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e3be4c44616aec592dc33b9ad91c25bb2ec00b38
biobox/target/executable/bcl_convert/bcl_convert
CI e3be4c4461 Build branch main with version main (b0db228) 
Build pipeline: viash-hub.biobox.main-nmzjs

Source commit: b0db228825

Source message: Update readme (#177)

* update image

* add changelog

* make readme more generic

* fix url

* make images relative again
2025-05-06 20:36:16 +00:00

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#!/usr/bin/env bash
# bcl_convert main
#
# This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
# work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
# Intuitive.
#
# The component may contain files which fall under a different license. The
# authors of this component should specify the license in the header of such
# files, or include a separate license file detailing the licenses of all included
# files.
#
# Component authors:
# * Toni Verbeiren (author, maintainer)
# * Dorien Roosen (author)
set -e
if [ -z "$VIASH_TEMP" ]; then
VIASH_TEMP=${VIASH_TEMP:-$VIASH_TMPDIR}
VIASH_TEMP=${VIASH_TEMP:-$VIASH_TEMPDIR}
VIASH_TEMP=${VIASH_TEMP:-$VIASH_TMP}
VIASH_TEMP=${VIASH_TEMP:-$TMPDIR}
VIASH_TEMP=${VIASH_TEMP:-$TMP}
VIASH_TEMP=${VIASH_TEMP:-$TEMPDIR}
VIASH_TEMP=${VIASH_TEMP:-$TEMP}
VIASH_TEMP=${VIASH_TEMP:-/tmp}
fi
# define helper functions
# ViashQuote: put quotes around non flag values
# $1 : unquoted string
# return : possibly quoted string
# examples:
# ViashQuote --foo # returns --foo
# ViashQuote bar # returns 'bar'
# Viashquote --foo=bar # returns --foo='bar'
function ViashQuote {
if [[ "$1" =~ ^-+[a-zA-Z0-9_\-]+=.+$ ]]; then
echo "$1" | sed "s#=\(.*\)#='\1'#"
elif [[ "$1" =~ ^-+[a-zA-Z0-9_\-]+$ ]]; then
echo "$1"
else
echo "'$1'"
fi
}
# ViashRemoveFlags: Remove leading flag
# $1 : string with a possible leading flag
# return : string without possible leading flag
# examples:
# ViashRemoveFlags --foo=bar # returns bar
function ViashRemoveFlags {
echo "$1" | sed 's/^--*[a-zA-Z0-9_\-]*=//'
}
# ViashSourceDir: return the path of a bash file, following symlinks
# usage : ViashSourceDir ${BASH_SOURCE[0]}
# $1 : Should always be set to ${BASH_SOURCE[0]}
# returns : The absolute path of the bash file
function ViashSourceDir {
local source="$1"
while [ -h "$source" ]; do
local dir="$( cd -P "$( dirname "$source" )" >/dev/null 2>&1 && pwd )"
source="$(readlink "$source")"
[[ $source != /* ]] && source="$dir/$source"
done
cd -P "$( dirname "$source" )" >/dev/null 2>&1 && pwd
}
# ViashFindTargetDir: return the path of the '.build.yaml' file, following symlinks
# usage : ViashFindTargetDir 'ScriptPath'
# $1 : The location from where to start the upward search
# returns : The absolute path of the '.build.yaml' file
function ViashFindTargetDir {
local source="$1"
while [[ "$source" != "" && ! -e "$source/.build.yaml" ]]; do
source=${source%/*}
done
echo $source
}
# see https://en.wikipedia.org/wiki/Syslog#Severity_level
VIASH_LOGCODE_EMERGENCY=0
VIASH_LOGCODE_ALERT=1
VIASH_LOGCODE_CRITICAL=2
VIASH_LOGCODE_ERROR=3
VIASH_LOGCODE_WARNING=4
VIASH_LOGCODE_NOTICE=5
VIASH_LOGCODE_INFO=6
VIASH_LOGCODE_DEBUG=7
VIASH_VERBOSITY=$VIASH_LOGCODE_NOTICE
# ViashLog: Log events depending on the verbosity level
# usage: ViashLog 1 alert Oh no something went wrong!
# $1: required verbosity level
# $2: display tag
# $3+: messages to display
# stdout: Your input, prepended by '[$2] '.
function ViashLog {
local required_level="$1"
local display_tag="$2"
shift 2
if [ $VIASH_VERBOSITY -ge $required_level ]; then
>&2 echo "[$display_tag]" "$@"
fi
}
# ViashEmergency: log events when the system is unstable
# usage: ViashEmergency Oh no something went wrong.
# stdout: Your input, prepended by '[emergency] '.
function ViashEmergency {
ViashLog $VIASH_LOGCODE_EMERGENCY emergency "$@"
}
# ViashAlert: log events when actions must be taken immediately (e.g. corrupted system database)
# usage: ViashAlert Oh no something went wrong.
# stdout: Your input, prepended by '[alert] '.
function ViashAlert {
ViashLog $VIASH_LOGCODE_ALERT alert "$@"
}
# ViashCritical: log events when a critical condition occurs
# usage: ViashCritical Oh no something went wrong.
# stdout: Your input, prepended by '[critical] '.
function ViashCritical {
ViashLog $VIASH_LOGCODE_CRITICAL critical "$@"
}
# ViashError: log events when an error condition occurs
# usage: ViashError Oh no something went wrong.
# stdout: Your input, prepended by '[error] '.
function ViashError {
ViashLog $VIASH_LOGCODE_ERROR error "$@"
}
# ViashWarning: log potentially abnormal events
# usage: ViashWarning Something may have gone wrong.
# stdout: Your input, prepended by '[warning] '.
function ViashWarning {
ViashLog $VIASH_LOGCODE_WARNING warning "$@"
}
# ViashNotice: log significant but normal events
# usage: ViashNotice This just happened.
# stdout: Your input, prepended by '[notice] '.
function ViashNotice {
ViashLog $VIASH_LOGCODE_NOTICE notice "$@"
}
# ViashInfo: log normal events
# usage: ViashInfo This just happened.
# stdout: Your input, prepended by '[info] '.
function ViashInfo {
ViashLog $VIASH_LOGCODE_INFO info "$@"
}
# ViashDebug: log all events, for debugging purposes
# usage: ViashDebug This just happened.
# stdout: Your input, prepended by '[debug] '.
function ViashDebug {
ViashLog $VIASH_LOGCODE_DEBUG debug "$@"
}
# find source folder of this component
VIASH_META_RESOURCES_DIR=`ViashSourceDir ${BASH_SOURCE[0]}`
# find the root of the built components & dependencies
VIASH_TARGET_DIR=`ViashFindTargetDir $VIASH_META_RESOURCES_DIR`
# define meta fields
VIASH_META_NAME="bcl_convert"
VIASH_META_FUNCTIONALITY_NAME="bcl_convert"
VIASH_META_EXECUTABLE="$VIASH_META_RESOURCES_DIR/$VIASH_META_NAME"
VIASH_META_CONFIG="$VIASH_META_RESOURCES_DIR/.config.vsh.yaml"
VIASH_META_TEMP_DIR="$VIASH_TEMP"
# initialise variables
VIASH_MODE='run'
VIASH_ENGINE_ID='docker'
######## Helper functions for setting up Docker images for viash ########
# expects: ViashDockerBuild
# ViashDockerInstallationCheck: check whether Docker is installed correctly
#
# examples:
# ViashDockerInstallationCheck
function ViashDockerInstallationCheck {
ViashDebug "Checking whether Docker is installed"
if [ ! command -v docker &> /dev/null ]; then
ViashCritical "Docker doesn't seem to be installed. See 'https://docs.docker.com/get-docker/' for instructions."
exit 1
fi
ViashDebug "Checking whether the Docker daemon is running"
local save=$-; set +e
local docker_version=$(docker version --format '{{.Client.APIVersion}}' 2> /dev/null)
local out=$?
[[ $save =~ e ]] && set -e
if [ $out -ne 0 ]; then
ViashCritical "Docker daemon does not seem to be running. Try one of the following:"
ViashCritical "- Try running 'dockerd' in the command line"
ViashCritical "- See https://docs.docker.com/config/daemon/"
exit 1
fi
}
# ViashDockerRemoteTagCheck: check whether a Docker image is available
# on a remote. Assumes `docker login` has been performed, if relevant.
#
# $1 : image identifier with format `[registry/]image[:tag]`
# exit code $? : whether or not the image was found
# examples:
# ViashDockerRemoteTagCheck python:latest
# echo $? # returns '0'
# ViashDockerRemoteTagCheck sdaizudceahifu
# echo $? # returns '1'
function ViashDockerRemoteTagCheck {
docker manifest inspect $1 > /dev/null 2> /dev/null
}
# ViashDockerLocalTagCheck: check whether a Docker image is available locally
#
# $1 : image identifier with format `[registry/]image[:tag]`
# exit code $? : whether or not the image was found
# examples:
# docker pull python:latest
# ViashDockerLocalTagCheck python:latest
# echo $? # returns '0'
# ViashDockerLocalTagCheck sdaizudceahifu
# echo $? # returns '1'
function ViashDockerLocalTagCheck {
[ -n "$(docker images -q $1)" ]
}
# ViashDockerPull: pull a Docker image
#
# $1 : image identifier with format `[registry/]image[:tag]`
# exit code $? : whether or not the image was found
# examples:
# ViashDockerPull python:latest
# echo $? # returns '0'
# ViashDockerPull sdaizudceahifu
# echo $? # returns '1'
function ViashDockerPull {
ViashNotice "Checking if Docker image is available at '$1'"
if [ $VIASH_VERBOSITY -ge $VIASH_LOGCODE_INFO ]; then
docker pull $1 && return 0 || return 1
else
local save=$-; set +e
docker pull $1 2> /dev/null > /dev/null
local out=$?
[[ $save =~ e ]] && set -e
if [ $out -ne 0 ]; then
ViashWarning "Could not pull from '$1'. Docker image doesn't exist or is not accessible."
fi
return $out
fi
}
# ViashDockerPush: push a Docker image
#
# $1 : image identifier with format `[registry/]image[:tag]`
# exit code $? : whether or not the image was found
# examples:
# ViashDockerPush python:latest
# echo $? # returns '0'
# ViashDockerPush sdaizudceahifu
# echo $? # returns '1'
function ViashDockerPush {
ViashNotice "Pushing image to '$1'"
local save=$-; set +e
local out
if [ $VIASH_VERBOSITY -ge $VIASH_LOGCODE_INFO ]; then
docker push $1
out=$?
else
docker push $1 2> /dev/null > /dev/null
out=$?
fi
[[ $save =~ e ]] && set -e
if [ $out -eq 0 ]; then
ViashNotice "Container '$1' push succeeded."
else
ViashError "Container '$1' push errored. You might not be logged in or have the necessary permissions."
fi
return $out
}
# ViashDockerPullElseBuild: pull a Docker image, else build it
#
# $1 : image identifier with format `[registry/]image[:tag]`
# ViashDockerBuild : a Bash function which builds a docker image, takes image identifier as argument.
# examples:
# ViashDockerPullElseBuild mynewcomponent
function ViashDockerPullElseBuild {
local save=$-; set +e
ViashDockerPull $1
local out=$?
