CI
5af6804276
Build pipeline: viash-hub.biobox.add-trimgalore-8w9nv
Source commit: 90735159b7
Source message: separate input fastqc file arguments from other arguments
1986 lines
84 KiB
Bash
Executable File
1986 lines
84 KiB
Bash
Executable File
#!/usr/bin/env bash
|
|
|
|
# multiqc add_trimgalore
|
|
#
|
|
# This wrapper script is auto-generated by viash 0.9.0-RC7 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:
|
|
# * Dorien Roosen (author, maintainer)
|
|
|
|
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 $VIASH_META_RESOURCES_DIR`
|
|
|
|
# define meta fields
|
|
VIASH_META_NAME="multiqc"
|
|
VIASH_META_FUNCTIONALITY_NAME="multiqc"
|
|
VIASH_META_EXECUTABLE="$VIASH_META_RESOURCES_DIR/$VIASH_META_NAME"
|
|
VIASH_META_CONFIG="$VIASH_META_RESOURCES_DIR/.config.vsh.yaml"
|
|
VIASH_META_TEMP_DIR="$VIASH_TEMP"
|
|
|
|
|
|
# ViashHelp: Display helpful explanation about this executable
|
|
function ViashHelp {
|
|
echo "multiqc add_trimgalore"
|
|
echo ""
|
|
echo "MultiQC aggregates results from bioinformatics analyses across many samples into"
|
|
echo "a single report."
|
|
echo "It searches a given directory for analysis logs and compiles a HTML report. It's"
|
|
echo "a general use tool, perfect for summarising the output from numerous"
|
|
echo "bioinformatics tools."
|
|
echo ""
|
|
echo "Input:"
|
|
echo " --input"
|
|
echo " type: file, required parameter, multiple values allowed, file must exist"
|
|
echo " example: data/results"
|
|
echo " File paths to be searched for analysis results to be included in the"
|
|
echo " report."
|
|
echo ""
|
|
echo "Ouput:"
|
|
echo " --output_report"
|
|
echo " type: file, output"
|
|
echo " example: multiqc_report.html"
|
|
echo " Filepath of the generated report."
|
|
echo ""
|
|
echo " --output_data"
|
|
echo " type: file, output"
|
|
echo " example: multiqc_data"
|
|
echo " Output directory for parsed data files. If not provided, parsed data"
|
|
echo " will not be published."
|
|
echo ""
|
|
echo " --output_plots"
|
|
echo " type: file, output"
|
|
echo " example: multiqc_plots"
|
|
echo " Output directory for generated plots. If not provided, plots will not be"
|
|
echo " published."
|
|
echo ""
|
|
echo "Modules and analyses to run:"
|
|
echo " --include_modules"
|
|
echo " type: string, multiple values allowed"
|
|
echo " example: fastqc;cutadapt"
|
|
echo " Use only these module"
|
|
echo ""
|
|
echo " --exclude_modules"
|
|
echo " type: string, multiple values allowed"
|
|
echo " example: fastqc;cutadapt"
|
|
echo " Do not use only these modules"
|
|
echo ""
|
|
echo " --ignore_analysis"
|
|
echo " type: string, multiple values allowed"
|
|
echo " example: run_one/*;run_two/*"
|
|
echo ""
|
|
echo " --ignore_samples"
|
|
echo " type: string, multiple values allowed"
|
|
echo " example: sample_1*;sample_3*"
|
|
echo ""
|
|
echo " --ignore_symlinks"
|
|
echo " type: boolean_true"
|
|
echo " Ignore symlinked directories and files"
|
|
echo ""
|
|
echo "Sample name handling:"
|
|
echo " --dirs"
|
|
echo " type: boolean_true"
|
|
echo " Prepend directory to sample names to avoid clashing filenames"
|
|
echo ""
|
|
echo " --dirs_depth"
|
|
echo " type: integer"
|
|
echo " Prepend n directories to sample names. Negative number to take from"
|
|
echo " start of path."
|
|
echo ""
|
|
echo " --full_names"
|
|
echo " type: boolean_true"
|
|
echo " Do not clean the sample names (leave as full file name)"
|
|
echo ""
|
|
echo " --fn_as_s_name"
|
|
echo " type: boolean_true"
|
|
echo " Use the log filename as the sample name"
|
|
echo ""
|
|
echo " --replace_names"
|
|
echo " type: file, file must exist"
|
|
echo " example: replace_names.tsv"
|
|
echo " TSV file to rename sample names during report generation"
|
|
echo ""
|
|
echo "Report Customisation:"
|
|
echo " --title"
|
|
echo " type: string"
|
|
echo " Report title. Printed as page header, used for filename if not otherwise"
|
|
echo " specified."
|
|
echo ""
|
|
echo " --comment"
|
|
echo " type: string"
|
|
echo " Custom comment, will be printed at the top of the report."
|
|
echo ""
|
|
echo " --template"
|
|
echo " type: string"
|
|
echo " choices: [ default, gathered, geo, highcharts, sections, simple ]"
|
|
echo " Report template to use."
|
|
echo ""
|
|
echo " --sample_names"
|
|
echo " type: file, file must exist"
|
|
echo " example: sample_names.tsv"
|
|
echo " TSV file containing alternative sample names for renaming buttons in the"
|
|
echo " report."
|
|
echo ""
|
|
echo " --sample_filters"
|
|
echo " type: file, file must exist"
|
|
echo " example: sample_filters.tsv"
|
|
echo " TSV file containing show/hide patterns for the report"
|
|
echo ""
|
|
echo " --custom_css_file"
|
|
echo " type: file, file must exist"
|
|
echo " example: custom_style_sheet.css"
|
|
echo " Custom CSS file to add to the final report"
|
|
echo ""
|
|
echo " --profile_runtime"
|
|
echo " type: boolean_true"
|
|
echo " Add analysis of how long MultiQC takes to run to the report"
|
|
echo ""
|
|
echo "MultiQC behaviour:"
|
|
echo " --verbose"
|
|
echo " type: boolean_true"
|
|
echo " Increase output verbosity."
|
|
echo ""
|
|
echo " --quiet"
|
|
echo " type: boolean_true"
|
|
echo " Only show log warnings"
|
|
echo ""
|
|
echo " --strict"
|
|
echo " type: boolean_true"
|
|
echo " Don't catch exceptions, run additional code checks to help development."
|
|
echo ""
|
|
echo " --development"
|
|
echo " type: boolean_true"
|
|
echo " Development mode. Do not compress and minimise JS, export uncompressed"
|
|
echo " plot data."
|
|
echo ""
|
|
echo " --require_logs"
|
|
echo " type: boolean_true"
|
|
echo " Require all explicitly requested modules to have log files. If not,"
|
|
echo " MultiQC will exit with an error."
|
|
echo ""
|
|
echo " --no_megaqc_upload"
|
|
echo " type: boolean_true"
|
|
echo " Don't upload generated report to MegaQC, even if MegaQC options are"
|
|
echo " found."
|
|
echo ""
|
|
echo " --no_ansi"
|
|
echo " type: boolean_true"
|
|
echo " Disable coloured log output."
|
|
echo ""
|
|
echo " --cl_config"
|
|
echo " type: string"
|
|
echo " example: qualimap_config: { general_stats_coverage: [20,40,200] }"
|
|
echo " YAML formatted string that allows to customize MultiQC behaviour like"
|
|
echo " input file detection."
|
|
echo ""
|
|
echo "Output format:"
|
|
echo " --flat"
|
|
echo " type: boolean_true"
|
|
echo " Use only flat plots (static images)."
|
|
echo ""
|
|
echo " --interactive"
|
|
echo " type: boolean_true"
|
|
echo " Use only interactive plots (in-browser Javascript)."
|
|
echo ""
|
|
echo " --data_dir"
|
|
echo " type: boolean_true"
|
|
echo " Force the parsed data directory to be created."
|
|
echo ""
|
|
echo " --no_data_dir"
|
|
echo " type: boolean_true"
|
|
echo " Prevent the parsed data directory from being created."
|
|
echo ""
|
|
echo " --zip_data_dir"
|
|
echo " type: boolean_true"
|
|
echo " Compress the data directory."
|
|
echo ""
|
|
echo " --data_format"
|
|
echo " type: string"
|
|
echo " choices: [ tsv, csv, json, yaml ]"
|
|
echo " Output parsed data in a different format than the default 'txt'."
