CI
e3be4c4461
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
2367 lines
118 KiB
Bash
Executable File
2367 lines
118 KiB
Bash
Executable File
#!/usr/bin/env bash
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# arriba main
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#
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# This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
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# work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
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# Intuitive.
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#
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# The component may contain files which fall under a different license. The
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# authors of this component should specify the license in the header of such
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# files, or include a separate license file detailing the licenses of all included
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# files.
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#
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# Component authors:
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# * Robrecht Cannoodt (author, maintainer)
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set -e
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if [ -z "$VIASH_TEMP" ]; then
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VIASH_TEMP=${VIASH_TEMP:-$VIASH_TMPDIR}
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VIASH_TEMP=${VIASH_TEMP:-$VIASH_TEMPDIR}
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VIASH_TEMP=${VIASH_TEMP:-$VIASH_TMP}
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VIASH_TEMP=${VIASH_TEMP:-$TMPDIR}
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VIASH_TEMP=${VIASH_TEMP:-$TMP}
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VIASH_TEMP=${VIASH_TEMP:-$TEMPDIR}
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VIASH_TEMP=${VIASH_TEMP:-$TEMP}
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VIASH_TEMP=${VIASH_TEMP:-/tmp}
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fi
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# define helper functions
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# ViashQuote: put quotes around non flag values
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# $1 : unquoted string
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# return : possibly quoted string
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# examples:
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# ViashQuote --foo # returns --foo
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# ViashQuote bar # returns 'bar'
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# Viashquote --foo=bar # returns --foo='bar'
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function ViashQuote {
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if [[ "$1" =~ ^-+[a-zA-Z0-9_\-]+=.+$ ]]; then
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echo "$1" | sed "s#=\(.*\)#='\1'#"
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elif [[ "$1" =~ ^-+[a-zA-Z0-9_\-]+$ ]]; then
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echo "$1"
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else
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echo "'$1'"
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fi
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}
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# ViashRemoveFlags: Remove leading flag
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# $1 : string with a possible leading flag
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# return : string without possible leading flag
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# examples:
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# ViashRemoveFlags --foo=bar # returns bar
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function ViashRemoveFlags {
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echo "$1" | sed 's/^--*[a-zA-Z0-9_\-]*=//'
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}
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# ViashSourceDir: return the path of a bash file, following symlinks
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# usage : ViashSourceDir ${BASH_SOURCE[0]}
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# $1 : Should always be set to ${BASH_SOURCE[0]}
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# returns : The absolute path of the bash file
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function ViashSourceDir {
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local source="$1"
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while [ -h "$source" ]; do
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local dir="$( cd -P "$( dirname "$source" )" >/dev/null 2>&1 && pwd )"
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source="$(readlink "$source")"
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[[ $source != /* ]] && source="$dir/$source"
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done
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cd -P "$( dirname "$source" )" >/dev/null 2>&1 && pwd
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}
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# ViashFindTargetDir: return the path of the '.build.yaml' file, following symlinks
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# usage : ViashFindTargetDir 'ScriptPath'
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# $1 : The location from where to start the upward search
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# returns : The absolute path of the '.build.yaml' file
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function ViashFindTargetDir {
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local source="$1"
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while [[ "$source" != "" && ! -e "$source/.build.yaml" ]]; do
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source=${source%/*}
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done
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echo $source
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}
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# see https://en.wikipedia.org/wiki/Syslog#Severity_level
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VIASH_LOGCODE_EMERGENCY=0
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VIASH_LOGCODE_ALERT=1
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VIASH_LOGCODE_CRITICAL=2
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VIASH_LOGCODE_ERROR=3
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VIASH_LOGCODE_WARNING=4
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VIASH_LOGCODE_NOTICE=5
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VIASH_LOGCODE_INFO=6
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VIASH_LOGCODE_DEBUG=7
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VIASH_VERBOSITY=$VIASH_LOGCODE_NOTICE
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# ViashLog: Log events depending on the verbosity level
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# usage: ViashLog 1 alert Oh no something went wrong!
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# $1: required verbosity level
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# $2: display tag
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# $3+: messages to display
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# stdout: Your input, prepended by '[$2] '.
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function ViashLog {
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local required_level="$1"
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local display_tag="$2"
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shift 2
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if [ $VIASH_VERBOSITY -ge $required_level ]; then
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>&2 echo "[$display_tag]" "$@"
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fi
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}
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# ViashEmergency: log events when the system is unstable
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# usage: ViashEmergency Oh no something went wrong.
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# stdout: Your input, prepended by '[emergency] '.
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function ViashEmergency {
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ViashLog $VIASH_LOGCODE_EMERGENCY emergency "$@"
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}
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# ViashAlert: log events when actions must be taken immediately (e.g. corrupted system database)
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# usage: ViashAlert Oh no something went wrong.
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# stdout: Your input, prepended by '[alert] '.
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function ViashAlert {
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ViashLog $VIASH_LOGCODE_ALERT alert "$@"
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}
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# ViashCritical: log events when a critical condition occurs
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# usage: ViashCritical Oh no something went wrong.
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# stdout: Your input, prepended by '[critical] '.
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function ViashCritical {
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ViashLog $VIASH_LOGCODE_CRITICAL critical "$@"
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}
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# ViashError: log events when an error condition occurs
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# usage: ViashError Oh no something went wrong.
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# stdout: Your input, prepended by '[error] '.
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function ViashError {
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ViashLog $VIASH_LOGCODE_ERROR error "$@"
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}
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# ViashWarning: log potentially abnormal events
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# usage: ViashWarning Something may have gone wrong.
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# stdout: Your input, prepended by '[warning] '.