[[ $save =~ e ]] && set -e
if [ $out -ne 0 ]; then
ViashDockerBuild $@
fi
}
# ViashDockerSetup: create a Docker image, according to specified docker setup strategy
#
# $1 : image identifier with format `[registry/]image[:tag]`
# $2 : docker setup strategy, see DockerSetupStrategy.scala
# examples:
# ViashDockerSetup mynewcomponent alwaysbuild
function ViashDockerSetup {
local image_id="$1"
local setup_strategy="$2"
if [ "$setup_strategy" == "alwaysbuild" -o "$setup_strategy" == "build" -o "$setup_strategy" == "b" ]; then
ViashDockerBuild $image_id --no-cache $(ViashDockerBuildArgs "$engine_id")
elif [ "$setup_strategy" == "alwayspull" -o "$setup_strategy" == "pull" -o "$setup_strategy" == "p" ]; then
ViashDockerPull $image_id
elif [ "$setup_strategy" == "alwayspullelsebuild" -o "$setup_strategy" == "pullelsebuild" ]; then
ViashDockerPullElseBuild $image_id --no-cache $(ViashDockerBuildArgs "$engine_id")
elif [ "$setup_strategy" == "alwayspullelsecachedbuild" -o "$setup_strategy" == "pullelsecachedbuild" ]; then
ViashDockerPullElseBuild $image_id $(ViashDockerBuildArgs "$engine_id")
elif [ "$setup_strategy" == "alwayscachedbuild" -o "$setup_strategy" == "cachedbuild" -o "$setup_strategy" == "cb" ]; then
ViashDockerBuild $image_id $(ViashDockerBuildArgs "$engine_id")
elif [[ "$setup_strategy" =~ ^ifneedbe ]]; then
local save=$-; set +e
ViashDockerLocalTagCheck $image_id
local outCheck=$?
[[ $save =~ e ]] && set -e
if [ $outCheck -eq 0 ]; then
ViashInfo "Image $image_id already exists"
elif [ "$setup_strategy" == "ifneedbebuild" ]; then
ViashDockerBuild $image_id --no-cache $(ViashDockerBuildArgs "$engine_id")
elif [ "$setup_strategy" == "ifneedbecachedbuild" ]; then
ViashDockerBuild $image_id $(ViashDockerBuildArgs "$engine_id")
elif [ "$setup_strategy" == "ifneedbepull" ]; then
ViashDockerPull $image_id
elif [ "$setup_strategy" == "ifneedbepullelsebuild" ]; then
ViashDockerPullElseBuild $image_id --no-cache $(ViashDockerBuildArgs "$engine_id")
elif [ "$setup_strategy" == "ifneedbepullelsecachedbuild" ]; then
ViashDockerPullElseBuild $image_id $(ViashDockerBuildArgs "$engine_id")
else
ViashError "Unrecognised Docker strategy: $setup_strategy"
exit 1
fi
elif [ "$setup_strategy" == "push" -o "$setup_strategy" == "forcepush" -o "$setup_strategy" == "alwayspush" ]; then
ViashDockerPush "$image_id"
elif [ "$setup_strategy" == "pushifnotpresent" -o "$setup_strategy" == "gentlepush" -o "$setup_strategy" == "maybepush" ]; then
local save=$-; set +e
ViashDockerRemoteTagCheck $image_id
local outCheck=$?
[[ $save =~ e ]] && set -e
if [ $outCheck -eq 0 ]; then
ViashNotice "Container '$image_id' exists, doing nothing."
else
ViashNotice "Container '$image_id' does not yet exist."
ViashDockerPush "$image_id"
fi
elif [ "$setup_strategy" == "donothing" -o "$setup_strategy" == "meh" ]; then
ViashNotice "Skipping setup."
else
ViashError "Unrecognised Docker strategy: $setup_strategy"
exit 1
fi
}
# ViashDockerCheckCommands: Check whether a docker container has the required commands
#
# $1 : image identifier with format `[registry/]image[:tag]`
# $@ : commands to verify being present
# examples:
# ViashDockerCheckCommands bash:4.0 bash ps foo
function ViashDockerCheckCommands {
local image_id="$1"
shift 1
local commands="$@"
local save=$-; set +e
local missing # mark 'missing' as local in advance, otherwise the exit code of the command will be missing and always be '0'
missing=$(docker run --rm --entrypoint=sh "$image_id" -c "for command in $commands; do command -v \$command >/dev/null 2>&1; if [ \$? -ne 0 ]; then echo \$command; exit 1; fi; done")
local outCheck=$?
[[ $save =~ e ]] && set -e
if [ $outCheck -ne 0 ]; then
ViashError "Docker container '$image_id' does not contain command '$missing'."
exit 1
fi
}
# ViashDockerBuild: build a docker image
# $1 : image identifier with format `[registry/]image[:tag]`
# $... : additional arguments to pass to docker build
# $VIASH_META_TEMP_DIR : temporary directory to store dockerfile & optional resources in
# $VIASH_META_NAME : name of the component
# $VIASH_META_RESOURCES_DIR : directory containing the resources
# $VIASH_VERBOSITY : verbosity level
# exit code $? : whether or not the image was built successfully
function ViashDockerBuild {
local image_id="$1"
shift 1
# create temporary directory to store dockerfile & optional resources in
local tmpdir=$(mktemp -d "$VIASH_META_TEMP_DIR/dockerbuild-$VIASH_META_NAME-XXXXXX")
local dockerfile="$tmpdir/Dockerfile"
function clean_up {
rm -rf "$tmpdir"
}
trap clean_up EXIT
# store dockerfile and resources
ViashDockerfile "$VIASH_ENGINE_ID" > "$dockerfile"
# generate the build command
local docker_build_cmd="docker build -t '$image_id' $@ '$VIASH_META_RESOURCES_DIR' -f '$dockerfile'"
# build the container
ViashNotice "Building container '$image_id' with Dockerfile"
ViashInfo "$docker_build_cmd"
local save=$-; set +e
if [ $VIASH_VERBOSITY -ge $VIASH_LOGCODE_INFO ]; then
eval $docker_build_cmd
else
eval $docker_build_cmd &> "$tmpdir/docker_build.log"
fi
# check exit code
local out=$?
[[ $save =~ e ]] && set -e
if [ $out -ne 0 ]; then
ViashError "Error occurred while building container '$image_id'"
if [ $VIASH_VERBOSITY -lt $VIASH_LOGCODE_INFO ]; then
ViashError "Transcript: --------------------------------"
cat "$tmpdir/docker_build.log"
ViashError "End of transcript --------------------------"
fi
exit 1
fi
}
######## End of helper functions for setting up Docker images for viash ########
# ViashDockerFile: print the dockerfile to stdout
# $1 : engine identifier
# return : dockerfile required to run this component
# examples:
# ViashDockerFile
function ViashDockerfile {
local engine_id="$1"
if [[ "$engine_id" == "docker" ]]; then
cat << 'VIASHDOCKER'
FROM debian:trixie-slim
ENTRYPOINT []
RUN apt-get update && \
DEBIAN_FRONTEND=noninteractive apt-get install -y wget gdb which hostname alien procps && \
rm -rf /var/lib/apt/lists/*
RUN wget https://s3.amazonaws.com/webdata.illumina.com/downloads/software/bcl-convert/bcl-convert-4.2.7-2.el8.x86_64.rpm -O /tmp/bcl-convert.rpm && \
alien -i /tmp/bcl-convert.rpm && \
rm -rf /var/lib/apt/lists/* && \
rm /tmp/bcl-convert.rpm
RUN echo "bcl-convert: \"$(bcl-convert -V 2>&1 >/dev/null | sed -n '/Version/ s/^bcl-convert\ Version //p')\"" > /var/software_versions.txt
LABEL org.opencontainers.image.authors="Toni Verbeiren, Dorien Roosen"
LABEL org.opencontainers.image.description="Companion container for running component bcl_convert"
LABEL org.opencontainers.image.created="2025-05-06T20:11:35Z"
LABEL org.opencontainers.image.source="https://github.com/viash-hub/biobox"
LABEL org.opencontainers.image.revision="b0db228825f3441b4651527e8775e8fc87d06e60"
LABEL org.opencontainers.image.version="main"
VIASHDOCKER
fi
}
# ViashDockerBuildArgs: return the arguments to pass to docker build
# $1 : engine identifier
# return : arguments to pass to docker build
function ViashDockerBuildArgs {
local engine_id="$1"
if [[ "$engine_id" == "docker" ]]; then
echo ""
fi
}
# ViashAbsolutePath: generate absolute path from relative path
# borrowed from https://stackoverflow.com/a/21951256
# $1 : relative filename
# return : absolute path
# examples:
# ViashAbsolutePath some_file.txt # returns /path/to/some_file.txt
# ViashAbsolutePath /foo/bar/.. # returns /foo
function ViashAbsolutePath {
local thePath
local parr
local outp
local len
if [[ ! "$1" =~ ^/ ]]; then
thePath="$PWD/$1"
else
thePath="$1"
fi
echo "$thePath" | (
IFS=/
read -a parr
declare -a outp
for i in "${parr[@]}"; do
case "$i" in
''|.) continue ;;
..)
len=${#outp[@]}
if ((len==0)); then
continue
else
unset outp[$((len-1))]
fi
;;
*)
len=${#outp[@]}
outp[$len]="$i"
;;
esac
done
echo /"${outp[*]}"
)
}
# ViashDockerAutodetectMount: auto configuring docker mounts from parameters
# $1 : The parameter value
# returns : New parameter
# $VIASH_DIRECTORY_MOUNTS : Added another parameter to be passed to docker
# $VIASH_DOCKER_AUTOMOUNT_PREFIX : The prefix to be used for the automounts
# examples:
# ViashDockerAutodetectMount /path/to/bar # returns '/viash_automount/path/to/bar'
# ViashDockerAutodetectMountArg /path/to/bar # returns '--volume="/path/to:/viash_automount/path/to"'
function ViashDockerAutodetectMount {
local abs_path=$(ViashAbsolutePath "$1")
local mount_source
local base_name
if [ -d "$abs_path" ]; then
mount_source="$abs_path"
base_name=""
else
mount_source=`dirname "$abs_path"`
base_name=`basename "$abs_path"`
fi
local mount_target="$VIASH_DOCKER_AUTOMOUNT_PREFIX$mount_source"
if [ -z "$base_name" ]; then
echo "$mount_target"
else
echo "$mount_target/$base_name"
fi
}
function ViashDockerAutodetectMountArg {
local abs_path=$(ViashAbsolutePath "$1")
local mount_source
local base_name
if [ -d "$abs_path" ]; then
mount_source="$abs_path"
base_name=""
else
mount_source=`dirname "$abs_path"`
base_name=`basename "$abs_path"`
fi
local mount_target="$VIASH_DOCKER_AUTOMOUNT_PREFIX$mount_source"
ViashDebug "ViashDockerAutodetectMountArg $1 -> $mount_source -> $mount_target"
echo "--volume=\"$mount_source:$mount_target\""
}
function ViashDockerStripAutomount {
local abs_path=$(ViashAbsolutePath "$1")
echo "${abs_path#$VIASH_DOCKER_AUTOMOUNT_PREFIX}"
}
# initialise variables
VIASH_DIRECTORY_MOUNTS=()
# configure default docker automount prefix if it is unset
if [ -z "${VIASH_DOCKER_AUTOMOUNT_PREFIX+x}" ]; then
VIASH_DOCKER_AUTOMOUNT_PREFIX="/viash_automount"
fi
# initialise docker variables
VIASH_DOCKER_RUN_ARGS=(-i --rm)
# ViashHelp: Display helpful explanation about this executable
function ViashHelp {
echo "bcl_convert main"
echo ""
echo "Convert bcl files to fastq files using bcl-convert."
