/MobiCNVvcfs/ and loop on it and launch mobicnv
# for LIBRARY in "${OUTPUT_PATH}${RUN}/MobiDL/MobiCNVvcfs/*"
for LIBRARY in ${!ROI_TYPES[@]}
do
# check if at least 3 samples / library => count number of tsv file in the folder
NUMBER_OF_SAMPLE=$(ls -l ${OUTPUT_PATH}${RUN}/MobiDL/MobiCNVtsvs/${LIBRARY}/*.tsv | wc -l)
if [ ${NUMBER_OF_SAMPLE} -gt 2 ];then
info "Launching MobiCNV on run ${RUN}, library ${LIBRARY}"
srun -N1 -c1 "${PYTHON}" "${MOBICNV}" -i "${OUTPUT_PATH}${RUN}/MobiDL/MobiCNVtsvs/${LIBRARY}/" -t tsv -o "${OUTPUT_PATH}${RUN}/MobiDL/${RUN}_${LIBRARY}_MobiCNV.xlsx"
debug "srun -N1 -c1 ${PYTHON} ${MOBICNV} -i ${OUTPUT_PATH}${RUN}/MobiDL/MobiCNVtsvs/${LIBRARY}/ -t tsv -o ${OUTPUT_PATH}${RUN}/MobiDL/${RUN}_${LIBRARY}_MobiCNV.xlsx"
# here prepare and launch gatk_cnv
# sed a gatk_cnv.yaml located in ${AUTODL_DIR} file with proper paths, loads the conda env and launches snakemake
# removed 20220420 as does not work as expected
# prepareGatkCnv "${OUTPUT_PATH}${RUN}/MobiDL/alignment_files/${LIBRARY}/" "${LIBRARY}\/"
# ${SNAKEMAKE} --cluster "sbatch -p monster -N 1 -J gatk-cnv --output=/dev/null" --jobs 1 -s ${GATK_SNAKEFILE} -j 8 --use-conda --configfile "${OUTPUT_PATH}${RUN}/MobiDL/alignment_files/${LIBRARY}/gatk_cnv.yaml" --resources cnv_caller=4
# info "${SNAKEMAKE} --cluster "sbatch -p monster -N 1 -J gatk-cnv --output=/dev/null" --jobs 1 -s ${GATK_SNAKEFILE} -j 8 --use-conda --configfile ${OUTPUT_PATH}${RUN}/MobiDL/alignment_files/${LIBRARY}/gatk_cnv.yaml --resources cnv_caller=4"
else
info "Not enough samples for Library ${LIBRARY} to launch MobiCNV (${NUMBER_OF_SAMPLE} samples)"
fi
done
else
info "Launching MobiCNV on run ${RUN}"
srun -N1 -c1 "${PYTHON}" "${MOBICNV}" -i "${OUTPUT_PATH}${RUN}/MobiDL/MobiCNVtsvs/" -t tsv -o "${OUTPUT_PATH}${RUN}/MobiDL/${RUN}_MobiCNV.xlsx"
debug "srun -N1 -c1 ${PYTHON} ${MOBICNV} -i ${OUTPUT_PATH}${RUN}/MobiDL/MobiCNVtsvs/ -t tsv -o ${OUTPUT_PATH}${RUN}/MobiDL/${RUN}_MobiCNV.xlsx"
# here prepare and launch gatk_cnv
# sed a gatk_cnv.yaml located in ${AUTODL_DIR} file with proper paths, loads the conda env and launches snakemake
# removed 20220420 as does not work as expected
# prepareGatkCnv "${OUTPUT_PATH}${RUN}/MobiDL/alignment_files/" ""
# ${SNAKEMAKE} --cluster "sbatch -p monster -N 1 -J gatk-cnv --output=/dev/null" --jobs 1 -s ${GATK_SNAKEFILE} -j 8 --use-conda --configfile "${OUTPUT_PATH}${RUN}/MobiDL/alignment_files/gatk_cnv.yaml" --resources cnv_caller=4
# debug "${SNAKEMAKE} --cluster "sbatch -p monster -N 1 -J gatk-cnv --output=/dev/null" --jobs 1 -s ${GATK_SNAKEFILE} -j 8 --use-conda --configfile ${OUTPUT_PATH}${RUN}/MobiDL/alignment_files/gatk_cnv.yaml --resources cnv_caller=4"
# ifCNV
BED_FILE_NAME=$(basename ${BED} .bed)