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function ViashWarning {
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ViashLog $VIASH_LOGCODE_WARNING warning "$@"
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}
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# ViashNotice: log significant but normal events
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# usage: ViashNotice This just happened.
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# stdout: Your input, prepended by '[notice] '.
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function ViashNotice {
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ViashLog $VIASH_LOGCODE_NOTICE notice "$@"
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}
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# ViashInfo: log normal events
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# usage: ViashInfo This just happened.
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# stdout: Your input, prepended by '[info] '.
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function ViashInfo {
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ViashLog $VIASH_LOGCODE_INFO info "$@"
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}
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# ViashDebug: log all events, for debugging purposes
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# usage: ViashDebug This just happened.
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# stdout: Your input, prepended by '[debug] '.
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function ViashDebug {
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ViashLog $VIASH_LOGCODE_DEBUG debug "$@"
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}
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# find source folder of this component
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VIASH_META_RESOURCES_DIR=`ViashSourceDir ${BASH_SOURCE[0]}`
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# find the root of the built components & dependencies
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VIASH_TARGET_DIR=`ViashFindTargetDir $VIASH_META_RESOURCES_DIR`
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# define meta fields
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VIASH_META_NAME="arriba"
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VIASH_META_FUNCTIONALITY_NAME="arriba"
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VIASH_META_EXECUTABLE="$VIASH_META_RESOURCES_DIR/$VIASH_META_NAME"
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VIASH_META_CONFIG="$VIASH_META_RESOURCES_DIR/.config.vsh.yaml"
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VIASH_META_TEMP_DIR="$VIASH_TEMP"
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# initialise variables
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VIASH_MODE='run'
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VIASH_ENGINE_ID='docker'
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######## Helper functions for setting up Docker images for viash ########
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# expects: ViashDockerBuild
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# ViashDockerInstallationCheck: check whether Docker is installed correctly
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#
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# examples:
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# ViashDockerInstallationCheck
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function ViashDockerInstallationCheck {
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ViashDebug "Checking whether Docker is installed"
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if [ ! command -v docker &> /dev/null ]; then
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ViashCritical "Docker doesn't seem to be installed. See 'https://docs.docker.com/get-docker/' for instructions."
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exit 1
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fi
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ViashDebug "Checking whether the Docker daemon is running"
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local save=$-; set +e
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local docker_version=$(docker version --format '{{.Client.APIVersion}}' 2> /dev/null)
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local out=$?
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[[ $save =~ e ]] && set -e
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if [ $out -ne 0 ]; then
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ViashCritical "Docker daemon does not seem to be running. Try one of the following:"
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ViashCritical "- Try running 'dockerd' in the command line"
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ViashCritical "- See https://docs.docker.com/config/daemon/"
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exit 1
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fi
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}
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# ViashDockerRemoteTagCheck: check whether a Docker image is available
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# on a remote. Assumes `docker login` has been performed, if relevant.
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#
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# $1 : image identifier with format `[registry/]image[:tag]`
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# exit code $? : whether or not the image was found
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# examples:
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# ViashDockerRemoteTagCheck python:latest
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# echo $? # returns '0'
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# ViashDockerRemoteTagCheck sdaizudceahifu
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# echo $? # returns '1'
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function ViashDockerRemoteTagCheck {
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docker manifest inspect $1 > /dev/null 2> /dev/null
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}
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# ViashDockerLocalTagCheck: check whether a Docker image is available locally
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#
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# $1 : image identifier with format `[registry/]image[:tag]`
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# exit code $? : whether or not the image was found
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# examples:
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# docker pull python:latest
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# ViashDockerLocalTagCheck python:latest
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# echo $? # returns '0'
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# ViashDockerLocalTagCheck sdaizudceahifu
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# echo $? # returns '1'
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function ViashDockerLocalTagCheck {
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[ -n "$(docker images -q $1)" ]
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}
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# ViashDockerPull: pull a Docker image
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#
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# $1 : image identifier with format `[registry/]image[:tag]`
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# exit code $? : whether or not the image was found
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# examples:
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# ViashDockerPull python:latest
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# echo $? # returns '0'
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# ViashDockerPull sdaizudceahifu
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# echo $? # returns '1'
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function ViashDockerPull {
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ViashNotice "Checking if Docker image is available at '$1'"
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if [ $VIASH_VERBOSITY -ge $VIASH_LOGCODE_INFO ]; then
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docker pull $1 && return 0 || return 1
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else
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local save=$-; set +e
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docker pull $1 2> /dev/null > /dev/null
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local out=$?
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[[ $save =~ e ]] && set -e
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if [ $out -ne 0 ]; then
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ViashWarning "Could not pull from '$1'. Docker image doesn't exist or is not accessible."
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fi
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return $out
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fi
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}
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# ViashDockerPush: push a Docker image
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#
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# $1 : image identifier with format `[registry/]image[:tag]`
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# exit code $? : whether or not the image was found
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# examples:
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# ViashDockerPush python:latest
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# echo $? # returns '0'
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# ViashDockerPush sdaizudceahifu
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# echo $? # returns '1'
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function ViashDockerPush {
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ViashNotice "Pushing image to '$1'"
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local save=$-; set +e
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local out
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if [ $VIASH_VERBOSITY -ge $VIASH_LOGCODE_INFO ]; then
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docker push $1
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out=$?
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else
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docker push $1 2> /dev/null > /dev/null
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out=$?
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fi
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[[ $save =~ e ]] && set -e
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if [ $out -eq 0 ]; then
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ViashNotice "Container '$1' push succeeded."
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else
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ViashError "Container '$1' push errored. You might not be logged in or have the necessary permissions."