echo "Information about upgrading from bcl2fastq via"
echo "[Upgrading from bcl2fastq to BCL"
echo "Convert](https://emea.support.illumina.com/bulletins/2020/10/upgrading-from-bcl2fastq-to-bcl-convert.html)"
echo "and [BCL Convert Compatible"
echo "Products](https://support.illumina.com/sequencing/sequencing_software/bcl-convert/compatibility.html)"
echo ""
echo "Input arguments:"
echo " -i, --bcl_input_directory"
echo " type: file, required parameter, file must exist"
echo " example: bcl_dir"
echo " Input run directory"
echo ""
echo " -s, --sample_sheet"
echo " type: file, file must exist"
echo " example: bcl_dir/sample_sheet.csv"
echo " Path to SampleSheet.csv file (default searched for in"
echo " --bcl_input_directory)"
echo ""
echo " --run_info"
echo " type: file, file must exist"
echo " example: bcl_dir/RunInfo.xml"
echo " Path to RunInfo.xml file (default root of BCL input directory)"
echo ""
echo "Lane and tile settings:"
echo " --bcl_only_lane"
echo " type: integer"
echo " example: 1"
echo " Convert only specified lane number (default all lanes)"
echo ""
echo " --first_tile_only"
echo " type: boolean"
echo " example: true"
echo " Only convert first tile of input (for testing & debugging)"
echo ""
echo " --tiles"
echo " type: string"
echo " example: s_[0-9]+_1"
echo " Process only a subset of tiles by a regular expression"
echo ""
echo " --exclude_tiles"
echo " type: string"
echo " example: s_[0-9]+_1"
echo " Exclude set of tiles by a regular expression"
echo ""
echo "Resource arguments:"
echo " --shared_thread_odirect_output"
echo " type: boolean"
echo " example: true"
echo " Use linux native asynchronous io (io_submit) for file output"
echo " (Default=false)"
echo ""
echo " --bcl_num_parallel_tiles"
echo " type: integer"
echo " example: 1"
echo " \\# of tiles to process in parallel (default 1)"
echo ""
echo " --bcl_num_conversion_threads"
echo " type: integer"
echo " example: 1"
echo " \\# of threads for conversion (per tile, default # cpu threads)"
echo ""
echo " --bcl_num_compression_threads"
echo " type: integer"
echo " example: 1"
echo " \\# of threads for fastq.gz output compression (per tile, default # cpu"
echo " threads, or HW+12)"
echo ""
echo " --bcl_num_decompression_threads"
echo " type: integer"
echo " example: 1"
echo " \\# of threads for bcl/cbcl input decompression (per tile, default half #"
echo " cpu threads, or HW+8). Only applies when preloading files"
echo ""
echo "Run arguments:"
echo " --bcl_only_matched_reads"
echo " type: boolean"
echo " example: true"
echo " For pure BCL conversion, do not output files for 'Undetermined'"
echo " [unmatched] reads (output by default)"
echo ""
echo " --no_lane_splitting"
echo " type: boolean"
echo " example: true"
echo " Do not split FASTQ file by lane (false by default)"
echo ""
echo " --num_unknown_barcodes_reported"
echo " type: integer"
echo " example: 1000"
echo " \\# of Top Unknown Barcodes to output (1000 by default)"
echo ""
echo " --bcl_validate_sample_sheet_only"
echo " type: boolean"
echo " example: true"
echo " Only validate RunInfo.xml & SampleSheet files (produce no FASTQ files)"
echo ""
echo " --strict_mode"
echo " type: boolean"
echo " example: true"
echo " Abort if any files are missing (false by default)"
echo ""
echo " --sample_name_column_enabled"
echo " type: boolean"
echo " example: true"
echo " Use sample sheet 'Sample_Name' column when naming fastq files &"
echo " subdirectories"
echo ""
echo "Output arguments:"
echo " -o, --output_directory"
echo " type: file, required parameter, output, file must exist"
echo " example: fastq_dir"
echo " Output directory containig fastq files"
echo ""
echo " --bcl_sampleproject_subdirectories"
echo " type: boolean"
echo " example: true"
echo " Output to subdirectories based upon sample sheet 'Sample_Project' column"
echo ""
echo " --fastq_gzip_compression_level"
echo " type: integer"
echo " example: 1"
echo " Set fastq output compression level 0-9 (default 1)"
echo ""
echo " --reports"
echo " type: file, output, file must exist"
echo " example: reports_dir"
echo " Reports directory"
echo ""
echo " --logs"
echo " type: file, output, file must exist"
echo " example: logs_dir"
echo " Reports directory"
echo ""
echo " --force"
echo " type: boolean"
echo " example: true"
echo " Allow destination directory to already exist and overwrite files."
echo ""
echo "Viash built in Computational Requirements:"
echo " ---cpus=INT"
echo " Number of CPUs to use"
echo " ---memory=STRING"
echo " Amount of memory to use. Examples: 4GB, 3MiB."
echo ""
echo "Viash built in Docker:"
echo " ---setup=STRATEGY"
echo " Setup the docker container. Options are: alwaysbuild, alwayscachedbuild, ifneedbebuild, ifneedbecachedbuild, alwayspull, alwayspullelsebuild, alwayspullelsecachedbuild, ifneedbepull, ifneedbepullelsebuild, ifneedbepullelsecachedbuild, push, pushifnotpresent, donothing."
echo " Default: ifneedbepullelsecachedbuild"
echo " ---dockerfile"
echo " Print the dockerfile to stdout."
echo " ---docker_run_args=ARG"
echo " Provide runtime arguments to Docker. See the documentation on \`docker run\` for more information."
echo " ---docker_image_id"
echo " Print the docker image id to stdout."
echo " ---debug"
echo " Enter the docker container for debugging purposes."
echo ""
echo "Viash built in Engines:"
echo " ---engine=ENGINE_ID"
echo " Specify the engine to use. Options are: docker, native."
echo " Default: docker"
}
# initialise array
VIASH_POSITIONAL_ARGS=''
while [[ $# -gt 0 ]]; do
case "$1" in
-h|--help)
ViashHelp
exit
;;
---v|---verbose)
let "VIASH_VERBOSITY=VIASH_VERBOSITY+1"
shift 1
;;
---verbosity)
VIASH_VERBOSITY="$2"
shift 2
;;
---verbosity=*)
VIASH_VERBOSITY="$(ViashRemoveFlags "$1")"
shift 1
;;
--version)
echo "bcl_convert main"
exit
;;
--bcl_input_directory)
[ -n "$VIASH_PAR_BCL_INPUT_DIRECTORY" ] && ViashError Bad arguments for option \'--bcl_input_directory\': \'$VIASH_PAR_BCL_INPUT_DIRECTORY\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
VIASH_PAR_BCL_INPUT_DIRECTORY="$2"
[ $# -lt 2 ] && ViashError Not enough arguments passed to --bcl_input_directory. Use "--help" to get more information on the parameters. && exit 1
shift 2
;;
--bcl_input_directory=*)
[ -n "$VIASH_PAR_BCL_INPUT_DIRECTORY" ] && ViashError Bad arguments for option \'--bcl_input_directory=*\': \'$VIASH_PAR_BCL_INPUT_DIRECTORY\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
VIASH_PAR_BCL_INPUT_DIRECTORY=$(ViashRemoveFlags "$1")
shift 1
;;
-i)
[ -n "$VIASH_PAR_BCL_INPUT_DIRECTORY" ] && ViashError Bad arguments for option \'-i\': \'$VIASH_PAR_BCL_INPUT_DIRECTORY\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
VIASH_PAR_BCL_INPUT_DIRECTORY="$2"
[ $# -lt 2 ] && ViashError Not enough arguments passed to -i. Use "--help" to get more information on the parameters. && exit 1
shift 2
;;
--sample_sheet)
[ -n "$VIASH_PAR_SAMPLE_SHEET" ] && ViashError Bad arguments for option \'--sample_sheet\': \'$VIASH_PAR_SAMPLE_SHEET\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
VIASH_PAR_SAMPLE_SHEET="$2"
[ $# -lt 2 ] && ViashError Not enough arguments passed to --sample_sheet. Use "--help" to get more information on the parameters. && exit 1
shift 2
;;
--sample_sheet=*)
[ -n "$VIASH_PAR_SAMPLE_SHEET" ] && ViashError Bad arguments for option \'--sample_sheet=*\': \'$VIASH_PAR_SAMPLE_SHEET\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
VIASH_PAR_SAMPLE_SHEET=$(ViashRemoveFlags "$1")
shift 1
;;
-s)
[ -n "$VIASH_PAR_SAMPLE_SHEET" ] && ViashError Bad arguments for option \'-s\': \'$VIASH_PAR_SAMPLE_SHEET\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
VIASH_PAR_SAMPLE_SHEET="$2"
[ $# -lt 2 ] && ViashError Not enough arguments passed to -s. Use "--help" to get more information on the parameters. && exit 1
shift 2
;;
--run_info)
[ -n "$VIASH_PAR_RUN_INFO" ] && ViashError Bad arguments for option \'--run_info\': \'$VIASH_PAR_RUN_INFO\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
VIASH_PAR_RUN_INFO="$2"
[ $# -lt 2 ] && ViashError Not enough arguments passed to --run_info. Use "--help" to get more information on the parameters. && exit 1
shift 2
;;
--run_info=*)
[ -n "$VIASH_PAR_RUN_INFO" ] && ViashError Bad arguments for option \'--run_info=*\': \'$VIASH_PAR_RUN_INFO\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
VIASH_PAR_RUN_INFO=$(ViashRemoveFlags "$1")
shift 1
;;
--bcl_only_lane)
[ -n "$VIASH_PAR_BCL_ONLY_LANE" ] && ViashError Bad arguments for option \'--bcl_only_lane\': \'$VIASH_PAR_BCL_ONLY_LANE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
VIASH_PAR_BCL_ONLY_LANE="$2"
[ $# -lt 2 ] && ViashError Not enough arguments passed to --bcl_only_lane. Use "--help" to get more information on the parameters. && exit 1
shift 2
;;
--bcl_only_lane=*)
[ -n "$VIASH_PAR_BCL_ONLY_LANE" ] && ViashError Bad arguments for option \'--bcl_only_lane=*\': \'$VIASH_PAR_BCL_ONLY_LANE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
VIASH_PAR_BCL_ONLY_LANE=$(ViashRemoveFlags "$1")
shift 1
;;
--first_tile_only)
[ -n "$VIASH_PAR_FIRST_TILE_ONLY" ] && ViashError Bad arguments for option \'--first_tile_only\': \'$VIASH_PAR_FIRST_TILE_ONLY\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
VIASH_PAR_FIRST_TILE_ONLY="$2"
[ $# -lt 2 ] && ViashError Not enough arguments passed to --first_tile_only. Use "--help" to get more information on the parameters. && exit 1
shift 2
;;
--first_tile_only=*)
[ -n "$VIASH_PAR_FIRST_TILE_ONLY" ] && ViashError Bad arguments for option \'--first_tile_only=*\': \'$VIASH_PAR_FIRST_TILE_ONLY\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
VIASH_PAR_FIRST_TILE_ONLY=$(ViashRemoveFlags "$1")
shift 1
;;
--tiles)
[ -n "$VIASH_PAR_TILES" ] && ViashError Bad arguments for option \'--tiles\': \'$VIASH_PAR_TILES\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
VIASH_PAR_TILES="$2"