|
|
echo ""
|
|
echo " --pdf"
|
|
echo " type: boolean_true"
|
|
echo " Creates PDF report with the 'simple' template. Requires Pandoc to be"
|
|
echo " installed."
|
|
}
|
|
|
|
# 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 quay.io/biocontainers/multiqc:1.21--pyhdfd78af_0
|
|
ENTRYPOINT []
|
|
RUN multiqc --version | sed 's/multiqc, version\s\(.*\)/multiqc: "\1"/' > /var/software_versions.txt
|
|
|
|
LABEL org.opencontainers.image.authors="Dorien Roosen"
|
|
LABEL org.opencontainers.image.description="Companion container for running component multiqc"
|
|
LABEL org.opencontainers.image.created="2024-09-19T08:36:08Z"
|
|
LABEL org.opencontainers.image.source="https://github.com/viash-hub/biobox"
|
|
LABEL org.opencontainers.image.revision="90735159b7bafa4aa8643eb132534d078ea299cf"
|
|
LABEL org.opencontainers.image.version="add_trimgalore"
|
|
|
|
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)
|
|
|
|
# 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 "$1")"
|
|
shift 1
|
|
;;
|
|
--version)
|
|
echo "multiqc add_trimgalore"
|
|
exit
|
|
;;
|
|
--input)
|
|
if [ -z "$VIASH_PAR_INPUT" ]; then
|
|
VIASH_PAR_INPUT="$2"
|
|
else
|
|
VIASH_PAR_INPUT="$VIASH_PAR_INPUT;""$2"
|
|
fi
|
|
[ $# -lt 2 ] && ViashError Not enough arguments passed to --input. Use "--help" to get more information on the parameters. && exit 1
|
|
shift 2
|
|
;;
|
|
--input=*)
|
|
if [ -z "$VIASH_PAR_INPUT" ]; then
|
|
VIASH_PAR_INPUT=$(ViashRemoveFlags "$1")
|
|
else
|
|
VIASH_PAR_INPUT="$VIASH_PAR_INPUT;"$(ViashRemoveFlags "$1")
|
|
fi
|
|
shift 1
|
|
;;
|
|
--output_report)
|
|
[ -n "$VIASH_PAR_OUTPUT_REPORT" ] && ViashError Bad arguments for option \'--output_report\': \'$VIASH_PAR_OUTPUT_REPORT\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_OUTPUT_REPORT="$2"
|
|
[ $# -lt 2 ] && ViashError Not enough arguments passed to --output_report. Use "--help" to get more information on the parameters. && exit 1
|
|
shift 2
|
|
;;
|
|
--output_report=*)
|
|
[ -n "$VIASH_PAR_OUTPUT_REPORT" ] && ViashError Bad arguments for option \'--output_report=*\': \'$VIASH_PAR_OUTPUT_REPORT\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_OUTPUT_REPORT=$(ViashRemoveFlags "$1")
|
|
shift 1
|
|
;;
|
|
--output_data)
|
|
[ -n "$VIASH_PAR_OUTPUT_DATA" ] && ViashError Bad arguments for option \'--output_data\': \'$VIASH_PAR_OUTPUT_DATA\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_OUTPUT_DATA="$2"
|
|
[ $# -lt 2 ] && ViashError Not enough arguments passed to --output_data. Use "--help" to get more information on the parameters. && exit 1
|
|
shift 2
|
|
;;
|
|
--output_data=*)
|
|
[ -n "$VIASH_PAR_OUTPUT_DATA" ] && ViashError Bad arguments for option \'--output_data=*\': \'$VIASH_PAR_OUTPUT_DATA\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_OUTPUT_DATA=$(ViashRemoveFlags "$1")
|
|
shift 1
|
|
;;
|
|
--output_plots)
|
|
[ -n "$VIASH_PAR_OUTPUT_PLOTS" ] && ViashError Bad arguments for option \'--output_plots\': \'$VIASH_PAR_OUTPUT_PLOTS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_OUTPUT_PLOTS="$2"
|
|
[ $# -lt 2 ] && ViashError Not enough arguments passed to --output_plots. Use "--help" to get more information on the parameters. && exit 1
|
|
shift 2
|
|
;;
|
|
--output_plots=*)
|
|
[ -n "$VIASH_PAR_OUTPUT_PLOTS" ] && ViashError Bad arguments for option \'--output_plots=*\': \'$VIASH_PAR_OUTPUT_PLOTS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_OUTPUT_PLOTS=$(ViashRemoveFlags "$1")
|
|
shift 1
|
|
;;
|
|
--include_modules)
|
|
if [ -z "$VIASH_PAR_INCLUDE_MODULES" ]; then
|
|
VIASH_PAR_INCLUDE_MODULES="$2"
|
|
else
|
|
VIASH_PAR_INCLUDE_MODULES="$VIASH_PAR_INCLUDE_MODULES;""$2"
|
|
fi
|
|
[ $# -lt 2 ] && ViashError Not enough arguments passed to --include_modules. Use "--help" to get more information on the parameters. && exit 1
|
|
shift 2
|
|
;;
|
|
--include_modules=*)
|
|
if [ -z "$VIASH_PAR_INCLUDE_MODULES" ]; then
|
|
VIASH_PAR_INCLUDE_MODULES=$(ViashRemoveFlags "$1")
|
|
else
|
|
VIASH_PAR_INCLUDE_MODULES="$VIASH_PAR_INCLUDE_MODULES;"$(ViashRemoveFlags "$1")
|
|
fi
|
|
shift 1
|
|
;;
|
|
--exclude_modules)
|
|
if [ -z "$VIASH_PAR_EXCLUDE_MODULES" ]; then
|
|
VIASH_PAR_EXCLUDE_MODULES="$2"
|
|
else
|
|
VIASH_PAR_EXCLUDE_MODULES="$VIASH_PAR_EXCLUDE_MODULES;""$2"
|
|
fi
|
|
[ $# -lt 2 ] && ViashError Not enough arguments passed to --exclude_modules. Use "--help" to get more information on the parameters. && exit 1
|
|
shift 2
|
|
;;
|
|
--exclude_modules=*)
|
|
if [ -z "$VIASH_PAR_EXCLUDE_MODULES" ]; then
|
|
VIASH_PAR_EXCLUDE_MODULES=$(ViashRemoveFlags "$1")
|
|
else
|
|
VIASH_PAR_EXCLUDE_MODULES="$VIASH_PAR_EXCLUDE_MODULES;"$(ViashRemoveFlags "$1")
|
|
fi
|
|
shift 1
|
|
;;
|
|
--ignore_analysis)
|
|
if [ -z "$VIASH_PAR_IGNORE_ANALYSIS" ]; then
|
|
VIASH_PAR_IGNORE_ANALYSIS="$2"
|
|
else
|
|
VIASH_PAR_IGNORE_ANALYSIS="$VIASH_PAR_IGNORE_ANALYSIS;""$2"
|
|
fi
|
|
[ $# -lt 2 ] && ViashError Not enough arguments passed to --ignore_analysis. Use "--help" to get more information on the parameters. && exit 1
|
|
shift 2
|
|
;;
|
|
--ignore_analysis=*)
|
|
if [ -z "$VIASH_PAR_IGNORE_ANALYSIS" ]; then
|
|
VIASH_PAR_IGNORE_ANALYSIS=$(ViashRemoveFlags "$1")
|
|
else
|
|
VIASH_PAR_IGNORE_ANALYSIS="$VIASH_PAR_IGNORE_ANALYSIS;"$(ViashRemoveFlags "$1")
|
|
fi
|
|
shift 1
|
|
;;
|
|
--ignore_samples)
|
|
if [ -z "$VIASH_PAR_IGNORE_SAMPLES" ]; then
|
|
VIASH_PAR_IGNORE_SAMPLES="$2"
|
|
else
|
|
VIASH_PAR_IGNORE_SAMPLES="$VIASH_PAR_IGNORE_SAMPLES;""$2"
|
|
fi
|
|
[ $# -lt 2 ] && ViashError Not enough arguments passed to --ignore_samples. Use "--help" to get more information on the parameters. && exit 1
|
|
shift 2
|
|
;;
|
|
--ignore_samples=*)
|
|
if [ -z "$VIASH_PAR_IGNORE_SAMPLES" ]; then
|
|
VIASH_PAR_IGNORE_SAMPLES=$(ViashRemoveFlags "$1")
|
|
else
|
|
VIASH_PAR_IGNORE_SAMPLES="$VIASH_PAR_IGNORE_SAMPLES;"$(ViashRemoveFlags "$1")
|
|
fi
|
|
shift 1
|
|
;;
|
|
--ignore_symlinks)
|
|
[ -n "$VIASH_PAR_IGNORE_SYMLINKS" ] && ViashError Bad arguments for option \'--ignore_symlinks\': \'$VIASH_PAR_IGNORE_SYMLINKS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_IGNORE_SYMLINKS=true