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fi
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return $out
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}
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# ViashDockerPullElseBuild: pull a Docker image, else build it
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#
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# $1 : image identifier with format `[registry/]image[:tag]`
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# ViashDockerBuild : a Bash function which builds a docker image, takes image identifier as argument.
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# examples:
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# ViashDockerPullElseBuild mynewcomponent
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function ViashDockerPullElseBuild {
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local save=$-; set +e
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ViashDockerPull $1
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local out=$?
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[[ $save =~ e ]] && set -e
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if [ $out -ne 0 ]; then
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ViashDockerBuild $@
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fi
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}
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# ViashDockerSetup: create a Docker image, according to specified docker setup strategy
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#
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# $1 : image identifier with format `[registry/]image[:tag]`
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# $2 : docker setup strategy, see DockerSetupStrategy.scala
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# examples:
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# ViashDockerSetup mynewcomponent alwaysbuild
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function ViashDockerSetup {
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local image_id="$1"
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local setup_strategy="$2"
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if [ "$setup_strategy" == "alwaysbuild" -o "$setup_strategy" == "build" -o "$setup_strategy" == "b" ]; then
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ViashDockerBuild $image_id --no-cache $(ViashDockerBuildArgs "$engine_id")
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elif [ "$setup_strategy" == "alwayspull" -o "$setup_strategy" == "pull" -o "$setup_strategy" == "p" ]; then
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ViashDockerPull $image_id
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elif [ "$setup_strategy" == "alwayspullelsebuild" -o "$setup_strategy" == "pullelsebuild" ]; then
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ViashDockerPullElseBuild $image_id --no-cache $(ViashDockerBuildArgs "$engine_id")
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elif [ "$setup_strategy" == "alwayspullelsecachedbuild" -o "$setup_strategy" == "pullelsecachedbuild" ]; then
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ViashDockerPullElseBuild $image_id $(ViashDockerBuildArgs "$engine_id")
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elif [ "$setup_strategy" == "alwayscachedbuild" -o "$setup_strategy" == "cachedbuild" -o "$setup_strategy" == "cb" ]; then
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ViashDockerBuild $image_id $(ViashDockerBuildArgs "$engine_id")
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elif [[ "$setup_strategy" =~ ^ifneedbe ]]; then
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local save=$-; set +e
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ViashDockerLocalTagCheck $image_id
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local outCheck=$?
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[[ $save =~ e ]] && set -e
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if [ $outCheck -eq 0 ]; then
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ViashInfo "Image $image_id already exists"
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elif [ "$setup_strategy" == "ifneedbebuild" ]; then
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ViashDockerBuild $image_id --no-cache $(ViashDockerBuildArgs "$engine_id")
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elif [ "$setup_strategy" == "ifneedbecachedbuild" ]; then
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ViashDockerBuild $image_id $(ViashDockerBuildArgs "$engine_id")
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elif [ "$setup_strategy" == "ifneedbepull" ]; then
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ViashDockerPull $image_id
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elif [ "$setup_strategy" == "ifneedbepullelsebuild" ]; then
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ViashDockerPullElseBuild $image_id --no-cache $(ViashDockerBuildArgs "$engine_id")
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elif [ "$setup_strategy" == "ifneedbepullelsecachedbuild" ]; then
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ViashDockerPullElseBuild $image_id $(ViashDockerBuildArgs "$engine_id")
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else
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ViashError "Unrecognised Docker strategy: $setup_strategy"
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exit 1
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fi
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elif [ "$setup_strategy" == "push" -o "$setup_strategy" == "forcepush" -o "$setup_strategy" == "alwayspush" ]; then
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ViashDockerPush "$image_id"
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elif [ "$setup_strategy" == "pushifnotpresent" -o "$setup_strategy" == "gentlepush" -o "$setup_strategy" == "maybepush" ]; then
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local save=$-; set +e
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ViashDockerRemoteTagCheck $image_id
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local outCheck=$?
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[[ $save =~ e ]] && set -e
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if [ $outCheck -eq 0 ]; then
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ViashNotice "Container '$image_id' exists, doing nothing."
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else
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ViashNotice "Container '$image_id' does not yet exist."
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ViashDockerPush "$image_id"
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fi
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elif [ "$setup_strategy" == "donothing" -o "$setup_strategy" == "meh" ]; then
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ViashNotice "Skipping setup."
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else
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ViashError "Unrecognised Docker strategy: $setup_strategy"
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exit 1
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fi
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}
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# ViashDockerCheckCommands: Check whether a docker container has the required commands
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#
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# $1 : image identifier with format `[registry/]image[:tag]`
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# $@ : commands to verify being present
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# examples:
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# ViashDockerCheckCommands bash:4.0 bash ps foo
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function ViashDockerCheckCommands {
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local image_id="$1"
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shift 1
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local commands="$@"
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local save=$-; set +e
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local missing # mark 'missing' as local in advance, otherwise the exit code of the command will be missing and always be '0'
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missing=$(docker run --rm --entrypoint=sh "$image_id" -c "for command in $commands; do command -v \$command >/dev/null 2>&1; if [ \$? -ne 0 ]; then echo \$command; exit 1; fi; done")
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local outCheck=$?
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[[ $save =~ e ]] && set -e
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if [ $outCheck -ne 0 ]; then
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ViashError "Docker container '$image_id' does not contain command '$missing'."