[ $# -lt 2 ] && ViashError Not enough arguments passed to --tiles. Use "--help" to get more information on the parameters. && exit 1
shift 2
;;
--tiles=*)
[ -n "$VIASH_PAR_TILES" ] && ViashError Bad arguments for option \'--tiles=*\': \'$VIASH_PAR_TILES\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
VIASH_PAR_TILES=$(ViashRemoveFlags "$1")
shift 1
;;
--exclude_tiles)
[ -n "$VIASH_PAR_EXCLUDE_TILES" ] && ViashError Bad arguments for option \'--exclude_tiles\': \'$VIASH_PAR_EXCLUDE_TILES\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
VIASH_PAR_EXCLUDE_TILES="$2"
[ $# -lt 2 ] && ViashError Not enough arguments passed to --exclude_tiles. Use "--help" to get more information on the parameters. && exit 1
shift 2
;;
--exclude_tiles=*)
[ -n "$VIASH_PAR_EXCLUDE_TILES" ] && ViashError Bad arguments for option \'--exclude_tiles=*\': \'$VIASH_PAR_EXCLUDE_TILES\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
VIASH_PAR_EXCLUDE_TILES=$(ViashRemoveFlags "$1")
shift 1
;;
--shared_thread_odirect_output)
[ -n "$VIASH_PAR_SHARED_THREAD_ODIRECT_OUTPUT" ] && ViashError Bad arguments for option \'--shared_thread_odirect_output\': \'$VIASH_PAR_SHARED_THREAD_ODIRECT_OUTPUT\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
VIASH_PAR_SHARED_THREAD_ODIRECT_OUTPUT="$2"
[ $# -lt 2 ] && ViashError Not enough arguments passed to --shared_thread_odirect_output. Use "--help" to get more information on the parameters. && exit 1
shift 2
;;
--shared_thread_odirect_output=*)
[ -n "$VIASH_PAR_SHARED_THREAD_ODIRECT_OUTPUT" ] && ViashError Bad arguments for option \'--shared_thread_odirect_output=*\': \'$VIASH_PAR_SHARED_THREAD_ODIRECT_OUTPUT\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
VIASH_PAR_SHARED_THREAD_ODIRECT_OUTPUT=$(ViashRemoveFlags "$1")
shift 1
;;
--bcl_num_parallel_tiles)
[ -n "$VIASH_PAR_BCL_NUM_PARALLEL_TILES" ] && ViashError Bad arguments for option \'--bcl_num_parallel_tiles\': \'$VIASH_PAR_BCL_NUM_PARALLEL_TILES\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
VIASH_PAR_BCL_NUM_PARALLEL_TILES="$2"
[ $# -lt 2 ] && ViashError Not enough arguments passed to --bcl_num_parallel_tiles. Use "--help" to get more information on the parameters. && exit 1
shift 2
;;
--bcl_num_parallel_tiles=*)
[ -n "$VIASH_PAR_BCL_NUM_PARALLEL_TILES" ] && ViashError Bad arguments for option \'--bcl_num_parallel_tiles=*\': \'$VIASH_PAR_BCL_NUM_PARALLEL_TILES\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
VIASH_PAR_BCL_NUM_PARALLEL_TILES=$(ViashRemoveFlags "$1")
shift 1
;;
--bcl_num_conversion_threads)
[ -n "$VIASH_PAR_BCL_NUM_CONVERSION_THREADS" ] && ViashError Bad arguments for option \'--bcl_num_conversion_threads\': \'$VIASH_PAR_BCL_NUM_CONVERSION_THREADS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
VIASH_PAR_BCL_NUM_CONVERSION_THREADS="$2"
[ $# -lt 2 ] && ViashError Not enough arguments passed to --bcl_num_conversion_threads. Use "--help" to get more information on the parameters. && exit 1
shift 2
;;
--bcl_num_conversion_threads=*)
[ -n "$VIASH_PAR_BCL_NUM_CONVERSION_THREADS" ] && ViashError Bad arguments for option \'--bcl_num_conversion_threads=*\': \'$VIASH_PAR_BCL_NUM_CONVERSION_THREADS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
VIASH_PAR_BCL_NUM_CONVERSION_THREADS=$(ViashRemoveFlags "$1")
shift 1
;;
--bcl_num_compression_threads)
[ -n "$VIASH_PAR_BCL_NUM_COMPRESSION_THREADS" ] && ViashError Bad arguments for option \'--bcl_num_compression_threads\': \'$VIASH_PAR_BCL_NUM_COMPRESSION_THREADS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
VIASH_PAR_BCL_NUM_COMPRESSION_THREADS="$2"
[ $# -lt 2 ] && ViashError Not enough arguments passed to --bcl_num_compression_threads. Use "--help" to get more information on the parameters. && exit 1
shift 2
;;
--bcl_num_compression_threads=*)
[ -n "$VIASH_PAR_BCL_NUM_COMPRESSION_THREADS" ] && ViashError Bad arguments for option \'--bcl_num_compression_threads=*\': \'$VIASH_PAR_BCL_NUM_COMPRESSION_THREADS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
VIASH_PAR_BCL_NUM_COMPRESSION_THREADS=$(ViashRemoveFlags "$1")
shift 1
;;
--bcl_num_decompression_threads)
[ -n "$VIASH_PAR_BCL_NUM_DECOMPRESSION_THREADS" ] && ViashError Bad arguments for option \'--bcl_num_decompression_threads\': \'$VIASH_PAR_BCL_NUM_DECOMPRESSION_THREADS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
VIASH_PAR_BCL_NUM_DECOMPRESSION_THREADS="$2"
[ $# -lt 2 ] && ViashError Not enough arguments passed to --bcl_num_decompression_threads. Use "--help" to get more information on the parameters. && exit 1
shift 2
;;
--bcl_num_decompression_threads=*)
[ -n "$VIASH_PAR_BCL_NUM_DECOMPRESSION_THREADS" ] && ViashError Bad arguments for option \'--bcl_num_decompression_threads=*\': \'$VIASH_PAR_BCL_NUM_DECOMPRESSION_THREADS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
VIASH_PAR_BCL_NUM_DECOMPRESSION_THREADS=$(ViashRemoveFlags "$1")
shift 1
;;
--bcl_only_matched_reads)
[ -n "$VIASH_PAR_BCL_ONLY_MATCHED_READS" ] && ViashError Bad arguments for option \'--bcl_only_matched_reads\': \'$VIASH_PAR_BCL_ONLY_MATCHED_READS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
VIASH_PAR_BCL_ONLY_MATCHED_READS="$2"
[ $# -lt 2 ] && ViashError Not enough arguments passed to --bcl_only_matched_reads. Use "--help" to get more information on the parameters. && exit 1
shift 2
;;
--bcl_only_matched_reads=*)
[ -n "$VIASH_PAR_BCL_ONLY_MATCHED_READS" ] && ViashError Bad arguments for option \'--bcl_only_matched_reads=*\': \'$VIASH_PAR_BCL_ONLY_MATCHED_READS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
VIASH_PAR_BCL_ONLY_MATCHED_READS=$(ViashRemoveFlags "$1")
shift 1
;;
--no_lane_splitting)
[ -n "$VIASH_PAR_NO_LANE_SPLITTING" ] && ViashError Bad arguments for option \'--no_lane_splitting\': \'$VIASH_PAR_NO_LANE_SPLITTING\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
VIASH_PAR_NO_LANE_SPLITTING="$2"
[ $# -lt 2 ] && ViashError Not enough arguments passed to --no_lane_splitting. Use "--help" to get more information on the parameters. && exit 1
shift 2
;;
--no_lane_splitting=*)
[ -n "$VIASH_PAR_NO_LANE_SPLITTING" ] && ViashError Bad arguments for option \'--no_lane_splitting=*\': \'$VIASH_PAR_NO_LANE_SPLITTING\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
VIASH_PAR_NO_LANE_SPLITTING=$(ViashRemoveFlags "$1")
shift 1
;;
--num_unknown_barcodes_reported)
[ -n "$VIASH_PAR_NUM_UNKNOWN_BARCODES_REPORTED" ] && ViashError Bad arguments for option \'--num_unknown_barcodes_reported\': \'$VIASH_PAR_NUM_UNKNOWN_BARCODES_REPORTED\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
VIASH_PAR_NUM_UNKNOWN_BARCODES_REPORTED="$2"
[ $# -lt 2 ] && ViashError Not enough arguments passed to --num_unknown_barcodes_reported. Use "--help" to get more information on the parameters. && exit 1
shift 2
;;
--num_unknown_barcodes_reported=*)
[ -n "$VIASH_PAR_NUM_UNKNOWN_BARCODES_REPORTED" ] && ViashError Bad arguments for option \'--num_unknown_barcodes_reported=*\': \'$VIASH_PAR_NUM_UNKNOWN_BARCODES_REPORTED\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
VIASH_PAR_NUM_UNKNOWN_BARCODES_REPORTED=$(ViashRemoveFlags "$1")
shift 1
;;
--bcl_validate_sample_sheet_only)
[ -n "$VIASH_PAR_BCL_VALIDATE_SAMPLE_SHEET_ONLY" ] && ViashError Bad arguments for option \'--bcl_validate_sample_sheet_only\': \'$VIASH_PAR_BCL_VALIDATE_SAMPLE_SHEET_ONLY\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
VIASH_PAR_BCL_VALIDATE_SAMPLE_SHEET_ONLY="$2"
[ $# -lt 2 ] && ViashError Not enough arguments passed to --bcl_validate_sample_sheet_only. Use "--help" to get more information on the parameters. && exit 1
shift 2
;;
--bcl_validate_sample_sheet_only=*)
[ -n "$VIASH_PAR_BCL_VALIDATE_SAMPLE_SHEET_ONLY" ] && ViashError Bad arguments for option \'--bcl_validate_sample_sheet_only=*\': \'$VIASH_PAR_BCL_VALIDATE_SAMPLE_SHEET_ONLY\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
VIASH_PAR_BCL_VALIDATE_SAMPLE_SHEET_ONLY=$(ViashRemoveFlags "$1")
shift 1
;;
--strict_mode)
[ -n "$VIASH_PAR_STRICT_MODE" ] && ViashError Bad arguments for option \'--strict_mode\': \'$VIASH_PAR_STRICT_MODE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
VIASH_PAR_STRICT_MODE="$2"
[ $# -lt 2 ] && ViashError Not enough arguments passed to --strict_mode. Use "--help" to get more information on the parameters. && exit 1
shift 2
;;
--strict_mode=*)
[ -n "$VIASH_PAR_STRICT_MODE" ] && ViashError Bad arguments for option \'--strict_mode=*\': \'$VIASH_PAR_STRICT_MODE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
VIASH_PAR_STRICT_MODE=$(ViashRemoveFlags "$1")
shift 1
;;
--sample_name_column_enabled)
[ -n "$VIASH_PAR_SAMPLE_NAME_COLUMN_ENABLED" ] && ViashError Bad arguments for option \'--sample_name_column_enabled\': \'$VIASH_PAR_SAMPLE_NAME_COLUMN_ENABLED\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
VIASH_PAR_SAMPLE_NAME_COLUMN_ENABLED="$2"
[ $# -lt 2 ] && ViashError Not enough arguments passed to --sample_name_column_enabled. Use "--help" to get more information on the parameters. && exit 1
shift 2
;;
--sample_name_column_enabled=*)
[ -n "$VIASH_PAR_SAMPLE_NAME_COLUMN_ENABLED" ] && ViashError Bad arguments for option \'--sample_name_column_enabled=*\': \'$VIASH_PAR_SAMPLE_NAME_COLUMN_ENABLED\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
VIASH_PAR_SAMPLE_NAME_COLUMN_ENABLED=$(ViashRemoveFlags "$1")
shift 1
;;
--output_directory)
[ -n "$VIASH_PAR_OUTPUT_DIRECTORY" ] && ViashError Bad arguments for option \'--output_directory\': \'$VIASH_PAR_OUTPUT_DIRECTORY\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
VIASH_PAR_OUTPUT_DIRECTORY="$2"
[ $# -lt 2 ] && ViashError Not enough arguments passed to --output_directory. Use "--help" to get more information on the parameters. && exit 1
shift 2
;;
--output_directory=*)
[ -n "$VIASH_PAR_OUTPUT_DIRECTORY" ] && ViashError Bad arguments for option \'--output_directory=*\': \'$VIASH_PAR_OUTPUT_DIRECTORY\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