|
|
shift 1
|
|
;;
|
|
--dirs)
|
|
[ -n "$VIASH_PAR_DIRS" ] && ViashError Bad arguments for option \'--dirs\': \'$VIASH_PAR_DIRS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_DIRS=true
|
|
shift 1
|
|
;;
|
|
--dirs_depth)
|
|
[ -n "$VIASH_PAR_DIRS_DEPTH" ] && ViashError Bad arguments for option \'--dirs_depth\': \'$VIASH_PAR_DIRS_DEPTH\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_DIRS_DEPTH="$2"
|
|
[ $# -lt 2 ] && ViashError Not enough arguments passed to --dirs_depth. Use "--help" to get more information on the parameters. && exit 1
|
|
shift 2
|
|
;;
|
|
--dirs_depth=*)
|
|
[ -n "$VIASH_PAR_DIRS_DEPTH" ] && ViashError Bad arguments for option \'--dirs_depth=*\': \'$VIASH_PAR_DIRS_DEPTH\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_DIRS_DEPTH=$(ViashRemoveFlags "$1")
|
|
shift 1
|
|
;;
|
|
--full_names)
|
|
[ -n "$VIASH_PAR_FULL_NAMES" ] && ViashError Bad arguments for option \'--full_names\': \'$VIASH_PAR_FULL_NAMES\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_FULL_NAMES=true
|
|
shift 1
|
|
;;
|
|
--fn_as_s_name)
|
|
[ -n "$VIASH_PAR_FN_AS_S_NAME" ] && ViashError Bad arguments for option \'--fn_as_s_name\': \'$VIASH_PAR_FN_AS_S_NAME\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_FN_AS_S_NAME=true
|
|
shift 1
|
|
;;
|
|
--replace_names)
|
|
[ -n "$VIASH_PAR_REPLACE_NAMES" ] && ViashError Bad arguments for option \'--replace_names\': \'$VIASH_PAR_REPLACE_NAMES\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_REPLACE_NAMES="$2"
|
|
[ $# -lt 2 ] && ViashError Not enough arguments passed to --replace_names. Use "--help" to get more information on the parameters. && exit 1
|
|
shift 2
|
|
;;
|
|
--replace_names=*)
|
|
[ -n "$VIASH_PAR_REPLACE_NAMES" ] && ViashError Bad arguments for option \'--replace_names=*\': \'$VIASH_PAR_REPLACE_NAMES\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_REPLACE_NAMES=$(ViashRemoveFlags "$1")
|
|
shift 1
|
|
;;
|
|
--title)
|
|
[ -n "$VIASH_PAR_TITLE" ] && ViashError Bad arguments for option \'--title\': \'$VIASH_PAR_TITLE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_TITLE="$2"
|
|
[ $# -lt 2 ] && ViashError Not enough arguments passed to --title. Use "--help" to get more information on the parameters. && exit 1
|
|
shift 2
|
|
;;
|
|
--title=*)
|
|
[ -n "$VIASH_PAR_TITLE" ] && ViashError Bad arguments for option \'--title=*\': \'$VIASH_PAR_TITLE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_TITLE=$(ViashRemoveFlags "$1")
|
|
shift 1
|
|
;;
|
|
--comment)
|
|
[ -n "$VIASH_PAR_COMMENT" ] && ViashError Bad arguments for option \'--comment\': \'$VIASH_PAR_COMMENT\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_COMMENT="$2"
|
|
[ $# -lt 2 ] && ViashError Not enough arguments passed to --comment. Use "--help" to get more information on the parameters. && exit 1
|
|
shift 2
|
|
;;
|
|
--comment=*)
|
|
[ -n "$VIASH_PAR_COMMENT" ] && ViashError Bad arguments for option \'--comment=*\': \'$VIASH_PAR_COMMENT\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_COMMENT=$(ViashRemoveFlags "$1")
|
|
shift 1
|
|
;;
|
|
--template)
|
|
[ -n "$VIASH_PAR_TEMPLATE" ] && ViashError Bad arguments for option \'--template\': \'$VIASH_PAR_TEMPLATE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_TEMPLATE="$2"
|
|
[ $# -lt 2 ] && ViashError Not enough arguments passed to --template. Use "--help" to get more information on the parameters. && exit 1
|
|
shift 2
|
|
;;
|
|
--template=*)
|
|
[ -n "$VIASH_PAR_TEMPLATE" ] && ViashError Bad arguments for option \'--template=*\': \'$VIASH_PAR_TEMPLATE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_TEMPLATE=$(ViashRemoveFlags "$1")
|
|
shift 1
|
|
;;
|
|
--sample_names)
|
|
[ -n "$VIASH_PAR_SAMPLE_NAMES" ] && ViashError Bad arguments for option \'--sample_names\': \'$VIASH_PAR_SAMPLE_NAMES\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_SAMPLE_NAMES="$2"
|
|
[ $# -lt 2 ] && ViashError Not enough arguments passed to --sample_names. Use "--help" to get more information on the parameters. && exit 1
|
|
shift 2
|
|
;;
|
|
--sample_names=*)
|
|
[ -n "$VIASH_PAR_SAMPLE_NAMES" ] && ViashError Bad arguments for option \'--sample_names=*\': \'$VIASH_PAR_SAMPLE_NAMES\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_SAMPLE_NAMES=$(ViashRemoveFlags "$1")
|
|
shift 1
|
|
;;
|
|
--sample_filters)
|
|
[ -n "$VIASH_PAR_SAMPLE_FILTERS" ] && ViashError Bad arguments for option \'--sample_filters\': \'$VIASH_PAR_SAMPLE_FILTERS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_SAMPLE_FILTERS="$2"
|
|
[ $# -lt 2 ] && ViashError Not enough arguments passed to --sample_filters. Use "--help" to get more information on the parameters. && exit 1
|
|
shift 2
|
|
;;
|
|
--sample_filters=*)
|
|
[ -n "$VIASH_PAR_SAMPLE_FILTERS" ] && ViashError Bad arguments for option \'--sample_filters=*\': \'$VIASH_PAR_SAMPLE_FILTERS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_SAMPLE_FILTERS=$(ViashRemoveFlags "$1")
|
|
shift 1
|
|
;;
|
|
--custom_css_file)
|
|
[ -n "$VIASH_PAR_CUSTOM_CSS_FILE" ] && ViashError Bad arguments for option \'--custom_css_file\': \'$VIASH_PAR_CUSTOM_CSS_FILE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_CUSTOM_CSS_FILE="$2"
|
|
[ $# -lt 2 ] && ViashError Not enough arguments passed to --custom_css_file. Use "--help" to get more information on the parameters. && exit 1
|
|
shift 2
|
|
;;
|
|
--custom_css_file=*)
|
|
[ -n "$VIASH_PAR_CUSTOM_CSS_FILE" ] && ViashError Bad arguments for option \'--custom_css_file=*\': \'$VIASH_PAR_CUSTOM_CSS_FILE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_CUSTOM_CSS_FILE=$(ViashRemoveFlags "$1")
|
|
shift 1
|
|
;;
|
|
--profile_runtime)
|
|
[ -n "$VIASH_PAR_PROFILE_RUNTIME" ] && ViashError Bad arguments for option \'--profile_runtime\': \'$VIASH_PAR_PROFILE_RUNTIME\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_PROFILE_RUNTIME=true
|
|
shift 1
|
|
;;
|
|
--verbose)
|
|