BED_IFCNV="${ROI_DIR}${BED_FILE_NAME}_ifcnv.bed"
if [ -e ${BED_IFCNV} ];then
info "Activating env ${IFCNV_ENV} and launching ifCNV on run ${RUN}"
# activates conda
# eval "$(${CONDA} 'shell.bash' 'hook')"
# https://unix.stackexchange.com/questions/454957/cron-job-to-run-under-conda-virtual-environment/572951#572951
# activates ifcnv env
source "${CONDA_ACTIVATE}" "${IFCNV_ENV}"
# "${CONDA}" activate "${IFCNV_ENV}"
debug "srun -N1 -c1 ${IFCNV} -i ${OUTPUT_PATH}${RUN}/MobiDL/alignment_files/ -b ${BED_IFCNV} -o ${OUTPUT_PATH}${RUN}/MobiDL/alignment_files/ifCNV/ -r ${RUN} -sT 0 -ct 0.01"
srun -N1 -c1 "${IFCNV}" -i "${OUTPUT_PATH}${RUN}/MobiDL/alignment_files/" -b "${BED_IFCNV}" -o "${OUTPUT_PATH}${RUN}/MobiDL/alignment_files/ifCNV/" -r "${RUN}" -sT 0 -ct 0.01 && "${CONDA} deactivate"
# deactivates conda env
# "${CONDA_DEACTIVATE}"
fi
fi
info "Launching MultiQC on run ${RUN}"
srun -N1 -c1 "${MULTIQC}" "${OUTPUT_PATH}${RUN}/MobiDL/" -n "${RUN}_multiqc.html" -o "${OUTPUT_PATH}${RUN}/MobiDL/"
debug "srun -N1 -c1 ${MULTIQC} ${OUTPUT_PATH}${RUN}/MobiDL/ -n ${RUN}_multiqc.html -o ${OUTPUT_PATH}${RUN}/MobiDL/"
# may not be needed anymore with NFS share TEST ME
chmod -R 777 "${OUTPUT_PATH}${RUN}/MobiDL/"
sed -i -e "s/${RUN}=1/${RUN}=2/" "${RUNS_FILE}"
RUN_ARRAY[${RUN}]=2
info "RUN ${RUN} treated"
touch "${OUTPUT_PATH}${RUN}/MobiDL/panelCaptureComplete.txt"
echo "[`date +'%Y-%m-%d %H:%M:%S'`] [INFO] - autoDL version : ${VERSION} - MobiDL panelCapture complete for run ${RUN}" > "${OUTPUT_PATH}${RUN}/MobiDL/panelCaptureComplete.txt"
rm -r "${TMP_OUTPUT_DIR2}"
else
info "Nothing done for run ${RUN_PATH}${RUN}"
if [ -z "${RUN_ARRAY[${RUN}]}" ];then
echo ${RUN}=2 >> ${RUNS_FILE}
RUN_ARRAY[${RUN}]=2
elif [ "${RUN_ARRAY[${RUN}]}" -eq 0 ];then
# Change value on array and file to done
sed -i -e "s/${RUN}=0/${RUN}=2/g" "${RUNS_FILE}"
RUN_ARRAY[${RUN}]=2
fi
fi
else
info "Nothing done for ${RUN}"
if [ -z "${RUN_ARRAY[${RUN}]}" ];then
echo ${RUN}=2 >> ${RUNS_FILE}
RUN_ARRAY[${RUN}]=2
elif [ "${RUN_ARRAY[${RUN}]}" -eq 0 ];then
# Change value on array and file to done
sed -i -e "s/${RUN}=0/${RUN}=2/g" "${RUNS_FILE}"
RUN_ARRAY[${RUN}]=2
fi
fi
fi
fi
fi
done
done