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exit 1
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fi
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}
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# ViashDockerBuild: build a docker image
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# $1 : image identifier with format `[registry/]image[:tag]`
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# $... : additional arguments to pass to docker build
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# $VIASH_META_TEMP_DIR : temporary directory to store dockerfile & optional resources in
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# $VIASH_META_NAME : name of the component
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# $VIASH_META_RESOURCES_DIR : directory containing the resources
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# $VIASH_VERBOSITY : verbosity level
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# exit code $? : whether or not the image was built successfully
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function ViashDockerBuild {
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local image_id="$1"
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shift 1
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# create temporary directory to store dockerfile & optional resources in
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local tmpdir=$(mktemp -d "$VIASH_META_TEMP_DIR/dockerbuild-$VIASH_META_NAME-XXXXXX")
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local dockerfile="$tmpdir/Dockerfile"
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function clean_up {
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rm -rf "$tmpdir"
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}
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trap clean_up EXIT
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# store dockerfile and resources
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ViashDockerfile "$VIASH_ENGINE_ID" > "$dockerfile"
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# generate the build command
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local docker_build_cmd="docker build -t '$image_id' $@ '$VIASH_META_RESOURCES_DIR' -f '$dockerfile'"
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# build the container
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ViashNotice "Building container '$image_id' with Dockerfile"
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ViashInfo "$docker_build_cmd"
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local save=$-; set +e
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if [ $VIASH_VERBOSITY -ge $VIASH_LOGCODE_INFO ]; then
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eval $docker_build_cmd
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else
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eval $docker_build_cmd &> "$tmpdir/docker_build.log"
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fi
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# check exit code
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local out=$?
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[[ $save =~ e ]] && set -e
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if [ $out -ne 0 ]; then
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ViashError "Error occurred while building container '$image_id'"
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if [ $VIASH_VERBOSITY -lt $VIASH_LOGCODE_INFO ]; then
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ViashError "Transcript: --------------------------------"
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cat "$tmpdir/docker_build.log"
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ViashError "End of transcript --------------------------"
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fi
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exit 1
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fi
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}
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######## End of helper functions for setting up Docker images for viash ########
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# ViashDockerFile: print the dockerfile to stdout
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# $1 : engine identifier
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# return : dockerfile required to run this component
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# examples:
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# ViashDockerFile
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function ViashDockerfile {
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local engine_id="$1"
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|
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if [[ "$engine_id" == "docker" ]]; then
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cat << 'VIASHDOCKER'
|
|
FROM quay.io/biocontainers/arriba:2.4.0--h0033a41_2
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ENTRYPOINT []
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|
RUN arriba -h | grep 'Version:' 2>&1 | sed 's/Version:\s\(.*\)/arriba: "\1"/' > /var/software_versions.txt
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LABEL org.opencontainers.image.authors="Robrecht Cannoodt"
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LABEL org.opencontainers.image.description="Companion container for running component arriba"
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LABEL org.opencontainers.image.created="2025-05-06T20:11:41Z"
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LABEL org.opencontainers.image.source="https://github.com/suhrig/arriba"
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LABEL org.opencontainers.image.revision="b0db228825f3441b4651527e8775e8fc87d06e60"
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LABEL org.opencontainers.image.version="main"
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VIASHDOCKER
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fi
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}
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# ViashDockerBuildArgs: return the arguments to pass to docker build
|
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# $1 : engine identifier
|
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# return : arguments to pass to docker build
|
|
function ViashDockerBuildArgs {
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|
local engine_id="$1"
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|
|
if [[ "$engine_id" == "docker" ]]; then
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echo ""
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|
fi
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}
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# ViashAbsolutePath: generate absolute path from relative path
|
|
# borrowed from https://stackoverflow.com/a/21951256
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|
# $1 : relative filename
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# return : absolute path
|
|
# examples:
|
|
# ViashAbsolutePath some_file.txt # returns /path/to/some_file.txt
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# ViashAbsolutePath /foo/bar/.. # returns /foo
|
|
function ViashAbsolutePath {
|
|
local thePath
|
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local parr
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|
local outp
|
|
local len
|
|
if [[ ! "$1" =~ ^/ ]]; then
|
|
thePath="$PWD/$1"
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else
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|
thePath="$1"
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fi
|
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echo "$thePath" | (
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IFS=/
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read -a parr
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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
|
|
;;
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|
*)
|
|
len=${#outp[@]}
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|
outp[$len]="$i"
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|
;;
|
|
esac
|
|
done
|
|
echo /"${outp[*]}"
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|
)
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|
}
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|
# 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
|
|
# $VIASH_DOCKER_AUTOMOUNT_PREFIX : The prefix to be used for the automounts
|
|
# examples:
|
|
# ViashDockerAutodetectMount /path/to/bar # returns '/viash_automount/path/to/bar'
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|
# ViashDockerAutodetectMountArg /path/to/bar # returns '--volume="/path/to:/viash_automount/path/to"'
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|
function ViashDockerAutodetectMount {
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local abs_path=$(ViashAbsolutePath "$1")
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local mount_source
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local base_name
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if [ -d "$abs_path" ]; then
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mount_source="$abs_path"
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base_name=""
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else
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mount_source=`dirname "$abs_path"`
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base_name=`basename "$abs_path"`
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|
fi
|
|
local mount_target="$VIASH_DOCKER_AUTOMOUNT_PREFIX$mount_source"
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|
if [ -z "$base_name" ]; then
|
|
echo "$mount_target"
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else
|
|
echo "$mount_target/$base_name"
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fi
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}
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function ViashDockerAutodetectMountArg {
|
|
local abs_path=$(ViashAbsolutePath "$1")
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local mount_source
|
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local base_name
|
|
if [ -d "$abs_path" ]; then
|
|
mount_source="$abs_path"
|
|
base_name=""
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|
else
|
|
mount_source=`dirname "$abs_path"`
|
|
base_name=`basename "$abs_path"`
|
|
fi
|
|
local mount_target="$VIASH_DOCKER_AUTOMOUNT_PREFIX$mount_source"
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|
ViashDebug "ViashDockerAutodetectMountArg $1 -> $mount_source -> $mount_target"
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echo "--volume=\"$mount_source:$mount_target\""
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|
}
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function ViashDockerStripAutomount {
|
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local abs_path=$(ViashAbsolutePath "$1")
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echo "${abs_path#$VIASH_DOCKER_AUTOMOUNT_PREFIX}"
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}
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# initialise variables
|
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VIASH_DIRECTORY_MOUNTS=()
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# configure default docker automount prefix if it is unset
|
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if [ -z "${VIASH_DOCKER_AUTOMOUNT_PREFIX+x}" ]; then
|
|
VIASH_DOCKER_AUTOMOUNT_PREFIX="/viash_automount"
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fi
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|
|
|
# initialise docker variables
|
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VIASH_DOCKER_RUN_ARGS=(-i --rm)
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|
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# ViashHelp: Display helpful explanation about this executable
|
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function ViashHelp {
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echo "arriba main"
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echo ""
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|
echo "Detect gene fusions from RNA-Seq data"
|
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echo ""
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|
echo "Inputs:"
|
|
echo " -x, --bam"
|
|
echo " type: file, required parameter, file must exist"
|
|
echo " example: Aligned.out.bam"
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|
echo " File in SAM/BAM/CRAM format with main alignments as generated by STAR"
|
|
echo " (Aligned.out.sam). Arriba extracts candidate reads from this file."