[ -n "$VIASH_PAR_VERBOSE" ] && ViashError Bad arguments for option \'--verbose\': \'$VIASH_PAR_VERBOSE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_VERBOSE=true
|
|
shift 1
|
|
;;
|
|
--quiet)
|
|
[ -n "$VIASH_PAR_QUIET" ] && ViashError Bad arguments for option \'--quiet\': \'$VIASH_PAR_QUIET\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_QUIET=true
|
|
shift 1
|
|
;;
|
|
--strict)
|
|
[ -n "$VIASH_PAR_STRICT" ] && ViashError Bad arguments for option \'--strict\': \'$VIASH_PAR_STRICT\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_STRICT=true
|
|
shift 1
|
|
;;
|
|
--development)
|
|
[ -n "$VIASH_PAR_DEVELOPMENT" ] && ViashError Bad arguments for option \'--development\': \'$VIASH_PAR_DEVELOPMENT\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_DEVELOPMENT=true
|
|
shift 1
|
|
;;
|
|
--require_logs)
|
|
[ -n "$VIASH_PAR_REQUIRE_LOGS" ] && ViashError Bad arguments for option \'--require_logs\': \'$VIASH_PAR_REQUIRE_LOGS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_REQUIRE_LOGS=true
|
|
shift 1
|
|
;;
|
|
--no_megaqc_upload)
|
|
[ -n "$VIASH_PAR_NO_MEGAQC_UPLOAD" ] && ViashError Bad arguments for option \'--no_megaqc_upload\': \'$VIASH_PAR_NO_MEGAQC_UPLOAD\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_NO_MEGAQC_UPLOAD=true
|
|
shift 1
|
|
;;
|
|
--no_ansi)
|
|
[ -n "$VIASH_PAR_NO_ANSI" ] && ViashError Bad arguments for option \'--no_ansi\': \'$VIASH_PAR_NO_ANSI\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_NO_ANSI=true
|
|
shift 1
|
|
;;
|
|
--cl_config)
|
|
[ -n "$VIASH_PAR_CL_CONFIG" ] && ViashError Bad arguments for option \'--cl_config\': \'$VIASH_PAR_CL_CONFIG\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_CL_CONFIG="$2"
|
|
[ $# -lt 2 ] && ViashError Not enough arguments passed to --cl_config. Use "--help" to get more information on the parameters. && exit 1
|
|
shift 2
|
|
;;
|
|
--cl_config=*)
|
|
[ -n "$VIASH_PAR_CL_CONFIG" ] && ViashError Bad arguments for option \'--cl_config=*\': \'$VIASH_PAR_CL_CONFIG\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_CL_CONFIG=$(ViashRemoveFlags "$1")
|
|
shift 1
|
|
;;
|
|
--flat)
|
|
[ -n "$VIASH_PAR_FLAT" ] && ViashError Bad arguments for option \'--flat\': \'$VIASH_PAR_FLAT\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_FLAT=true
|
|
shift 1
|
|
;;
|
|
--interactive)
|
|
[ -n "$VIASH_PAR_INTERACTIVE" ] && ViashError Bad arguments for option \'--interactive\': \'$VIASH_PAR_INTERACTIVE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_INTERACTIVE=true
|
|
shift 1
|
|
;;
|
|
--data_dir)
|
|
[ -n "$VIASH_PAR_DATA_DIR" ] && ViashError Bad arguments for option \'--data_dir\': \'$VIASH_PAR_DATA_DIR\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_DATA_DIR=true
|
|
shift 1
|
|
;;
|
|
--no_data_dir)
|
|
[ -n "$VIASH_PAR_NO_DATA_DIR" ] && ViashError Bad arguments for option \'--no_data_dir\': \'$VIASH_PAR_NO_DATA_DIR\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_NO_DATA_DIR=true
|
|
shift 1
|
|
;;
|
|
--zip_data_dir)
|
|
[ -n "$VIASH_PAR_ZIP_DATA_DIR" ] && ViashError Bad arguments for option \'--zip_data_dir\': \'$VIASH_PAR_ZIP_DATA_DIR\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_ZIP_DATA_DIR=true
|
|
shift 1
|
|
;;
|
|
--data_format)
|
|
[ -n "$VIASH_PAR_DATA_FORMAT" ] && ViashError Bad arguments for option \'--data_format\': \'$VIASH_PAR_DATA_FORMAT\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_DATA_FORMAT="$2"
|
|
[ $# -lt 2 ] && ViashError Not enough arguments passed to --data_format. Use "--help" to get more information on the parameters. && exit 1
|
|
shift 2
|
|
;;
|
|
--data_format=*)
|
|
[ -n "$VIASH_PAR_DATA_FORMAT" ] && ViashError Bad arguments for option \'--data_format=*\': \'$VIASH_PAR_DATA_FORMAT\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_DATA_FORMAT=$(ViashRemoveFlags "$1")
|
|
shift 1
|
|
;;
|
|
--pdf)
|
|
[ -n "$VIASH_PAR_PDF" ] && ViashError Bad arguments for option \'--pdf\': \'$VIASH_PAR_PDF\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_PDF=true
|
|
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/multiqc:add_trimgalore'
|
|
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_INPUT+x} ]; then
|
|
ViashError '--input' 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
|
|
|
|
# filling in defaults
|
|
if [ -z ${VIASH_PAR_IGNORE_SYMLINKS+x} ]; then
|
|
VIASH_PAR_IGNORE_SYMLINKS="false"
|
|
fi
|
|
if [ -z ${VIASH_PAR_DIRS+x} ]; then
|
|
VIASH_PAR_DIRS="false"
|
|
fi
|
|
if [ -z ${VIASH_PAR_FULL_NAMES+x} ]; then
|
|
VIASH_PAR_FULL_NAMES="false"
|
|
fi
|
|
if [ -z ${VIASH_PAR_FN_AS_S_NAME+x} ]; then
|
|
VIASH_PAR_FN_AS_S_NAME="false"
|
|
fi
|
|
if [ -z ${VIASH_PAR_PROFILE_RUNTIME+x} ]; then
|
|
VIASH_PAR_PROFILE_RUNTIME="false"
|
|
fi
|
|
if [ -z ${VIASH_PAR_VERBOSE+x} ]; then
|
|
VIASH_PAR_VERBOSE="false"
|
|
fi
|
|
if [ -z ${VIASH_PAR_QUIET+x} ]; then
|
|
VIASH_PAR_QUIET="false"
|
|
fi
|
|
if [ -z ${VIASH_PAR_STRICT+x} ]; then
|
|
VIASH_PAR_STRICT="false"
|
|
fi
|
|
if [ -z ${VIASH_PAR_DEVELOPMENT+x} ]; then
|
|
VIASH_PAR_DEVELOPMENT="false"
|
|
fi
|
|
if [ -z ${VIASH_PAR_REQUIRE_LOGS+x} ]; then
|
|
VIASH_PAR_REQUIRE_LOGS="false"
|
|
fi
|
|
if [ -z ${VIASH_PAR_NO_MEGAQC_UPLOAD+x} ]; then
|
|
VIASH_PAR_NO_MEGAQC_UPLOAD="false"
|
|
fi
|
|
if [ -z ${VIASH_PAR_NO_ANSI+x} ]; then
|
|
VIASH_PAR_NO_ANSI="false"
|
|
fi
|
|
if [ -z ${VIASH_PAR_FLAT+x} ]; then
|
|
VIASH_PAR_FLAT="false"
|
|
fi
|
|
if [ -z ${VIASH_PAR_INTERACTIVE+x} ]; then
|
|
VIASH_PAR_INTERACTIVE="false"
|
|
fi
|
|
if [ -z ${VIASH_PAR_DATA_DIR+x} ]; then
|
|
VIASH_PAR_DATA_DIR="false"
|
|
fi
|
|
if [ -z ${VIASH_PAR_NO_DATA_DIR+x} ]; then
|
|
VIASH_PAR_NO_DATA_DIR="false"
|
|
fi
|
|
if [ -z ${VIASH_PAR_ZIP_DATA_DIR+x} ]; then
|
|
VIASH_PAR_ZIP_DATA_DIR="false"
|
|
fi
|
|
if [ -z ${VIASH_PAR_PDF+x} ]; then
|
|
VIASH_PAR_PDF="false"
|
|
fi
|
|
|
|
# check whether required files exist
|
|
if [ ! -z "$VIASH_PAR_INPUT" ]; then
|
|
IFS=';'
|
|
set -f
|
|
for file in $VIASH_PAR_INPUT; do
|
|
unset IFS
|
|
if [ ! -e "$file" ]; then
|
|
ViashError "Input file '$file' does not exist."