VIASH_PAR_OUTPUT_DIRECTORY=$(ViashRemoveFlags "$1")
shift 1
;;
-o)
[ -n "$VIASH_PAR_OUTPUT_DIRECTORY" ] && ViashError Bad arguments for option \'-o\': \'$VIASH_PAR_OUTPUT_DIRECTORY\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
VIASH_PAR_OUTPUT_DIRECTORY="$2"
[ $# -lt 2 ] && ViashError Not enough arguments passed to -o. Use "--help" to get more information on the parameters. && exit 1
shift 2
;;
--bcl_sampleproject_subdirectories)
[ -n "$VIASH_PAR_BCL_SAMPLEPROJECT_SUBDIRECTORIES" ] && ViashError Bad arguments for option \'--bcl_sampleproject_subdirectories\': \'$VIASH_PAR_BCL_SAMPLEPROJECT_SUBDIRECTORIES\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
VIASH_PAR_BCL_SAMPLEPROJECT_SUBDIRECTORIES="$2"
[ $# -lt 2 ] && ViashError Not enough arguments passed to --bcl_sampleproject_subdirectories. Use "--help" to get more information on the parameters. && exit 1
shift 2
;;
--bcl_sampleproject_subdirectories=*)
[ -n "$VIASH_PAR_BCL_SAMPLEPROJECT_SUBDIRECTORIES" ] && ViashError Bad arguments for option \'--bcl_sampleproject_subdirectories=*\': \'$VIASH_PAR_BCL_SAMPLEPROJECT_SUBDIRECTORIES\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
VIASH_PAR_BCL_SAMPLEPROJECT_SUBDIRECTORIES=$(ViashRemoveFlags "$1")
shift 1
;;
--fastq_gzip_compression_level)
[ -n "$VIASH_PAR_FASTQ_GZIP_COMPRESSION_LEVEL" ] && ViashError Bad arguments for option \'--fastq_gzip_compression_level\': \'$VIASH_PAR_FASTQ_GZIP_COMPRESSION_LEVEL\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
VIASH_PAR_FASTQ_GZIP_COMPRESSION_LEVEL="$2"
[ $# -lt 2 ] && ViashError Not enough arguments passed to --fastq_gzip_compression_level. Use "--help" to get more information on the parameters. && exit 1
shift 2
;;
--fastq_gzip_compression_level=*)
[ -n "$VIASH_PAR_FASTQ_GZIP_COMPRESSION_LEVEL" ] && ViashError Bad arguments for option \'--fastq_gzip_compression_level=*\': \'$VIASH_PAR_FASTQ_GZIP_COMPRESSION_LEVEL\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
VIASH_PAR_FASTQ_GZIP_COMPRESSION_LEVEL=$(ViashRemoveFlags "$1")
shift 1
;;
--reports)
[ -n "$VIASH_PAR_REPORTS" ] && ViashError Bad arguments for option \'--reports\': \'$VIASH_PAR_REPORTS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
VIASH_PAR_REPORTS="$2"
[ $# -lt 2 ] && ViashError Not enough arguments passed to --reports. Use "--help" to get more information on the parameters. && exit 1
shift 2
;;
--reports=*)
[ -n "$VIASH_PAR_REPORTS" ] && ViashError Bad arguments for option \'--reports=*\': \'$VIASH_PAR_REPORTS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
VIASH_PAR_REPORTS=$(ViashRemoveFlags "$1")
shift 1
;;
--logs)
[ -n "$VIASH_PAR_LOGS" ] && ViashError Bad arguments for option \'--logs\': \'$VIASH_PAR_LOGS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
VIASH_PAR_LOGS="$2"
[ $# -lt 2 ] && ViashError Not enough arguments passed to --logs. Use "--help" to get more information on the parameters. && exit 1
shift 2
;;
--logs=*)
[ -n "$VIASH_PAR_LOGS" ] && ViashError Bad arguments for option \'--logs=*\': \'$VIASH_PAR_LOGS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
VIASH_PAR_LOGS=$(ViashRemoveFlags "$1")
shift 1
;;
--force)
[ -n "$VIASH_PAR_FORCE" ] && ViashError Bad arguments for option \'--force\': \'$VIASH_PAR_FORCE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
VIASH_PAR_FORCE="$2"
[ $# -lt 2 ] && ViashError Not enough arguments passed to --force. Use "--help" to get more information on the parameters. && exit 1
shift 2
;;
--force=*)
[ -n "$VIASH_PAR_FORCE" ] && ViashError Bad arguments for option \'--force=*\': \'$VIASH_PAR_FORCE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
VIASH_PAR_FORCE=$(ViashRemoveFlags "$1")
shift 1
;;
---engine)
VIASH_ENGINE_ID="$2"
shift 2
;;
---engine=*)
VIASH_ENGINE_ID="$(ViashRemoveFlags "$1")"
shift 1
;;
---setup)
VIASH_MODE='setup'
VIASH_SETUP_STRATEGY="$2"
shift 2
;;
---setup=*)
VIASH_MODE='setup'
VIASH_SETUP_STRATEGY="$(ViashRemoveFlags "$1")"
shift 1
;;
---dockerfile)
VIASH_MODE='dockerfile'
shift 1
;;
---docker_run_args)
VIASH_DOCKER_RUN_ARGS+=("$2")
shift 2
;;
---docker_run_args=*)
VIASH_DOCKER_RUN_ARGS+=("$(ViashRemoveFlags "$1")")
shift 1
;;
---docker_image_id)
VIASH_MODE='docker_image_id'
shift 1
;;
---debug)
VIASH_MODE='debug'
shift 1
;;
---cpus)
[ -n "$VIASH_META_CPUS" ] && ViashError Bad arguments for option \'---cpus\': \'$VIASH_META_CPUS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
VIASH_META_CPUS="$2"
[ $# -lt 2 ] && ViashError Not enough arguments passed to ---cpus. Use "--help" to get more information on the parameters. && exit 1
shift 2
;;
---cpus=*)
[ -n "$VIASH_META_CPUS" ] && ViashError Bad arguments for option \'---cpus=*\': \'$VIASH_META_CPUS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
VIASH_META_CPUS=$(ViashRemoveFlags "$1")
shift 1
;;
---memory)
[ -n "$VIASH_META_MEMORY" ] && ViashError Bad arguments for option \'---memory\': \'$VIASH_META_MEMORY\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
VIASH_META_MEMORY="$2"
[ $# -lt 2 ] && ViashError Not enough arguments passed to ---memory. Use "--help" to get more information on the parameters. && exit 1
shift 2
;;
---memory=*)
[ -n "$VIASH_META_MEMORY" ] && ViashError Bad arguments for option \'---memory=*\': \'$VIASH_META_MEMORY\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
VIASH_META_MEMORY=$(ViashRemoveFlags "$1")
shift 1
;;
*) # positional arg or unknown option
# since the positional args will be eval'd, can we always quote, instead of using ViashQuote
VIASH_POSITIONAL_ARGS="$VIASH_POSITIONAL_ARGS '$1'"
[[ $1 == -* ]] && ViashWarning $1 looks like a parameter but is not a defined parameter and will instead be treated as a positional argument. Use "--help" to get more information on the parameters.
shift # past argument
;;
esac
done
# parse positional parameters
eval set -- $VIASH_POSITIONAL_ARGS
if [ "$VIASH_ENGINE_ID" == "native" ] ; then
VIASH_ENGINE_TYPE='native'
elif [ "$VIASH_ENGINE_ID" == "docker" ] ; then
VIASH_ENGINE_TYPE='docker'
else
ViashError "Engine '$VIASH_ENGINE_ID' is not recognized. Options are: docker, native."
exit 1
fi
if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then
# check if docker is installed properly
ViashDockerInstallationCheck
# determine docker image id
if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then
VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/biobox/bcl_convert:main'
fi
# print dockerfile
if [ "$VIASH_MODE" == "dockerfile" ]; then
ViashDockerfile "$VIASH_ENGINE_ID"
exit 0
elif [ "$VIASH_MODE" == "docker_image_id" ]; then
echo "$VIASH_DOCKER_IMAGE_ID"
exit 0
# enter docker container
elif [[ "$VIASH_MODE" == "debug" ]]; then
VIASH_CMD="docker run --entrypoint=bash ${VIASH_DOCKER_RUN_ARGS[@]} -v '$(pwd)':/pwd --workdir /pwd -t $VIASH_DOCKER_IMAGE_ID"
ViashNotice "+ $VIASH_CMD"
eval $VIASH_CMD
exit
# build docker image
elif [ "$VIASH_MODE" == "setup" ]; then
ViashDockerSetup "$VIASH_DOCKER_IMAGE_ID" "$VIASH_SETUP_STRATEGY"
ViashDockerCheckCommands "$VIASH_DOCKER_IMAGE_ID" 'ps' 'bash'
exit 0
fi
# check if docker image exists
ViashDockerSetup "$VIASH_DOCKER_IMAGE_ID" ifneedbepullelsecachedbuild
ViashDockerCheckCommands "$VIASH_DOCKER_IMAGE_ID" 'ps' 'bash'
fi
# setting computational defaults
# helper function for parsing memory strings
function ViashMemoryAsBytes {
local memory=`echo "$1" | tr '[:upper:]' '[:lower:]' | tr -d '[:space:]'`
local memory_regex='^([0-9]+)([kmgtp]i?b?|b)$'
if [[ $memory =~ $memory_regex ]]; then
local number=${memory/[^0-9]*/}
local symbol=${memory/*[0-9]/}
case $symbol in
b) memory_b=$number ;;
kb|k) memory_b=$(( $number * 1000 )) ;;
mb|m) memory_b=$(( $number * 1000 * 1000 )) ;;
gb|g) memory_b=$(( $number * 1000 * 1000 * 1000 )) ;;
tb|t) memory_b=$(( $number * 1000 * 1000 * 1000 * 1000 )) ;;
pb|p) memory_b=$(( $number * 1000 * 1000 * 1000 * 1000 * 1000 )) ;;
kib|ki) memory_b=$(( $number * 1024 )) ;;
mib|mi) memory_b=$(( $number * 1024 * 1024 )) ;;
gib|gi) memory_b=$(( $number * 1024 * 1024 * 1024 )) ;;
tib|ti) memory_b=$(( $number * 1024 * 1024 * 1024 * 1024 )) ;;
pib|pi) memory_b=$(( $number * 1024 * 1024 * 1024 * 1024 * 1024 )) ;;
esac
echo "$memory_b"
fi
}
# compute memory in different units
if [ ! -z ${VIASH_META_MEMORY+x} ]; then
VIASH_META_MEMORY_B=`ViashMemoryAsBytes $VIASH_META_MEMORY`
# do not define other variables if memory_b is an empty string
if [ ! -z "$VIASH_META_MEMORY_B" ]; then
VIASH_META_MEMORY_KB=$(( ($VIASH_META_MEMORY_B+999) / 1000 ))
VIASH_META_MEMORY_MB=$(( ($VIASH_META_MEMORY_KB+999) / 1000 ))
VIASH_META_MEMORY_GB=$(( ($VIASH_META_MEMORY_MB+999) / 1000 ))
VIASH_META_MEMORY_TB=$(( ($VIASH_META_MEMORY_GB+999) / 1000 ))
VIASH_META_MEMORY_PB=$(( ($VIASH_META_MEMORY_TB+999) / 1000 ))
VIASH_META_MEMORY_KIB=$(( ($VIASH_META_MEMORY_B+1023) / 1024 ))
VIASH_META_MEMORY_MIB=$(( ($VIASH_META_MEMORY_KIB+1023) / 1024 ))
VIASH_META_MEMORY_GIB=$(( ($VIASH_META_MEMORY_MIB+1023) / 1024 ))
VIASH_META_MEMORY_TIB=$(( ($VIASH_META_MEMORY_GIB+1023) / 1024 ))
VIASH_META_MEMORY_PIB=$(( ($VIASH_META_MEMORY_TIB+1023) / 1024 ))
else
# unset memory if string is empty
unset $VIASH_META_MEMORY_B
fi
fi
# unset nproc if string is empty
if [ -z "$VIASH_META_CPUS" ]; then
unset $VIASH_META_CPUS
fi
# check whether required parameters exist
if [ -z ${VIASH_PAR_BCL_INPUT_DIRECTORY+x} ]; then
ViashError '--bcl_input_directory' is a required argument. Use "--help" to get more information on the parameters.
exit 1
fi
if [ -z ${VIASH_PAR_OUTPUT_DIRECTORY+x} ]; then
ViashError '--output_directory' is a required argument. Use "--help" to get more information on the parameters.
exit 1
fi
if [ -z ${VIASH_META_NAME+x} ]; then
ViashError 'name' is a required argument. Use "--help" to get more information on the parameters.
exit 1
fi
if [ -z ${VIASH_META_FUNCTIONALITY_NAME+x} ]; then
ViashError 'functionality_name' is a required argument. Use "--help" to get more information on the parameters.