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|
echo ""
|
|
echo " -a, --genome"
|
|
echo " type: file, required parameter, file must exist"
|
|
echo " example: assembly.fa"
|
|
echo " FastA file with genome sequence (assembly). The file may be"
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|
echo " gzip-compressed. An"
|
|
echo " index with the file extension .fai must exist only if CRAM files are"
|
|
echo " processed."
|
|
echo ""
|
|
echo " -g, --gene_annotation"
|
|
echo " type: file, required parameter, file must exist"
|
|
echo " example: annotation.gtf"
|
|
echo " GTF file with gene annotation. The file may be gzip-compressed."
|
|
echo ""
|
|
echo " -k, --known_fusions"
|
|
echo " type: file, file must exist"
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|
echo " example: known_fusions.tsv"
|
|
echo " File containing known/recurrent fusions. Some cancer entities are often"
|
|
echo " characterized by fusions between the same pair of genes. In order to"
|
|
echo " boost"
|
|
echo " sensitivity, a list of known fusions can be supplied using this"
|
|
echo " parameter. The list"
|
|
echo " must contain two columns with the names of the fused genes, separated by"
|
|
echo " tabs."
|
|
echo ""
|
|
echo " -b, --blacklist"
|
|
echo " type: file, file must exist"
|
|
echo " example: blacklist.tsv"
|
|
echo " File containing blacklisted events (recurrent artifacts and transcripts"
|
|
echo " observed in healthy tissue)."
|
|
echo ""
|
|
echo " -d, --structural_variants"
|
|
echo " type: file, file must exist"
|
|
echo " example: structural_variants_from_WGS.tsv"
|
|
echo " Tab-separated file with coordinates of structural variants found using"
|
|
echo " whole-genome sequencing data. These coordinates serve to increase"
|
|
echo " sensitivity"
|
|
echo " towards weakly expressed fusions and to eliminate fusions with low"
|
|
echo " evidence."
|
|
echo ""
|
|
echo " -t, --tags"
|
|
echo " type: file, file must exist"
|
|
echo " example: tags.tsv"
|
|
echo " Tab-separated file containing fusions to annotate with tags in the"
|
|
echo " 'tags' column."
|
|
echo " The first two columns specify the genes; the third column specifies the"
|
|
echo " tag. The"
|
|
echo " file may be gzip-compressed."
|
|
echo ""
|
|
echo " -p, --protein_domains"
|
|
echo " type: file, file must exist"
|
|
echo " example: protein_domains.gff3"
|
|
echo " File in GFF3 format containing coordinates of the protein domains of"
|
|
echo " genes. The"
|
|
echo " protein domains retained in a fusion are listed in the column"
|
|
echo " 'retained_protein_domains'. The file may be gzip-compressed."
|
|
echo ""
|
|
echo "Outputs:"
|
|
echo " -o, --fusions"
|
|
echo " type: file, required parameter, output, file must exist"
|
|
echo " example: fusions.tsv"
|
|
echo " Output file with fusions that have passed all filters."
|
|
echo ""
|
|
echo " -O, --fusions_discarded"
|
|
echo " type: file, output, file must exist"
|
|
echo " example: fusions.discarded.tsv"
|
|
echo " Output file with fusions that were discarded due to filtering."
|
|
echo ""
|
|
echo "Arguments:"
|
|
echo " -D, --max_genomic_breakpoint_distance"
|
|
echo " type: long"
|
|
echo " When a file with genomic breakpoints obtained via"
|
|
echo " whole-genome sequencing is supplied via the --structural_variants"
|
|
echo " parameter, this parameter determines how far a"
|
|
echo " genomic breakpoint may be away from a"
|
|
echo " transcriptomic breakpoint to consider it as a"
|
|
echo " related event. For events inside genes, the"
|
|
echo " distance is added to the end of the gene; for"
|
|
echo " intergenic events, the distance threshold is"
|
|
echo " applied as is. Default: 100000."