|
|
exit 1
|
|
fi
|
|
done
|
|
set +f
|
|
fi
|
|
if [ ! -z "$VIASH_PAR_REPLACE_NAMES" ] && [ ! -e "$VIASH_PAR_REPLACE_NAMES" ]; then
|
|
ViashError "Input file '$VIASH_PAR_REPLACE_NAMES' does not exist."
|
|
exit 1
|
|
fi
|
|
if [ ! -z "$VIASH_PAR_SAMPLE_NAMES" ] && [ ! -e "$VIASH_PAR_SAMPLE_NAMES" ]; then
|
|
ViashError "Input file '$VIASH_PAR_SAMPLE_NAMES' does not exist."
|
|
exit 1
|
|
fi
|
|
if [ ! -z "$VIASH_PAR_SAMPLE_FILTERS" ] && [ ! -e "$VIASH_PAR_SAMPLE_FILTERS" ]; then
|
|
ViashError "Input file '$VIASH_PAR_SAMPLE_FILTERS' does not exist."
|
|
exit 1
|
|
fi
|
|
if [ ! -z "$VIASH_PAR_CUSTOM_CSS_FILE" ] && [ ! -e "$VIASH_PAR_CUSTOM_CSS_FILE" ]; then
|
|
ViashError "Input file '$VIASH_PAR_CUSTOM_CSS_FILE' does not exist."
|
|
exit 1
|
|
fi
|
|
|
|
# check whether parameters values are of the right type
|
|
if [[ -n "$VIASH_PAR_IGNORE_SYMLINKS" ]]; then
|
|
if ! [[ "$VIASH_PAR_IGNORE_SYMLINKS" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then
|
|
ViashError '--ignore_symlinks' has to be a boolean_true. Use "--help" to get more information on the parameters.
|
|
exit 1
|
|
fi
|
|
fi
|
|
if [[ -n "$VIASH_PAR_DIRS" ]]; then
|
|
if ! [[ "$VIASH_PAR_DIRS" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then
|
|
ViashError '--dirs' has to be a boolean_true. Use "--help" to get more information on the parameters.
|
|
exit 1
|
|
fi
|
|
fi
|
|
if [[ -n "$VIASH_PAR_DIRS_DEPTH" ]]; then
|
|
if ! [[ "$VIASH_PAR_DIRS_DEPTH" =~ ^[-+]?[0-9]+$ ]]; then
|
|
ViashError '--dirs_depth' has to be an integer. Use "--help" to get more information on the parameters.
|
|
exit 1
|
|
fi
|
|
fi
|
|
if [[ -n "$VIASH_PAR_FULL_NAMES" ]]; then
|
|
if ! [[ "$VIASH_PAR_FULL_NAMES" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then
|
|
ViashError '--full_names' has to be a boolean_true. Use "--help" to get more information on the parameters.
|
|
exit 1
|
|
fi
|
|
fi
|
|
if [[ -n "$VIASH_PAR_FN_AS_S_NAME" ]]; then
|
|
if ! [[ "$VIASH_PAR_FN_AS_S_NAME" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then
|
|
ViashError '--fn_as_s_name' has to be a boolean_true. Use "--help" to get more information on the parameters.
|
|
exit 1
|
|
fi
|
|
fi
|
|
if [[ -n "$VIASH_PAR_PROFILE_RUNTIME" ]]; then
|
|
if ! [[ "$VIASH_PAR_PROFILE_RUNTIME" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then
|
|
ViashError '--profile_runtime' has to be a boolean_true. Use "--help" to get more information on the parameters.
|
|
exit 1
|
|
fi
|
|
fi
|
|
if [[ -n "$VIASH_PAR_VERBOSE" ]]; then
|
|
if ! [[ "$VIASH_PAR_VERBOSE" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then
|
|
ViashError '--verbose' has to be a boolean_true. Use "--help" to get more information on the parameters.
|
|
exit 1
|
|
fi
|
|
fi
|
|
if [[ -n "$VIASH_PAR_QUIET" ]]; then
|
|
if ! [[ "$VIASH_PAR_QUIET" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then
|
|
ViashError '--quiet' has to be a boolean_true. Use "--help" to get more information on the parameters.
|
|
exit 1
|
|
fi
|
|
fi
|
|
if [[ -n "$VIASH_PAR_STRICT" ]]; then
|
|
if ! [[ "$VIASH_PAR_STRICT" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then
|
|
ViashError '--strict' has to be a boolean_true. Use "--help" to get more information on the parameters.
|
|
exit 1
|
|
fi
|
|
fi
|
|
if [[ -n "$VIASH_PAR_DEVELOPMENT" ]]; then
|
|
if ! [[ "$VIASH_PAR_DEVELOPMENT" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then
|
|
ViashError '--development' has to be a boolean_true. Use "--help" to get more information on the parameters.
|
|
exit 1
|
|
fi
|
|
fi
|
|
if [[ -n "$VIASH_PAR_REQUIRE_LOGS" ]]; then
|
|
if ! [[ "$VIASH_PAR_REQUIRE_LOGS" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then
|
|
ViashError '--require_logs' has to be a boolean_true. Use "--help" to get more information on the parameters.
|
|
exit 1
|
|
fi
|
|
fi
|
|
if [[ -n "$VIASH_PAR_NO_MEGAQC_UPLOAD" ]]; then
|
|
if ! [[ "$VIASH_PAR_NO_MEGAQC_UPLOAD" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then
|
|
ViashError '--no_megaqc_upload' has to be a boolean_true. Use "--help" to get more information on the parameters.
|
|
exit 1
|
|
fi
|
|
fi
|
|
if [[ -n "$VIASH_PAR_NO_ANSI" ]]; then
|
|
if ! [[ "$VIASH_PAR_NO_ANSI" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then
|
|
ViashError '--no_ansi' has to be a boolean_true. Use "--help" to get more information on the parameters.
|
|
exit 1
|
|
fi
|
|
fi
|
|
if [[ -n "$VIASH_PAR_FLAT" ]]; then
|
|
if ! [[ "$VIASH_PAR_FLAT" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then
|
|
ViashError '--flat' has to be a boolean_true. Use "--help" to get more information on the parameters.
|
|
exit 1
|
|
fi
|
|
fi
|
|
if [[ -n "$VIASH_PAR_INTERACTIVE" ]]; then
|
|
if ! [[ "$VIASH_PAR_INTERACTIVE" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then
|
|
ViashError '--interactive' has to be a boolean_true. Use "--help" to get more information on the parameters.
|
|
exit 1
|
|
fi
|
|
fi
|
|
if [[ -n "$VIASH_PAR_DATA_DIR" ]]; then
|
|
if ! [[ "$VIASH_PAR_DATA_DIR" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then
|
|
ViashError '--data_dir' has to be a boolean_true. Use "--help" to get more information on the parameters.
|
|
exit 1
|
|
fi
|
|
fi
|
|
if [[ -n "$VIASH_PAR_NO_DATA_DIR" ]]; then
|
|
if ! [[ "$VIASH_PAR_NO_DATA_DIR" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then
|
|
ViashError '--no_data_dir' has to be a boolean_true. Use "--help" to get more information on the parameters.
|
|
exit 1
|
|
fi
|
|
fi
|
|
if [[ -n "$VIASH_PAR_ZIP_DATA_DIR" ]]; then
|
|
if ! [[ "$VIASH_PAR_ZIP_DATA_DIR" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then
|
|
ViashError '--zip_data_dir' has to be a boolean_true. Use "--help" to get more information on the parameters.
|
|
exit 1
|
|
fi
|
|
fi
|
|
if [[ -n "$VIASH_PAR_PDF" ]]; then
|
|
if ! [[ "$VIASH_PAR_PDF" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then
|
|
ViashError '--pdf' has to be a boolean_true. 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
|
|
|
|
# check whether value is belongs to a set of choices
|
|
if [ ! -z "$VIASH_PAR_TEMPLATE" ]; then
|
|
VIASH_PAR_TEMPLATE_CHOICES=("default;gathered;geo;highcharts;sections;simple")
|
|
IFS=';'
|
|
set -f
|
|
if ! [[ ";${VIASH_PAR_TEMPLATE_CHOICES[*]};" =~ ";$VIASH_PAR_TEMPLATE;" ]]; then
|
|
ViashError '--template' specified value of \'$VIASH_PAR_TEMPLATE\' is not in the list of allowed values. Use "--help" to get more information on the parameters.