exit 1
fi
if [ -z ${VIASH_META_RESOURCES_DIR+x} ]; then
ViashError 'resources_dir' is a required argument. Use "--help" to get more information on the parameters.
exit 1
fi
if [ -z ${VIASH_META_EXECUTABLE+x} ]; then
ViashError 'executable' is a required argument. Use "--help" to get more information on the parameters.
exit 1
fi
if [ -z ${VIASH_META_CONFIG+x} ]; then
ViashError 'config' is a required argument. Use "--help" to get more information on the parameters.
exit 1
fi
if [ -z ${VIASH_META_TEMP_DIR+x} ]; then
ViashError 'temp_dir' is a required argument. Use "--help" to get more information on the parameters.
exit 1
fi
# check whether required files exist
if [ ! -z "$VIASH_PAR_BCL_INPUT_DIRECTORY" ] && [ ! -e "$VIASH_PAR_BCL_INPUT_DIRECTORY" ]; then
ViashError "Input file '$VIASH_PAR_BCL_INPUT_DIRECTORY' does not exist."
exit 1
fi
if [ ! -z "$VIASH_PAR_SAMPLE_SHEET" ] && [ ! -e "$VIASH_PAR_SAMPLE_SHEET" ]; then
ViashError "Input file '$VIASH_PAR_SAMPLE_SHEET' does not exist."
exit 1
fi
if [ ! -z "$VIASH_PAR_RUN_INFO" ] && [ ! -e "$VIASH_PAR_RUN_INFO" ]; then
ViashError "Input file '$VIASH_PAR_RUN_INFO' does not exist."
exit 1
fi
# check whether parameters values are of the right type
if [[ -n "$VIASH_PAR_BCL_ONLY_LANE" ]]; then
if ! [[ "$VIASH_PAR_BCL_ONLY_LANE" =~ ^[-+]?[0-9]+$ ]]; then
ViashError '--bcl_only_lane' has to be an integer. Use "--help" to get more information on the parameters.
exit 1
fi
fi
if [[ -n "$VIASH_PAR_FIRST_TILE_ONLY" ]]; then
if ! [[ "$VIASH_PAR_FIRST_TILE_ONLY" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then
ViashError '--first_tile_only' has to be a boolean. Use "--help" to get more information on the parameters.
exit 1
fi
fi
if [[ -n "$VIASH_PAR_SHARED_THREAD_ODIRECT_OUTPUT" ]]; then
if ! [[ "$VIASH_PAR_SHARED_THREAD_ODIRECT_OUTPUT" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then
ViashError '--shared_thread_odirect_output' has to be a boolean. Use "--help" to get more information on the parameters.
exit 1
fi
fi
if [[ -n "$VIASH_PAR_BCL_NUM_PARALLEL_TILES" ]]; then
if ! [[ "$VIASH_PAR_BCL_NUM_PARALLEL_TILES" =~ ^[-+]?[0-9]+$ ]]; then
ViashError '--bcl_num_parallel_tiles' has to be an integer. Use "--help" to get more information on the parameters.
exit 1
fi
fi
if [[ -n "$VIASH_PAR_BCL_NUM_CONVERSION_THREADS" ]]; then
if ! [[ "$VIASH_PAR_BCL_NUM_CONVERSION_THREADS" =~ ^[-+]?[0-9]+$ ]]; then
ViashError '--bcl_num_conversion_threads' has to be an integer. Use "--help" to get more information on the parameters.
exit 1
fi
fi
if [[ -n "$VIASH_PAR_BCL_NUM_COMPRESSION_THREADS" ]]; then
if ! [[ "$VIASH_PAR_BCL_NUM_COMPRESSION_THREADS" =~ ^[-+]?[0-9]+$ ]]; then
ViashError '--bcl_num_compression_threads' has to be an integer. Use "--help" to get more information on the parameters.
exit 1
fi
fi
if [[ -n "$VIASH_PAR_BCL_NUM_DECOMPRESSION_THREADS" ]]; then
if ! [[ "$VIASH_PAR_BCL_NUM_DECOMPRESSION_THREADS" =~ ^[-+]?[0-9]+$ ]]; then
ViashError '--bcl_num_decompression_threads' has to be an integer. Use "--help" to get more information on the parameters.
exit 1
fi
fi
if [[ -n "$VIASH_PAR_BCL_ONLY_MATCHED_READS" ]]; then
if ! [[ "$VIASH_PAR_BCL_ONLY_MATCHED_READS" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then
ViashError '--bcl_only_matched_reads' has to be a boolean. Use "--help" to get more information on the parameters.
exit 1
fi
fi
if [[ -n "$VIASH_PAR_NO_LANE_SPLITTING" ]]; then
if ! [[ "$VIASH_PAR_NO_LANE_SPLITTING" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then
ViashError '--no_lane_splitting' has to be a boolean. Use "--help" to get more information on the parameters.
exit 1
fi
fi
if [[ -n "$VIASH_PAR_NUM_UNKNOWN_BARCODES_REPORTED" ]]; then
if ! [[ "$VIASH_PAR_NUM_UNKNOWN_BARCODES_REPORTED" =~ ^[-+]?[0-9]+$ ]]; then
ViashError '--num_unknown_barcodes_reported' has to be an integer. Use "--help" to get more information on the parameters.
exit 1
fi
fi
if [[ -n "$VIASH_PAR_BCL_VALIDATE_SAMPLE_SHEET_ONLY" ]]; then
if ! [[ "$VIASH_PAR_BCL_VALIDATE_SAMPLE_SHEET_ONLY" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then
ViashError '--bcl_validate_sample_sheet_only' has to be a boolean. Use "--help" to get more information on the parameters.
exit 1
fi
fi
if [[ -n "$VIASH_PAR_STRICT_MODE" ]]; then
if ! [[ "$VIASH_PAR_STRICT_MODE" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then
ViashError '--strict_mode' has to be a boolean. Use "--help" to get more information on the parameters.
exit 1
fi
fi
if [[ -n "$VIASH_PAR_SAMPLE_NAME_COLUMN_ENABLED" ]]; then
if ! [[ "$VIASH_PAR_SAMPLE_NAME_COLUMN_ENABLED" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then
ViashError '--sample_name_column_enabled' has to be a boolean. Use "--help" to get more information on the parameters.
exit 1
fi
fi
if [[ -n "$VIASH_PAR_BCL_SAMPLEPROJECT_SUBDIRECTORIES" ]]; then
if ! [[ "$VIASH_PAR_BCL_SAMPLEPROJECT_SUBDIRECTORIES" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then
ViashError '--bcl_sampleproject_subdirectories' has to be a boolean. Use "--help" to get more information on the parameters.
exit 1
fi
fi
if [[ -n "$VIASH_PAR_FASTQ_GZIP_COMPRESSION_LEVEL" ]]; then
if ! [[ "$VIASH_PAR_FASTQ_GZIP_COMPRESSION_LEVEL" =~ ^[-+]?[0-9]+$ ]]; then
ViashError '--fastq_gzip_compression_level' has to be an integer. Use "--help" to get more information on the parameters.
exit 1
fi
fi
if [[ -n "$VIASH_PAR_FORCE" ]]; then
if ! [[ "$VIASH_PAR_FORCE" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then
ViashError '--force' has to be a boolean. Use "--help" to get more information on the parameters.
exit 1
fi
fi
if [[ -n "$VIASH_META_CPUS" ]]; then
if ! [[ "$VIASH_META_CPUS" =~ ^[-+]?[0-9]+$ ]]; then
ViashError 'cpus' has to be an integer. Use "--help" to get more information on the parameters.
exit 1
fi
fi
if [[ -n "$VIASH_META_MEMORY_B" ]]; then
if ! [[ "$VIASH_META_MEMORY_B" =~ ^[-+]?[0-9]+$ ]]; then
ViashError 'memory_b' has to be a long. Use "--help" to get more information on the parameters.
exit 1
fi
fi
if [[ -n "$VIASH_META_MEMORY_KB" ]]; then
if ! [[ "$VIASH_META_MEMORY_KB" =~ ^[-+]?[0-9]+$ ]]; then
ViashError 'memory_kb' has to be a long. Use "--help" to get more information on the parameters.
exit 1
fi
fi
if [[ -n "$VIASH_META_MEMORY_MB" ]]; then
if ! [[ "$VIASH_META_MEMORY_MB" =~ ^[-+]?[0-9]+$ ]]; then
ViashError 'memory_mb' has to be a long. Use "--help" to get more information on the parameters.
exit 1
fi
fi
if [[ -n "$VIASH_META_MEMORY_GB" ]]; then
if ! [[ "$VIASH_META_MEMORY_GB" =~ ^[-+]?[0-9]+$ ]]; then
ViashError 'memory_gb' has to be a long. Use "--help" to get more information on the parameters.
exit 1
fi
fi
if [[ -n "$VIASH_META_MEMORY_TB" ]]; then
if ! [[ "$VIASH_META_MEMORY_TB" =~ ^[-+]?[0-9]+$ ]]; then
ViashError 'memory_tb' has to be a long. Use "--help" to get more information on the parameters.
exit 1
fi
fi
if [[ -n "$VIASH_META_MEMORY_PB" ]]; then
if ! [[ "$VIASH_META_MEMORY_PB" =~ ^[-+]?[0-9]+$ ]]; then
ViashError 'memory_pb' has to be a long. Use "--help" to get more information on the parameters.
exit 1
fi
fi
if [[ -n "$VIASH_META_MEMORY_KIB" ]]; then
if ! [[ "$VIASH_META_MEMORY_KIB" =~ ^[-+]?[0-9]+$ ]]; then
ViashError 'memory_kib' has to be a long. Use "--help" to get more information on the parameters.
exit 1
fi
fi
if [[ -n "$VIASH_META_MEMORY_MIB" ]]; then
if ! [[ "$VIASH_META_MEMORY_MIB" =~ ^[-+]?[0-9]+$ ]]; then
ViashError 'memory_mib' has to be a long. Use "--help" to get more information on the parameters.
exit 1
fi
fi
if [[ -n "$VIASH_META_MEMORY_GIB" ]]; then
if ! [[ "$VIASH_META_MEMORY_GIB" =~ ^[-+]?[0-9]+$ ]]; then
ViashError 'memory_gib' has to be a long. Use "--help" to get more information on the parameters.
exit 1
fi
fi
if [[ -n "$VIASH_META_MEMORY_TIB" ]]; then
if ! [[ "$VIASH_META_MEMORY_TIB" =~ ^[-+]?[0-9]+$ ]]; then
ViashError 'memory_tib' has to be a long. Use "--help" to get more information on the parameters.
exit 1
fi
fi
if [[ -n "$VIASH_META_MEMORY_PIB" ]]; then
if ! [[ "$VIASH_META_MEMORY_PIB" =~ ^[-+]?[0-9]+$ ]]; then
ViashError 'memory_pib' has to be a long. Use "--help" to get more information on the parameters.
exit 1
fi
fi
# create parent directories of output files, if so desired
if [ ! -z "$VIASH_PAR_OUTPUT_DIRECTORY" ] && [ ! -d "$(dirname "$VIASH_PAR_OUTPUT_DIRECTORY")" ]; then
mkdir -p "$(dirname "$VIASH_PAR_OUTPUT_DIRECTORY")"
fi
if [ ! -z "$VIASH_PAR_REPORTS" ] && [ ! -d "$(dirname "$VIASH_PAR_REPORTS")" ]; then
mkdir -p "$(dirname "$VIASH_PAR_REPORTS")"
fi
if [ ! -z "$VIASH_PAR_LOGS" ] && [ ! -d "$(dirname "$VIASH_PAR_LOGS")" ]; then
mkdir -p "$(dirname "$VIASH_PAR_LOGS")"
fi
if [ "$VIASH_ENGINE_ID" == "native" ] ; then
if [ "$VIASH_MODE" == "run" ]; then
VIASH_CMD="bash"
else
ViashError "Engine '$VIASH_ENGINE_ID' does not support mode '$VIASH_MODE'."