|
|
echo ""
|
|
echo " -s, --strandedness"
|
|
echo " type: string"
|
|
echo " choices: [ auto, yes, no, reverse ]"
|
|
echo " Whether a strand-specific protocol was used for library preparation,"
|
|
echo " and if so, the type of strandedness (auto/yes/no/reverse). When"
|
|
echo " unstranded data is processed, the strand can sometimes be inferred from"
|
|
echo " splice-patterns. But in unclear situations, stranded data helps"
|
|
echo " resolve ambiguities. Default: auto"
|
|
echo ""
|
|
echo " -i, --interesting_contigs"
|
|
echo " type: string, multiple values allowed"
|
|
echo " example: 1;2;AC_*;NC_*"
|
|
echo " List of interesting contigs. Fusions between genes"
|
|
echo " on other contigs are ignored. Contigs can be specified with or without"
|
|
echo " the"
|
|
echo " prefix \"chr\". Asterisks (*) are treated as wild-cards."
|
|
echo " Default: 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 X Y"
|
|
echo " AC_* NC_*"
|
|
echo ""
|
|
echo " -v, --viral_contigs"
|
|
echo " type: string, multiple values allowed"
|
|
echo " example: AC_*;NC_*"
|
|
echo " List of viral contigs. Asterisks (*) are treated as"
|
|
echo " wild-cards."
|
|
echo " Default: AC_* NC_*"
|
|
echo ""
|
|
echo " -f, --disable_filters"
|
|
echo " type: string, multiple values allowed"
|
|
echo " choices: [ homologs, low_entropy, isoforms, top_expressed_viral_contigs,"
|
|
echo "viral_contigs, uninteresting_contigs, non_coding_neighbors, mismatches,"
|
|
echo "duplicates, no_genomic_support, genomic_support, intronic, end_to_end,"
|
|
echo "relative_support, low_coverage_viral_contigs, merge_adjacent, mismappers,"
|
|
echo "multimappers, same_gene, long_gap, internal_tandem_duplication,"
|
|
echo "small_insert_size, read_through, inconsistently_clipped, intragenic_exonic,"
|
|
echo "marginal_read_through, spliced, hairpin, blacklist, min_support, select_best,"
|
|
echo "in_vitro, short_anchor, known_fusions, no_coverage, homopolymer, many_spliced ]"
|
|
echo " List of filters to disable. By default all filters are"
|
|
echo " enabled."
|
|
echo ""
|
|
echo " -E, --max_e_value"
|
|
echo " type: double"
|
|
echo " Arriba estimates the number of fusions with a given number of supporting"
|
|
echo " reads which one would expect to see by random chance. If the expected"
|
|
echo " number"
|
|
echo " of fusions (e-value) is higher than this threshold, the fusion is"
|
|
echo " discarded by the 'relative_support' filter. Note: Increasing this"
|
|
echo " threshold can dramatically increase the number of false positives and"
|
|
echo " may"
|
|
echo " increase the runtime of resource-intensive steps. Fractional values are"
|
|
echo " possible. Default: 0.300000"
|
|
echo ""
|
|
echo " -S, --min_supporting_reads"
|
|
echo " type: integer"
|
|
echo " example: 2"
|
|
echo " The 'min_support' filter discards all fusions with fewer than"
|
|
echo " this many supporting reads (split reads and discordant mates"
|
|
echo " combined). Default: 2"
|
|
echo ""
|
|
echo " -m, --max_mismappers"
|
|
echo " type: double"
|
|
echo " example: 0.8"
|
|
echo " When more than this fraction of supporting reads turns out to be"
|
|
echo " mismappers, the 'mismappers' filter discards the fusion. Default:"
|
|
echo " 0.800000"
|
|
echo ""
|
|
echo " -L, --max_homolog_identity"
|
|
echo " type: double"
|
|
echo " example: 0.3"
|
|
echo " Genes with more than the given fraction of sequence identity are"
|
|
echo " considered homologs and removed by the 'homologs' filter."
|
|
echo " Default: 0.300000"
|
|
echo ""
|
|
echo " -H, --homopolymer_length"
|
|
echo " type: integer"
|
|
echo " example: 6"
|
|
echo " The 'homopolymer' filter removes breakpoints adjacent to"
|
|
echo " homopolymers of the given length or more. Default: 6"
|
|
echo ""
|
|
echo " -R, --read_through_distance"
|
|
echo " type: integer"
|
|
echo " example: 10000"
|
|
echo " The 'read_through' filter removes read-through fusions"
|
|
echo " where the breakpoints are less than the given distance away"
|
|
echo " from each other. Default: 10000"
|
|
echo ""
|
|
echo " -A, --min_anchor_length"
|
|
echo " type: integer"
|
|
echo " example: 23"
|
|
echo " Alignment artifacts are often characterized by split reads coming"
|
|
echo " from only one gene and no discordant mates. Moreover, the split"
|
|
echo " reads only align to a short stretch in one of the genes. The"
|
|
echo " 'short_anchor' filter removes these fusions. This parameter sets"
|
|
echo " the threshold in bp for what the filter considers short. Default: 23"
|
|
echo ""
|
|
echo " -M, --many_spliced_events"
|
|
echo " type: integer"
|
|
echo " example: 4"
|
|
echo " The 'many_spliced' filter recovers fusions between genes that"
|
|
echo " have at least this many spliced breakpoints. Default: 4"
|
|
echo ""
|
|
echo " -K, --max_kmer_content"
|
|
echo " type: double"
|
|
echo " example: 0.6"
|
|
echo " The 'low_entropy' filter removes reads with repetitive 3-mers. If"
|
|
echo " the 3-mers make up more than the given fraction of the sequence, then"
|
|
echo " the read is discarded. Default: 0.600000"
|
|
echo ""
|
|
echo " -V, --max_mismatch_pvalue"
|
|
echo " type: double"
|
|
echo " example: 0.05"
|
|
echo " The 'mismatches' filter uses a binomial model to calculate a"
|
|
echo " p-value for observing a given number of mismatches in a read. If"
|
|
echo " the number of mismatches is too high, the read is discarded."