|
|
exit 1
|
|
fi
|
|
set +f
|
|
unset IFS
|
|
fi
|
|
|
|
if [ ! -z "$VIASH_PAR_DATA_FORMAT" ]; then
|
|
VIASH_PAR_DATA_FORMAT_CHOICES=("tsv;csv;json;yaml")
|
|
IFS=';'
|
|
set -f
|
|
if ! [[ ";${VIASH_PAR_DATA_FORMAT_CHOICES[*]};" =~ ";$VIASH_PAR_DATA_FORMAT;" ]]; then
|
|
ViashError '--data_format' specified value of \'$VIASH_PAR_DATA_FORMAT\' is not in the list of allowed values. Use "--help" to get more information on the parameters.
|
|
exit 1
|
|
fi
|
|
set +f
|
|
unset IFS
|
|
fi
|
|
|
|
# create parent directories of output files, if so desired
|
|
if [ ! -z "$VIASH_PAR_OUTPUT_REPORT" ] && [ ! -d "$(dirname "$VIASH_PAR_OUTPUT_REPORT")" ]; then
|
|
mkdir -p "$(dirname "$VIASH_PAR_OUTPUT_REPORT")"
|
|
fi
|
|
if [ ! -z "$VIASH_PAR_OUTPUT_DATA" ] && [ ! -d "$(dirname "$VIASH_PAR_OUTPUT_DATA")" ]; then
|
|
mkdir -p "$(dirname "$VIASH_PAR_OUTPUT_DATA")"
|
|
fi
|
|
if [ ! -z "$VIASH_PAR_OUTPUT_PLOTS" ] && [ ! -d "$(dirname "$VIASH_PAR_OUTPUT_PLOTS")" ]; then
|
|
mkdir -p "$(dirname "$VIASH_PAR_OUTPUT_PLOTS")"
|
|
fi
|
|
|
|
if [ "$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_INPUT" ]; then
|
|
VIASH_TEST_INPUT=()
|
|
IFS=';'
|
|
for var in $VIASH_PAR_INPUT; do
|
|
unset IFS
|
|
VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$var")" )
|
|
var=$(ViashDockerAutodetectMount "$var")
|
|
VIASH_TEST_INPUT+=( "$var" )
|
|
done
|
|
VIASH_PAR_INPUT=$(IFS=';' ; echo "${VIASH_TEST_INPUT[*]}")
|
|
fi
|
|
if [ ! -z "$VIASH_PAR_OUTPUT_REPORT" ]; then
|
|
VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$VIASH_PAR_OUTPUT_REPORT")" )
|
|
VIASH_PAR_OUTPUT_REPORT=$(ViashDockerAutodetectMount "$VIASH_PAR_OUTPUT_REPORT")
|
|
VIASH_CHOWN_VARS+=( "$VIASH_PAR_OUTPUT_REPORT" )
|
|
fi
|
|
if [ ! -z "$VIASH_PAR_OUTPUT_DATA" ]; then
|
|
VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$VIASH_PAR_OUTPUT_DATA")" )
|
|
VIASH_PAR_OUTPUT_DATA=$(ViashDockerAutodetectMount "$VIASH_PAR_OUTPUT_DATA")
|
|
VIASH_CHOWN_VARS+=( "$VIASH_PAR_OUTPUT_DATA" )
|
|
fi
|
|
if [ ! -z "$VIASH_PAR_OUTPUT_PLOTS" ]; then
|
|
VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$VIASH_PAR_OUTPUT_PLOTS")" )
|
|
VIASH_PAR_OUTPUT_PLOTS=$(ViashDockerAutodetectMount "$VIASH_PAR_OUTPUT_PLOTS")
|
|
VIASH_CHOWN_VARS+=( "$VIASH_PAR_OUTPUT_PLOTS" )
|
|
fi
|
|
if [ ! -z "$VIASH_PAR_REPLACE_NAMES" ]; then
|
|
VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$VIASH_PAR_REPLACE_NAMES")" )
|
|
VIASH_PAR_REPLACE_NAMES=$(ViashDockerAutodetectMount "$VIASH_PAR_REPLACE_NAMES")
|
|
fi
|
|
if [ ! -z "$VIASH_PAR_SAMPLE_NAMES" ]; then
|
|
VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$VIASH_PAR_SAMPLE_NAMES")" )
|
|
VIASH_PAR_SAMPLE_NAMES=$(ViashDockerAutodetectMount "$VIASH_PAR_SAMPLE_NAMES")
|
|
fi
|
|
if [ ! -z "$VIASH_PAR_SAMPLE_FILTERS" ]; then
|
|
VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$VIASH_PAR_SAMPLE_FILTERS")" )
|
|
VIASH_PAR_SAMPLE_FILTERS=$(ViashDockerAutodetectMount "$VIASH_PAR_SAMPLE_FILTERS")
|
|
fi
|
|
if [ ! -z "$VIASH_PAR_CUSTOM_CSS_FILE" ]; then
|
|
VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$VIASH_PAR_CUSTOM_CSS_FILE")" )
|
|
VIASH_PAR_CUSTOM_CSS_FILE=$(ViashDockerAutodetectMount "$VIASH_PAR_CUSTOM_CSS_FILE")
|
|
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-multiqc-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 ${VIASH_PAR_INPUT+x} ]; then echo "${VIASH_PAR_INPUT}" | sed "s#'#'\"'\"'#g;s#.*#par_input='&'#" ; else echo "# par_input="; fi )
|
|
$( if [ ! -z ${VIASH_PAR_OUTPUT_REPORT+x} ]; then echo "${VIASH_PAR_OUTPUT_REPORT}" | sed "s#'#'\"'\"'#g;s#.*#par_output_report='&'#" ; else echo "# par_output_report="; fi )
|
|
$( if [ ! -z ${VIASH_PAR_OUTPUT_DATA+x} ]; then echo "${VIASH_PAR_OUTPUT_DATA}" | sed "s#'#'\"'\"'#g;s#.*#par_output_data='&'#" ; else echo "# par_output_data="; fi )
|
|
$( if [ ! -z ${VIASH_PAR_OUTPUT_PLOTS+x} ]; then echo "${VIASH_PAR_OUTPUT_PLOTS}" | sed "s#'#'\"'\"'#g;s#.*#par_output_plots='&'#" ; else echo "# par_output_plots="; fi )
|
|
$( if [ ! -z ${VIASH_PAR_INCLUDE_MODULES+x} ]; then echo "${VIASH_PAR_INCLUDE_MODULES}" | sed "s#'#'\"'\"'#g;s#.*#par_include_modules='&'#" ; else echo "# par_include_modules="; fi )
|
|
$( if [ ! -z ${VIASH_PAR_EXCLUDE_MODULES+x} ]; then echo "${VIASH_PAR_EXCLUDE_MODULES}" | sed "s#'#'\"'\"'#g;s#.*#par_exclude_modules='&'#" ; else echo "# par_exclude_modules="; fi )
|
|
$( if [ ! -z ${VIASH_PAR_IGNORE_ANALYSIS+x} ]; then echo "${VIASH_PAR_IGNORE_ANALYSIS}" | sed "s#'#'\"'\"'#g;s#.*#par_ignore_analysis='&'#" ; else echo "# par_ignore_analysis="; fi )
|
|
$( if [ ! -z ${VIASH_PAR_IGNORE_SAMPLES+x} ]; then echo "${VIASH_PAR_IGNORE_SAMPLES}" | sed "s#'#'\"'\"'#g;s#.*#par_ignore_samples='&'#" ; else echo "# par_ignore_samples="; fi )
|
|
$( if [ ! -z ${VIASH_PAR_IGNORE_SYMLINKS+x} ]; then echo "${VIASH_PAR_IGNORE_SYMLINKS}" | sed "s#'#'\"'\"'#g;s#.*#par_ignore_symlinks='&'#" ; else echo "# par_ignore_symlinks="; fi )
|
|
$( if [ ! -z ${VIASH_PAR_DIRS+x} ]; then echo "${VIASH_PAR_DIRS}" | sed "s#'#'\"'\"'#g;s#.*#par_dirs='&'#" ; else echo "# par_dirs="; fi )
|
|
$( if [ ! -z ${VIASH_PAR_DIRS_DEPTH+x} ]; then echo "${VIASH_PAR_DIRS_DEPTH}" | sed "s#'#'\"'\"'#g;s#.*#par_dirs_depth='&'#" ; else echo "# par_dirs_depth="; fi )