exit 1
fi
fi
if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then
# detect volumes from file arguments
VIASH_CHOWN_VARS=()
if [ ! -z "$VIASH_PAR_BCL_INPUT_DIRECTORY" ]; then
VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$VIASH_PAR_BCL_INPUT_DIRECTORY")" )
VIASH_PAR_BCL_INPUT_DIRECTORY=$(ViashDockerAutodetectMount "$VIASH_PAR_BCL_INPUT_DIRECTORY")
fi
if [ ! -z "$VIASH_PAR_SAMPLE_SHEET" ]; then
VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$VIASH_PAR_SAMPLE_SHEET")" )
VIASH_PAR_SAMPLE_SHEET=$(ViashDockerAutodetectMount "$VIASH_PAR_SAMPLE_SHEET")
fi
if [ ! -z "$VIASH_PAR_RUN_INFO" ]; then
VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$VIASH_PAR_RUN_INFO")" )
VIASH_PAR_RUN_INFO=$(ViashDockerAutodetectMount "$VIASH_PAR_RUN_INFO")
fi
if [ ! -z "$VIASH_PAR_OUTPUT_DIRECTORY" ]; then
VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$VIASH_PAR_OUTPUT_DIRECTORY")" )
VIASH_PAR_OUTPUT_DIRECTORY=$(ViashDockerAutodetectMount "$VIASH_PAR_OUTPUT_DIRECTORY")
VIASH_CHOWN_VARS+=( "$VIASH_PAR_OUTPUT_DIRECTORY" )
fi
if [ ! -z "$VIASH_PAR_REPORTS" ]; then
VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$VIASH_PAR_REPORTS")" )
VIASH_PAR_REPORTS=$(ViashDockerAutodetectMount "$VIASH_PAR_REPORTS")
VIASH_CHOWN_VARS+=( "$VIASH_PAR_REPORTS" )
fi
if [ ! -z "$VIASH_PAR_LOGS" ]; then
VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$VIASH_PAR_LOGS")" )
VIASH_PAR_LOGS=$(ViashDockerAutodetectMount "$VIASH_PAR_LOGS")
VIASH_CHOWN_VARS+=( "$VIASH_PAR_LOGS" )
fi
if [ ! -z "$VIASH_META_RESOURCES_DIR" ]; then
VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$VIASH_META_RESOURCES_DIR")" )
VIASH_META_RESOURCES_DIR=$(ViashDockerAutodetectMount "$VIASH_META_RESOURCES_DIR")
fi
if [ ! -z "$VIASH_META_EXECUTABLE" ]; then
VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$VIASH_META_EXECUTABLE")" )
VIASH_META_EXECUTABLE=$(ViashDockerAutodetectMount "$VIASH_META_EXECUTABLE")
fi
if [ ! -z "$VIASH_META_CONFIG" ]; then
VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$VIASH_META_CONFIG")" )
VIASH_META_CONFIG=$(ViashDockerAutodetectMount "$VIASH_META_CONFIG")
fi
if [ ! -z "$VIASH_META_TEMP_DIR" ]; then
VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$VIASH_META_TEMP_DIR")" )
VIASH_META_TEMP_DIR=$(ViashDockerAutodetectMount "$VIASH_META_TEMP_DIR")
fi
# get unique mounts
VIASH_UNIQUE_MOUNTS=($(for val in "${VIASH_DIRECTORY_MOUNTS[@]}"; do echo "$val"; done | sort -u))
fi
if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then
# change file ownership
function ViashPerformChown {
if (( ${#VIASH_CHOWN_VARS[@]} )); then
set +e
VIASH_CMD="docker run --entrypoint=bash --rm ${VIASH_UNIQUE_MOUNTS[@]} $VIASH_DOCKER_IMAGE_ID -c 'chown $(id -u):$(id -g) --silent --recursive ${VIASH_CHOWN_VARS[@]}'"
ViashDebug "+ $VIASH_CMD"
eval $VIASH_CMD
set -e
fi
}
trap ViashPerformChown EXIT
fi
if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then
# helper function for filling in extra docker args
if [ ! -z "$VIASH_META_MEMORY_B" ]; then
VIASH_DOCKER_RUN_ARGS+=("--memory=${VIASH_META_MEMORY_B}")
fi
if [ ! -z "$VIASH_META_CPUS" ]; then
VIASH_DOCKER_RUN_ARGS+=("--cpus=${VIASH_META_CPUS}")
fi
fi
if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then
VIASH_CMD="docker run --entrypoint=bash ${VIASH_DOCKER_RUN_ARGS[@]} ${VIASH_UNIQUE_MOUNTS[@]} $VIASH_DOCKER_IMAGE_ID"
fi
# set dependency paths
ViashDebug "Running command: $(echo $VIASH_CMD)"
cat << VIASHEOF | eval $VIASH_CMD
set -e
tempscript=\$(mktemp "$VIASH_META_TEMP_DIR/viash-run-bcl_convert-XXXXXX").sh
function clean_up {
rm "\$tempscript"
}
function interrupt {
echo -e "\nCTRL-C Pressed..."
exit 1
}
trap clean_up EXIT
trap interrupt INT SIGINT
cat > "\$tempscript" << 'VIASHMAIN'
## VIASH START
# The following code has been auto-generated by Viash.
$( if [ ! -z ${VIASH_PAR_BCL_INPUT_DIRECTORY+x} ]; then echo "${VIASH_PAR_BCL_INPUT_DIRECTORY}" | sed "s#'#'\"'\"'#g;s#.*#par_bcl_input_directory='&'#" ; else echo "# par_bcl_input_directory="; fi )
$( if [ ! -z ${VIASH_PAR_SAMPLE_SHEET+x} ]; then echo "${VIASH_PAR_SAMPLE_SHEET}" | sed "s#'#'\"'\"'#g;s#.*#par_sample_sheet='&'#" ; else echo "# par_sample_sheet="; fi )
$( if [ ! -z ${VIASH_PAR_RUN_INFO+x} ]; then echo "${VIASH_PAR_RUN_INFO}" | sed "s#'#'\"'\"'#g;s#.*#par_run_info='&'#" ; else echo "# par_run_info="; fi )
$( if [ ! -z ${VIASH_PAR_BCL_ONLY_LANE+x} ]; then echo "${VIASH_PAR_BCL_ONLY_LANE}" | sed "s#'#'\"'\"'#g;s#.*#par_bcl_only_lane='&'#" ; else echo "# par_bcl_only_lane="; fi )
$( if [ ! -z ${VIASH_PAR_FIRST_TILE_ONLY+x} ]; then echo "${VIASH_PAR_FIRST_TILE_ONLY}" | sed "s#'#'\"'\"'#g;s#.*#par_first_tile_only='&'#" ; else echo "# par_first_tile_only="; fi )
$( if [ ! -z ${VIASH_PAR_TILES+x} ]; then echo "${VIASH_PAR_TILES}" | sed "s#'#'\"'\"'#g;s#.*#par_tiles='&'#" ; else echo "# par_tiles="; fi )
$( if [ ! -z ${VIASH_PAR_EXCLUDE_TILES+x} ]; then echo "${VIASH_PAR_EXCLUDE_TILES}" | sed "s#'#'\"'\"'#g;s#.*#par_exclude_tiles='&'#" ; else echo "# par_exclude_tiles="; fi )
$( if [ ! -z ${VIASH_PAR_SHARED_THREAD_ODIRECT_OUTPUT+x} ]; then echo "${VIASH_PAR_SHARED_THREAD_ODIRECT_OUTPUT}" | sed "s#'#'\"'\"'#g;s#.*#par_shared_thread_odirect_output='&'#" ; else echo "# par_shared_thread_odirect_output="; fi )
$( if [ ! -z ${VIASH_PAR_BCL_NUM_PARALLEL_TILES+x} ]; then echo "${VIASH_PAR_BCL_NUM_PARALLEL_TILES}" | sed "s#'#'\"'\"'#g;s#.*#par_bcl_num_parallel_tiles='&'#" ; else echo "# par_bcl_num_parallel_tiles="; fi )
$( if [ ! -z ${VIASH_PAR_BCL_NUM_CONVERSION_THREADS+x} ]; then echo "${VIASH_PAR_BCL_NUM_CONVERSION_THREADS}" | sed "s#'#'\"'\"'#g;s#.*#par_bcl_num_conversion_threads='&'#" ; else echo "# par_bcl_num_conversion_threads="; fi )
$( if [ ! -z ${VIASH_PAR_BCL_NUM_COMPRESSION_THREADS+x} ]; then echo "${VIASH_PAR_BCL_NUM_COMPRESSION_THREADS}" | sed "s#'#'\"'\"'#g;s#.*#par_bcl_num_compression_threads='&'#" ; else echo "# par_bcl_num_compression_threads="; fi )
$( if [ ! -z ${VIASH_PAR_BCL_NUM_DECOMPRESSION_THREADS+x} ]; then echo "${VIASH_PAR_BCL_NUM_DECOMPRESSION_THREADS}" | sed "s#'#'\"'\"'#g;s#.*#par_bcl_num_decompression_threads='&'#" ; else echo "# par_bcl_num_decompression_threads="; fi )
$( if [ ! -z ${VIASH_PAR_BCL_ONLY_MATCHED_READS+x} ]; then echo "${VIASH_PAR_BCL_ONLY_MATCHED_READS}" | sed "s#'#'\"'\"'#g;s#.*#par_bcl_only_matched_reads='&'#" ; else echo "# par_bcl_only_matched_reads="; fi )
$( if [ ! -z ${VIASH_PAR_NO_LANE_SPLITTING+x} ]; then echo "${VIASH_PAR_NO_LANE_SPLITTING}" | sed "s#'#'\"'\"'#g;s#.*#par_no_lane_splitting='&'#" ; else echo "# par_no_lane_splitting="; fi )
$( if [ ! -z ${VIASH_PAR_NUM_UNKNOWN_BARCODES_REPORTED+x} ]; then echo "${VIASH_PAR_NUM_UNKNOWN_BARCODES_REPORTED}" | sed "s#'#'\"'\"'#g;s#.*#par_num_unknown_barcodes_reported='&'#" ; else echo "# par_num_unknown_barcodes_reported="; fi )
$( if [ ! -z ${VIASH_PAR_BCL_VALIDATE_SAMPLE_SHEET_ONLY+x} ]; then echo "${VIASH_PAR_BCL_VALIDATE_SAMPLE_SHEET_ONLY}" | sed "s#'#'\"'\"'#g;s#.*#par_bcl_validate_sample_sheet_only='&'#" ; else echo "# par_bcl_validate_sample_sheet_only="; fi )
$( if [ ! -z ${VIASH_PAR_STRICT_MODE+x} ]; then echo "${VIASH_PAR_STRICT_MODE}" | sed "s#'#'\"'\"'#g;s#.*#par_strict_mode='&'#" ; else echo "# par_strict_mode="; fi )
$( if [ ! -z ${VIASH_PAR_SAMPLE_NAME_COLUMN_ENABLED+x} ]; then echo "${VIASH_PAR_SAMPLE_NAME_COLUMN_ENABLED}" | sed "s#'#'\"'\"'#g;s#.*#par_sample_name_column_enabled='&'#" ; else echo "# par_sample_name_column_enabled="; fi )
$( if [ ! -z ${VIASH_PAR_OUTPUT_DIRECTORY+x} ]; then echo "${VIASH_PAR_OUTPUT_DIRECTORY}" | sed "s#'#'\"'\"'#g;s#.*#par_output_directory='&'#" ; else echo "# par_output_directory="; fi )
$( if [ ! -z ${VIASH_PAR_BCL_SAMPLEPROJECT_SUBDIRECTORIES+x} ]; then echo "${VIASH_PAR_BCL_SAMPLEPROJECT_SUBDIRECTORIES}" | sed "s#'#'\"'\"'#g;s#.*#par_bcl_sampleproject_subdirectories='&'#" ; else echo "# par_bcl_sampleproject_subdirectories="; fi )