|
|
echo " Default: 0.010000"
|
|
echo ""
|
|
echo " -F, --fragment_length"
|
|
echo " type: integer"
|
|
echo " example: 200"
|
|
echo " When paired-end data is given, the fragment length is estimated"
|
|
echo " automatically and this parameter has no effect. But when single-end"
|
|
echo " data is given, the mean fragment length should be specified to"
|
|
echo " effectively filter fusions that arise from hairpin structures."
|
|
echo " Default: 200"
|
|
echo ""
|
|
echo " -U, --max_reads"
|
|
echo " type: integer"
|
|
echo " example: 300"
|
|
echo " Subsample fusions with more than the given number of supporting reads."
|
|
echo " This"
|
|
echo " improves performance without compromising sensitivity, as long as the"
|
|
echo " threshold is high. Counting of supporting reads beyond the threshold is"
|
|
echo " inaccurate, obviously. Default: 300"
|
|
echo ""
|
|
echo " -Q, --quantile"
|
|
echo " type: double"
|
|
echo " example: 0.998"
|
|
echo " Highly expressed genes are prone to produce artifacts during library"
|
|
echo " preparation. Genes with an expression above the given quantile are"
|
|
echo " eligible"
|
|
echo " for filtering by the 'in_vitro' filter. Default: 0.998000"
|
|
echo ""
|
|
echo " -e, --exonic_fraction"
|
|
echo " type: double"
|
|
echo " example: 0.33"
|
|
echo " The breakpoints of false-positive predictions of intragenic events"
|
|
echo " are often both in exons. True predictions are more likely to have at"
|
|
echo " least one breakpoint in an intron, because introns are larger. If the"
|
|
echo " fraction of exonic sequence between two breakpoints is smaller than"
|
|
echo " the given fraction, the 'intragenic_exonic' filter discards the"
|
|
echo " event. Default: 0.330000"
|
|
echo ""
|
|
echo " -T, --top_n"
|
|
echo " type: integer"
|
|
echo " example: 5"
|
|
echo " Only report viral integration sites of the top N most highly expressed"
|
|
echo " viral"
|
|
echo " contigs. Default: 5"
|
|
echo ""
|
|
echo " -C, --covered_fraction"
|
|
echo " type: double"
|
|
echo " example: 0.05"
|
|
echo " Ignore virally associated events if the virus is not fully"
|
|
echo " expressed, i.e., less than the given fraction of the viral contig is"
|
|
echo " transcribed. Default: 0.050000"
|
|
echo ""
|
|
echo " -l, --max_itd_length"
|
|
echo " type: integer"
|
|
echo " example: 100"
|
|
echo " Maximum length of internal tandem duplications. Note: Increasing"
|
|
echo " this value beyond the default can impair performance and lead to many"
|
|
echo " false positives. Default: 100"
|
|
echo ""
|
|
echo " -z, --min_itd_allele_fraction"
|
|
echo " type: double"
|
|
echo " example: 0.07"
|
|
echo " Required fraction of supporting reads to report an internal"
|
|
echo " tandem duplication. Default: 0.070000"
|
|
echo ""
|
|
echo " -Z, --min_itd_supporting_reads"
|
|
echo " type: integer"
|
|
echo " example: 10"
|
|
echo " Required absolute number of supporting reads to report an"
|
|
echo " internal tandem duplication. Default: 10"
|
|
echo ""
|
|
echo " -u, --skip_duplicate_marking"
|
|
echo " type: boolean_true"
|
|
echo " Instead of performing duplicate marking itself, Arriba relies on"
|
|
echo " duplicate marking by a"
|
|
echo " preceding program using the BAM_FDUP flag. This makes sense when unique"
|
|
echo " molecular"
|
|
echo " identifiers (UMI) are used."
|
|
echo ""
|
|
echo " -X, --extra_information"
|
|
echo " type: boolean_true"
|
|
echo " To reduce the runtime and file size, by default, the columns"
|
|
echo " 'fusion_transcript',"
|
|
echo " 'peptide_sequence', and 'read_identifiers' are left empty in the file"
|
|
echo " containing"
|
|
echo " discarded fusion candidates (see parameter -O). When this flag is set,"
|
|
echo " this extra"
|
|
echo " information is reported in the discarded fusions file."
|
|
echo ""
|
|
echo " -I, --fill_gaps"
|
|
echo " type: boolean_true"
|
|
echo " If assembly of the fusion transcript sequence from the supporting reads"
|
|
echo " is incomplete"
|
|
echo " (denoted as '...'), fill the gaps using the assembly sequence wherever"
|
|
echo " possible."