|
|
$( if [ ! -z ${VIASH_PAR_FULL_NAMES+x} ]; then echo "${VIASH_PAR_FULL_NAMES}" | sed "s#'#'\"'\"'#g;s#.*#par_full_names='&'#" ; else echo "# par_full_names="; fi )
|
|
$( if [ ! -z ${VIASH_PAR_FN_AS_S_NAME+x} ]; then echo "${VIASH_PAR_FN_AS_S_NAME}" | sed "s#'#'\"'\"'#g;s#.*#par_fn_as_s_name='&'#" ; else echo "# par_fn_as_s_name="; fi )
|
|
$( if [ ! -z ${VIASH_PAR_REPLACE_NAMES+x} ]; then echo "${VIASH_PAR_REPLACE_NAMES}" | sed "s#'#'\"'\"'#g;s#.*#par_replace_names='&'#" ; else echo "# par_replace_names="; fi )
|
|
$( if [ ! -z ${VIASH_PAR_TITLE+x} ]; then echo "${VIASH_PAR_TITLE}" | sed "s#'#'\"'\"'#g;s#.*#par_title='&'#" ; else echo "# par_title="; fi )
|
|
$( if [ ! -z ${VIASH_PAR_COMMENT+x} ]; then echo "${VIASH_PAR_COMMENT}" | sed "s#'#'\"'\"'#g;s#.*#par_comment='&'#" ; else echo "# par_comment="; fi )
|
|
$( if [ ! -z ${VIASH_PAR_TEMPLATE+x} ]; then echo "${VIASH_PAR_TEMPLATE}" | sed "s#'#'\"'\"'#g;s#.*#par_template='&'#" ; else echo "# par_template="; fi )
|
|
$( if [ ! -z ${VIASH_PAR_SAMPLE_NAMES+x} ]; then echo "${VIASH_PAR_SAMPLE_NAMES}" | sed "s#'#'\"'\"'#g;s#.*#par_sample_names='&'#" ; else echo "# par_sample_names="; fi )
|
|
$( if [ ! -z ${VIASH_PAR_SAMPLE_FILTERS+x} ]; then echo "${VIASH_PAR_SAMPLE_FILTERS}" | sed "s#'#'\"'\"'#g;s#.*#par_sample_filters='&'#" ; else echo "# par_sample_filters="; fi )
|
|
$( if [ ! -z ${VIASH_PAR_CUSTOM_CSS_FILE+x} ]; then echo "${VIASH_PAR_CUSTOM_CSS_FILE}" | sed "s#'#'\"'\"'#g;s#.*#par_custom_css_file='&'#" ; else echo "# par_custom_css_file="; fi )
|
|
$( if [ ! -z ${VIASH_PAR_PROFILE_RUNTIME+x} ]; then echo "${VIASH_PAR_PROFILE_RUNTIME}" | sed "s#'#'\"'\"'#g;s#.*#par_profile_runtime='&'#" ; else echo "# par_profile_runtime="; fi )
|
|
$( if [ ! -z ${VIASH_PAR_VERBOSE+x} ]; then echo "${VIASH_PAR_VERBOSE}" | sed "s#'#'\"'\"'#g;s#.*#par_verbose='&'#" ; else echo "# par_verbose="; fi )
|
|
$( if [ ! -z ${VIASH_PAR_QUIET+x} ]; then echo "${VIASH_PAR_QUIET}" | sed "s#'#'\"'\"'#g;s#.*#par_quiet='&'#" ; else echo "# par_quiet="; fi )
|
|
$( if [ ! -z ${VIASH_PAR_STRICT+x} ]; then echo "${VIASH_PAR_STRICT}" | sed "s#'#'\"'\"'#g;s#.*#par_strict='&'#" ; else echo "# par_strict="; fi )
|
|
$( if [ ! -z ${VIASH_PAR_DEVELOPMENT+x} ]; then echo "${VIASH_PAR_DEVELOPMENT}" | sed "s#'#'\"'\"'#g;s#.*#par_development='&'#" ; else echo "# par_development="; fi )
|
|
$( if [ ! -z ${VIASH_PAR_REQUIRE_LOGS+x} ]; then echo "${VIASH_PAR_REQUIRE_LOGS}" | sed "s#'#'\"'\"'#g;s#.*#par_require_logs='&'#" ; else echo "# par_require_logs="; fi )
|
|
$( if [ ! -z ${VIASH_PAR_NO_MEGAQC_UPLOAD+x} ]; then echo "${VIASH_PAR_NO_MEGAQC_UPLOAD}" | sed "s#'#'\"'\"'#g;s#.*#par_no_megaqc_upload='&'#" ; else echo "# par_no_megaqc_upload="; fi )
|
|
$( if [ ! -z ${VIASH_PAR_NO_ANSI+x} ]; then echo "${VIASH_PAR_NO_ANSI}" | sed "s#'#'\"'\"'#g;s#.*#par_no_ansi='&'#" ; else echo "# par_no_ansi="; fi )
|
|
$( if [ ! -z ${VIASH_PAR_CL_CONFIG+x} ]; then echo "${VIASH_PAR_CL_CONFIG}" | sed "s#'#'\"'\"'#g;s#.*#par_cl_config='&'#" ; else echo "# par_cl_config="; fi )
|
|
$( if [ ! -z ${VIASH_PAR_FLAT+x} ]; then echo "${VIASH_PAR_FLAT}" | sed "s#'#'\"'\"'#g;s#.*#par_flat='&'#" ; else echo "# par_flat="; fi )
|
|
$( if [ ! -z ${VIASH_PAR_INTERACTIVE+x} ]; then echo "${VIASH_PAR_INTERACTIVE}" | sed "s#'#'\"'\"'#g;s#.*#par_interactive='&'#" ; else echo "# par_interactive="; fi )
|
|
$( if [ ! -z ${VIASH_PAR_DATA_DIR+x} ]; then echo "${VIASH_PAR_DATA_DIR}" | sed "s#'#'\"'\"'#g;s#.*#par_data_dir='&'#" ; else echo "# par_data_dir="; fi )
|
|
$( if [ ! -z ${VIASH_PAR_NO_DATA_DIR+x} ]; then echo "${VIASH_PAR_NO_DATA_DIR}" | sed "s#'#'\"'\"'#g;s#.*#par_no_data_dir='&'#" ; else echo "# par_no_data_dir="; fi )
|
|
$( if [ ! -z ${VIASH_PAR_ZIP_DATA_DIR+x} ]; then echo "${VIASH_PAR_ZIP_DATA_DIR}" | sed "s#'#'\"'\"'#g;s#.*#par_zip_data_dir='&'#" ; else echo "# par_zip_data_dir="; fi )
|
|
$( if [ ! -z ${VIASH_PAR_DATA_FORMAT+x} ]; then echo "${VIASH_PAR_DATA_FORMAT}" | sed "s#'#'\"'\"'#g;s#.*#par_data_format='&'#" ; else echo "# par_data_format="; fi )
|
|
$( if [ ! -z ${VIASH_PAR_PDF+x} ]; then echo "${VIASH_PAR_PDF}" | sed "s#'#'\"'\"'#g;s#.*#par_pdf='&'#" ; else echo "# par_pdf="; 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
|
|
|
|
# disable flags
|
|
unset_if_false=(
|
|
par_ignore_symlinks
|
|
par_dirs
|
|
par_full_names
|
|
par_fn_as_s_name
|
|
par_profile_runtime
|
|
par_verbose
|
|
par_quiet
|
|
par_strict
|
|
par_development
|
|
par_require_logs
|
|
par_no_megaqc_upload
|
|
par_no_ansi
|
|
par_flat
|
|
par_interactive
|
|
par_static_plot_export
|
|
par_data_dir
|
|
par_no_data_dir
|
|
par_zip_data_dir
|
|
par_pdf
|
|
)
|
|
|
|
for par in \${unset_if_false[@]}; do
|
|
test_val="\${!par}"
|
|
[[ "\$test_val" == "false" ]] && unset \$par
|
|
done
|
|
|
|
# handle inputs
|
|
out_dir=\$(dirname "\$par_output_report")
|
|
output_report_file=\$(basename "\$par_output_report")
|
|
report_name="\${output_report_file%.*}"
|
|
|
|
# handle outputs
|
|
[[ -z "\$par_output_report" ]] && no_report=true
|
|
[[ -z "\$par_output_data" ]] && no_data_dir=true
|
|
[[ ! -z "\$par_output_data" ]] && data_dir=true
|
|
[[ ! -z "\$par_output_plots" ]] && export=true
|
|
|
|
# handle multiples
|
|
IFS=";" read -ra inputs <<< \$par_input