$( if [ ! -z ${VIASH_PAR_FASTQ_GZIP_COMPRESSION_LEVEL+x} ]; then echo "${VIASH_PAR_FASTQ_GZIP_COMPRESSION_LEVEL}" | sed "s#'#'\"'\"'#g;s#.*#par_fastq_gzip_compression_level='&'#" ; else echo "# par_fastq_gzip_compression_level="; fi )
$( if [ ! -z ${VIASH_PAR_REPORTS+x} ]; then echo "${VIASH_PAR_REPORTS}" | sed "s#'#'\"'\"'#g;s#.*#par_reports='&'#" ; else echo "# par_reports="; fi )
$( if [ ! -z ${VIASH_PAR_LOGS+x} ]; then echo "${VIASH_PAR_LOGS}" | sed "s#'#'\"'\"'#g;s#.*#par_logs='&'#" ; else echo "# par_logs="; fi )
$( if [ ! -z ${VIASH_PAR_FORCE+x} ]; then echo "${VIASH_PAR_FORCE}" | sed "s#'#'\"'\"'#g;s#.*#par_force='&'#" ; else echo "# par_force="; fi )
$( if [ ! -z ${VIASH_META_NAME+x} ]; then echo "${VIASH_META_NAME}" | sed "s#'#'\"'\"'#g;s#.*#meta_name='&'#" ; else echo "# meta_name="; fi )
$( if [ ! -z ${VIASH_META_FUNCTIONALITY_NAME+x} ]; then echo "${VIASH_META_FUNCTIONALITY_NAME}" | sed "s#'#'\"'\"'#g;s#.*#meta_functionality_name='&'#" ; else echo "# meta_functionality_name="; fi )
$( if [ ! -z ${VIASH_META_RESOURCES_DIR+x} ]; then echo "${VIASH_META_RESOURCES_DIR}" | sed "s#'#'\"'\"'#g;s#.*#meta_resources_dir='&'#" ; else echo "# meta_resources_dir="; fi )
$( if [ ! -z ${VIASH_META_EXECUTABLE+x} ]; then echo "${VIASH_META_EXECUTABLE}" | sed "s#'#'\"'\"'#g;s#.*#meta_executable='&'#" ; else echo "# meta_executable="; fi )
$( if [ ! -z ${VIASH_META_CONFIG+x} ]; then echo "${VIASH_META_CONFIG}" | sed "s#'#'\"'\"'#g;s#.*#meta_config='&'#" ; else echo "# meta_config="; fi )
$( if [ ! -z ${VIASH_META_TEMP_DIR+x} ]; then echo "${VIASH_META_TEMP_DIR}" | sed "s#'#'\"'\"'#g;s#.*#meta_temp_dir='&'#" ; else echo "# meta_temp_dir="; fi )
$( if [ ! -z ${VIASH_META_CPUS+x} ]; then echo "${VIASH_META_CPUS}" | sed "s#'#'\"'\"'#g;s#.*#meta_cpus='&'#" ; else echo "# meta_cpus="; fi )
$( if [ ! -z ${VIASH_META_MEMORY_B+x} ]; then echo "${VIASH_META_MEMORY_B}" | sed "s#'#'\"'\"'#g;s#.*#meta_memory_b='&'#" ; else echo "# meta_memory_b="; fi )
$( if [ ! -z ${VIASH_META_MEMORY_KB+x} ]; then echo "${VIASH_META_MEMORY_KB}" | sed "s#'#'\"'\"'#g;s#.*#meta_memory_kb='&'#" ; else echo "# meta_memory_kb="; fi )
$( if [ ! -z ${VIASH_META_MEMORY_MB+x} ]; then echo "${VIASH_META_MEMORY_MB}" | sed "s#'#'\"'\"'#g;s#.*#meta_memory_mb='&'#" ; else echo "# meta_memory_mb="; fi )
$( if [ ! -z ${VIASH_META_MEMORY_GB+x} ]; then echo "${VIASH_META_MEMORY_GB}" | sed "s#'#'\"'\"'#g;s#.*#meta_memory_gb='&'#" ; else echo "# meta_memory_gb="; fi )
$( if [ ! -z ${VIASH_META_MEMORY_TB+x} ]; then echo "${VIASH_META_MEMORY_TB}" | sed "s#'#'\"'\"'#g;s#.*#meta_memory_tb='&'#" ; else echo "# meta_memory_tb="; fi )
$( if [ ! -z ${VIASH_META_MEMORY_PB+x} ]; then echo "${VIASH_META_MEMORY_PB}" | sed "s#'#'\"'\"'#g;s#.*#meta_memory_pb='&'#" ; else echo "# meta_memory_pb="; fi )
$( if [ ! -z ${VIASH_META_MEMORY_KIB+x} ]; then echo "${VIASH_META_MEMORY_KIB}" | sed "s#'#'\"'\"'#g;s#.*#meta_memory_kib='&'#" ; else echo "# meta_memory_kib="; fi )
$( if [ ! -z ${VIASH_META_MEMORY_MIB+x} ]; then echo "${VIASH_META_MEMORY_MIB}" | sed "s#'#'\"'\"'#g;s#.*#meta_memory_mib='&'#" ; else echo "# meta_memory_mib="; fi )
$( if [ ! -z ${VIASH_META_MEMORY_GIB+x} ]; then echo "${VIASH_META_MEMORY_GIB}" | sed "s#'#'\"'\"'#g;s#.*#meta_memory_gib='&'#" ; else echo "# meta_memory_gib="; fi )
$( if [ ! -z ${VIASH_META_MEMORY_TIB+x} ]; then echo "${VIASH_META_MEMORY_TIB}" | sed "s#'#'\"'\"'#g;s#.*#meta_memory_tib='&'#" ; else echo "# meta_memory_tib="; fi )
$( if [ ! -z ${VIASH_META_MEMORY_PIB+x} ]; then echo "${VIASH_META_MEMORY_PIB}" | sed "s#'#'\"'\"'#g;s#.*#meta_memory_pib='&'#" ; else echo "# meta_memory_pib="; fi )
## VIASH END
#!/bin/bash
set -eo pipefail
[[ "\$par_force" == "false" ]] && unset par_force
\$(which bcl-convert) \\
--bcl-input-directory "\$par_bcl_input_directory" \\
--output-directory "\$par_output_directory" \\
\${par_force:+--force} \\
\${par_sample_sheet:+ --sample-sheet "\$par_sample_sheet"} \\
\${par_run_info:+ --run-info "\$par_run_info"} \\
\${par_bcl_only_lane:+ --bcl-only-lane "\$par_bcl_only_lane"} \\
\${par_first_tile_only:+ --first-tile-only "\$par_first_tile_only"} \\
\${par_tiles:+ --tiles "\$par_tiles"} \\
\${par_exclude_tiles:+ --exclude-tiles "\$par_exclude_tiles"} \\
\${par_shared_thread_odirect_output:+ --shared-thread-odirect-output "\$par_shared_thread_odirect_output"} \\
\${par_bcl_num_parallel_tiles:+ --bcl-num-parallel-tiles "\$par_bcl_num_parallel_tiles"} \\
\${par_bcl_num_conversion_threads:+ --bcl-num-conversion-threads "\$par_bcl_num_conversion_threads"} \\
\${par_bcl_num_compression_threads:+ --bcl-num-compression-threads "\$par_bcl_num_compression_threads"} \\
\${par_bcl_num_decompression_threads:+ --bcl-num-decompression-threads "\$par_bcl_num_decompression_threads"} \\
\${par_bcl_only_matched_reads:+ --bcl-only-matched-reads "\$par_bcl_only_matched_reads"} \\
\${par_no_lane_splitting:+ --no-lane-splitting "\$par_no_lane_splitting"} \\
\${par_num_unknown_barcodes_reported:+ --num-unknown-barcodes-reported "\$par_num_unknown_barcodes_reported"} \\
\${par_bcl_validate_sample_sheet_only:+ --bcl-validate-sample-sheet-only "\$par_bcl_validate_sample_sheet_only"} \\
\${par_strict_mode:+ --strict-mode "\$par_strict_mode"} \\
\${par_sample_name_column_enabled:+ --sample-name-column-enabled "\$par_sample_name_column_enabled"} \\
\${par_bcl_sampleproject_subdirectories:+ --bcl-sampleproject-subdirectories "\$par_bcl_sampleproject_subdirectories"} \\
\${par_fastq_gzip_compression_level:+ --fastq-gzip-compression-level "\$par_fastq_gzip_compression_level"}
if [ ! -z "\$par_reports" ]; then
echo "Moving reports to their own location"
mv "\${par_output_directory}/Reports" "\$par_reports"
else
echo "Leaving reports alone"
fi
if [ ! -z "\$par_logs" ]; then
echo "Moving logs to their own location"
mv "\${par_output_directory}/Logs" "\$par_logs"
else
echo "Leaving logs alone"
fi
VIASHMAIN
bash "\$tempscript" &
wait "\$!"
VIASHEOF
if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then
# strip viash automount from file paths
if [ ! -z "$VIASH_PAR_BCL_INPUT_DIRECTORY" ]; then
VIASH_PAR_BCL_INPUT_DIRECTORY=$(ViashDockerStripAutomount "$VIASH_PAR_BCL_INPUT_DIRECTORY")
fi
if [ ! -z "$VIASH_PAR_SAMPLE_SHEET" ]; then
VIASH_PAR_SAMPLE_SHEET=$(ViashDockerStripAutomount "$VIASH_PAR_SAMPLE_SHEET")
fi
if [ ! -z "$VIASH_PAR_RUN_INFO" ]; then
VIASH_PAR_RUN_INFO=$(ViashDockerStripAutomount "$VIASH_PAR_RUN_INFO")
fi
if [ ! -z "$VIASH_PAR_OUTPUT_DIRECTORY" ]; then
VIASH_PAR_OUTPUT_DIRECTORY=$(ViashDockerStripAutomount "$VIASH_PAR_OUTPUT_DIRECTORY")
fi
if [ ! -z "$VIASH_PAR_REPORTS" ]; then
VIASH_PAR_REPORTS=$(ViashDockerStripAutomount "$VIASH_PAR_REPORTS")
fi
if [ ! -z "$VIASH_PAR_LOGS" ]; then
VIASH_PAR_LOGS=$(ViashDockerStripAutomount "$VIASH_PAR_LOGS")
fi
if [ ! -z "$VIASH_META_RESOURCES_DIR" ]; then
VIASH_META_RESOURCES_DIR=$(ViashDockerStripAutomount "$VIASH_META_RESOURCES_DIR")
fi
if [ ! -z "$VIASH_META_EXECUTABLE" ]; then
VIASH_META_EXECUTABLE=$(ViashDockerStripAutomount "$VIASH_META_EXECUTABLE")
fi
if [ ! -z "$VIASH_META_CONFIG" ]; then
VIASH_META_CONFIG=$(ViashDockerStripAutomount "$VIASH_META_CONFIG")
fi
if [ ! -z "$VIASH_META_TEMP_DIR" ]; then
VIASH_META_TEMP_DIR=$(ViashDockerStripAutomount "$VIASH_META_TEMP_DIR")
fi
fi
# check whether required files exist
if [ ! -z "$VIASH_PAR_OUTPUT_DIRECTORY" ] && [ ! -e "$VIASH_PAR_OUTPUT_DIRECTORY" ]; then
ViashError "Output file '$VIASH_PAR_OUTPUT_DIRECTORY' does not exist."
exit 1
fi
if [ ! -z "$VIASH_PAR_REPORTS" ] && [ ! -e "$VIASH_PAR_REPORTS" ]; then
ViashError "Output file '$VIASH_PAR_REPORTS' does not exist."
exit 1
fi
if [ ! -z "$VIASH_PAR_LOGS" ] && [ ! -e "$VIASH_PAR_LOGS" ]; then
ViashError "Output file '$VIASH_PAR_LOGS' does not exist."
exit 1
fi
exit 0
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