|
|
|
|
if [[ -n "\$par_include_modules" ]]; then
|
|
include_modules=""
|
|
IFS=";" read -ra incl_modules <<< \$par_include_modules
|
|
for i in "\${incl_modules[@]}"; do
|
|
include_modules+="--include \$i "
|
|
done
|
|
unset IFS
|
|
fi
|
|
|
|
if [[ -n "\$par_exclude_modules" ]]; then
|
|
exclude_modules=""
|
|
IFS=";" read -ra excl_modules <<< \$par_exclude_modules
|
|
for i in "\${excl_modules[@]}"; do
|
|
exclude_modules+="--exclude \$i"
|
|
done
|
|
unset IFS
|
|
fi
|
|
|
|
if [[ -n "\$par_ignore_analysis" ]]; then
|
|
ignore=""
|
|
IFS=";" read -ra ignore_analysis <<< \$par_ignore_analysis
|
|
for i in "\${ignore_analysis[@]}"; do
|
|
ignore+="--ignore \$i "
|
|
done
|
|
unset IFS
|
|
fi
|
|
|
|
if [[ -n "\$par_ignore_samples" ]]; then
|
|
ignore_samples=""
|
|
IFS=";" read -ra ign_samples <<< \$par_ignore_samples
|
|
for i in "\${ign_samples[@]}"; do
|
|
ignore_samples+="--ignore-samples \$i"
|
|
done
|
|
unset IFS
|
|
fi
|
|
|
|
# run multiqc
|
|
multiqc \\
|
|
\${par_output_report:+--filename "\$report_name"} \\
|
|
\${out_dir:+--outdir "\$out_dir"} \\
|
|
\${no_report:+--no-report} \\
|
|
\${no_data_dir:+--no-data-dir} \\
|
|
\${data_dir:+--data-dir} \\
|
|
\${export:+--export} \\
|
|
\${par_title:+--title "\$par_title"} \\
|
|
\${par_comment:+--comment "\$par_comment"} \\
|
|
\${par_template:+--template "\$par_template"} \\
|
|
\${par_sample_names:+--sample-names "\$par_sample_names"} \\
|
|
\${par_sample_filters:+--sample-filters "\$par_sample_filters"} \\
|
|
\${par_custom_css_file:+--custom-css-file "\$par_custom_css_file"} \\
|
|
\${par_profile_runtime:+--profile-runtime} \\
|
|
\${par_dirs:+--dirs} \\
|
|
\${par_dirs_depth:+--dirs-depth "\$par_dirs_depth"} \\
|
|
\${par_full_names:+--full-names} \\
|
|
\${par_fn_as_s_name:+--fn-as-s-name} \\
|
|
\${par_ignore_names:+--ignore-names "\$par_ignore_names"} \\
|
|
\${par_ignore_symlinks:+--ignore-symlinks} \\
|
|
\${ignore_samples} \\
|
|
\${ignore} \\
|
|
\${exclude_modules} \\
|
|
\${include_modules} \\
|
|
\${par_include_modules:+--include-modules "\$par_include_modules"} \\
|
|
\${par_data_format:+--data-format "\$par_data_format"} \\
|
|
\${par_cl_config:+--cl-config "\$par_cl_config"} \\
|
|
\${par_zip_data_dir:+--zip-data-dir} \\
|
|
\${par_pdf:+--pdf} \\
|
|
\${par_interactive:+--interactive} \\
|
|
\${par_flat:+--flat} \\
|
|
\${par_verbose:+--verbose} \\
|
|
\${par_quiet:+--quiet} \\
|
|
\${par_strict:+--strict} \\
|
|
\${par_no_megaqc_upload:+--no-megaqc-upload} \\
|
|
\${par_no_ansi:+--no-ansi} \\
|
|
\${par_profile_runtime:+--profile-runtime} \\
|
|
\${par_require_logs:+--require-logs} \\
|
|
\${par_development:+--development} \\
|
|
--force \\
|
|
"\${inputs[@]}"
|
|
|
|
# Move outputs
|
|
|
|
if [[ -n "\$par_output_data" ]] && [[ -d "\${out_dir}/\${report_name}_data" ]]; then
|
|
mv "\${out_dir}/\${report_name}_data" "\$par_output_data"
|
|
elif [[ -n "\$par_output_data" ]] && [[ ! -d "\${out_dir}/\${report_name}_data" ]]; then
|
|
echo "WARNING: Data could not be saved because data folder was not generated by multiqc. This could be due to filtering out of modules or samples."
|
|
fi
|
|
|
|
if [[ -n "\$par_output_plots" ]] && [[ -d "\${out_dir}/\${report_name}_plots" ]]; then
|
|
mv "\${out_dir}/\${report_name}_plots" "\$par_output_plots"
|
|
elif [[ -n "\$par_output_plots" ]] && [[ ! -d "\${out_dir}/\${report_name}_plots" ]]; then
|
|
echo "WARNING: Plots could not be saved because plots folder was not generated by multiqc. This could be due to filtering out of modules or samples."
|
|
fi
|
|
VIASHMAIN
|
|
bash "\$tempscript" &
|
|
wait "\$!"
|
|
|
|
VIASHEOF
|
|
|
|
|
|
if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then
|
|
# strip viash automount from file paths
|
|
|
|
if [ ! -z "$VIASH_PAR_INPUT" ]; then
|
|
unset VIASH_TEST_INPUT
|
|
IFS=';'
|
|
for var in $VIASH_PAR_INPUT; do
|
|
unset IFS
|
|
if [ -z "$VIASH_TEST_INPUT" ]; then
|
|
VIASH_TEST_INPUT="$(ViashDockerStripAutomount "$var")"
|
|
else
|
|
VIASH_TEST_INPUT="$VIASH_TEST_INPUT;""$(ViashDockerStripAutomount "$var")"
|
|
fi
|
|
done
|
|
VIASH_PAR_INPUT="$VIASH_TEST_INPUT"
|
|
fi
|
|
if [ ! -z "$VIASH_PAR_OUTPUT_REPORT" ]; then
|
|
VIASH_PAR_OUTPUT_REPORT=$(ViashDockerStripAutomount "$VIASH_PAR_OUTPUT_REPORT")
|
|
fi
|
|
if [ ! -z "$VIASH_PAR_OUTPUT_DATA" ]; then
|
|
VIASH_PAR_OUTPUT_DATA=$(ViashDockerStripAutomount "$VIASH_PAR_OUTPUT_DATA")
|
|
fi
|
|
if [ ! -z "$VIASH_PAR_OUTPUT_PLOTS" ]; then
|
|
VIASH_PAR_OUTPUT_PLOTS=$(ViashDockerStripAutomount "$VIASH_PAR_OUTPUT_PLOTS")
|
|
fi
|
|
if [ ! -z "$VIASH_PAR_REPLACE_NAMES" ]; then
|
|
VIASH_PAR_REPLACE_NAMES=$(ViashDockerStripAutomount "$VIASH_PAR_REPLACE_NAMES")
|
|
fi
|
|
if [ ! -z "$VIASH_PAR_SAMPLE_NAMES" ]; then
|
|
VIASH_PAR_SAMPLE_NAMES=$(ViashDockerStripAutomount "$VIASH_PAR_SAMPLE_NAMES")
|
|
fi
|
|
if [ ! -z "$VIASH_PAR_SAMPLE_FILTERS" ]; then
|
|
VIASH_PAR_SAMPLE_FILTERS=$(ViashDockerStripAutomount "$VIASH_PAR_SAMPLE_FILTERS")
|
|
fi
|
|
if [ ! -z "$VIASH_PAR_CUSTOM_CSS_FILE" ]; then
|
|
VIASH_PAR_CUSTOM_CSS_FILE=$(ViashDockerStripAutomount "$VIASH_PAR_CUSTOM_CSS_FILE")
|
|
fi
|
|
if [ ! -z "$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
|
|
|
|
|
|
exit 0
|