|
|
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 "$1")"
|
|
shift 1
|
|
;;
|
|
--version)
|
|
echo "arriba main"
|
|
exit
|
|
;;
|
|
--bam)
|
|
[ -n "$VIASH_PAR_BAM" ] && ViashError Bad arguments for option \'--bam\': \'$VIASH_PAR_BAM\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_BAM="$2"
|
|
[ $# -lt 2 ] && ViashError Not enough arguments passed to --bam. Use "--help" to get more information on the parameters. && exit 1
|
|
shift 2
|
|
;;
|
|
--bam=*)
|
|
[ -n "$VIASH_PAR_BAM" ] && ViashError Bad arguments for option \'--bam=*\': \'$VIASH_PAR_BAM\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_BAM=$(ViashRemoveFlags "$1")
|
|
shift 1
|
|
;;
|
|
-x)
|
|
[ -n "$VIASH_PAR_BAM" ] && ViashError Bad arguments for option \'-x\': \'$VIASH_PAR_BAM\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_BAM="$2"
|
|
[ $# -lt 2 ] && ViashError Not enough arguments passed to -x. Use "--help" to get more information on the parameters. && exit 1
|
|
shift 2
|
|
;;
|
|
--genome)
|
|
[ -n "$VIASH_PAR_GENOME" ] && ViashError Bad arguments for option \'--genome\': \'$VIASH_PAR_GENOME\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_GENOME="$2"
|
|
[ $# -lt 2 ] && ViashError Not enough arguments passed to --genome. Use "--help" to get more information on the parameters. && exit 1
|
|
shift 2
|
|
;;
|
|
--genome=*)
|
|
[ -n "$VIASH_PAR_GENOME" ] && ViashError Bad arguments for option \'--genome=*\': \'$VIASH_PAR_GENOME\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_GENOME=$(ViashRemoveFlags "$1")
|
|
shift 1
|
|
;;
|
|
-a)
|
|
[ -n "$VIASH_PAR_GENOME" ] && ViashError Bad arguments for option \'-a\': \'$VIASH_PAR_GENOME\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_GENOME="$2"
|
|
[ $# -lt 2 ] && ViashError Not enough arguments passed to -a. Use "--help" to get more information on the parameters. && exit 1
|
|
shift 2
|
|
;;
|
|
--gene_annotation)
|
|
[ -n "$VIASH_PAR_GENE_ANNOTATION" ] && ViashError Bad arguments for option \'--gene_annotation\': \'$VIASH_PAR_GENE_ANNOTATION\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_GENE_ANNOTATION="$2"
|
|
[ $# -lt 2 ] && ViashError Not enough arguments passed to --gene_annotation. Use "--help" to get more information on the parameters. && exit 1
|
|
shift 2
|
|
;;
|
|
--gene_annotation=*)
|
|
[ -n "$VIASH_PAR_GENE_ANNOTATION" ] && ViashError Bad arguments for option \'--gene_annotation=*\': \'$VIASH_PAR_GENE_ANNOTATION\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_GENE_ANNOTATION=$(ViashRemoveFlags "$1")
|
|
shift 1
|
|
;;
|
|
-g)
|
|
[ -n "$VIASH_PAR_GENE_ANNOTATION" ] && ViashError Bad arguments for option \'-g\': \'$VIASH_PAR_GENE_ANNOTATION\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_GENE_ANNOTATION="$2"
|
|
[ $# -lt 2 ] && ViashError Not enough arguments passed to -g. Use "--help" to get more information on the parameters. && exit 1
|
|
shift 2
|
|
;;
|
|
--known_fusions)
|
|
[ -n "$VIASH_PAR_KNOWN_FUSIONS" ] && ViashError Bad arguments for option \'--known_fusions\': \'$VIASH_PAR_KNOWN_FUSIONS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_KNOWN_FUSIONS="$2"
|
|
[ $# -lt 2 ] && ViashError Not enough arguments passed to --known_fusions. Use "--help" to get more information on the parameters. && exit 1
|
|
shift 2
|
|
;;
|
|
--known_fusions=*)
|
|
[ -n "$VIASH_PAR_KNOWN_FUSIONS" ] && ViashError Bad arguments for option \'--known_fusions=*\': \'$VIASH_PAR_KNOWN_FUSIONS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_KNOWN_FUSIONS=$(ViashRemoveFlags "$1")
|
|
shift 1
|
|
;;
|
|
-k)
|
|
[ -n "$VIASH_PAR_KNOWN_FUSIONS" ] && ViashError Bad arguments for option \'-k\': \'$VIASH_PAR_KNOWN_FUSIONS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_KNOWN_FUSIONS="$2"
|
|
[ $# -lt 2 ] && ViashError Not enough arguments passed to -k. Use "--help" to get more information on the parameters. && exit 1
|
|
shift 2
|
|
;;
|
|
--blacklist)
|
|
[ -n "$VIASH_PAR_BLACKLIST" ] && ViashError Bad arguments for option \'--blacklist\': \'$VIASH_PAR_BLACKLIST\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_BLACKLIST="$2"
|
|
[ $# -lt 2 ] && ViashError Not enough arguments passed to --blacklist. Use "--help" to get more information on the parameters. && exit 1
|
|
shift 2
|
|
;;
|
|
--blacklist=*)
|
|
[ -n "$VIASH_PAR_BLACKLIST" ] && ViashError Bad arguments for option \'--blacklist=*\': \'$VIASH_PAR_BLACKLIST\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_BLACKLIST=$(ViashRemoveFlags "$1")
|
|
shift 1
|
|
;;
|
|
-b)
|
|
[ -n "$VIASH_PAR_BLACKLIST" ] && ViashError Bad arguments for option \'-b\': \'$VIASH_PAR_BLACKLIST\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_BLACKLIST="$2"
|
|
[ $# -lt 2 ] && ViashError Not enough arguments passed to -b. Use "--help" to get more information on the parameters. && exit 1
|
|
shift 2
|
|
;;
|
|
--structural_variants)
|
|
[ -n "$VIASH_PAR_STRUCTURAL_VARIANTS" ] && ViashError Bad arguments for option \'--structural_variants\': \'$VIASH_PAR_STRUCTURAL_VARIANTS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_STRUCTURAL_VARIANTS="$2"
|
|
[ $# -lt 2 ] && ViashError Not enough arguments passed to --structural_variants. Use "--help" to get more information on the parameters. && exit 1
|
|
shift 2
|
|
;;
|
|
--structural_variants=*)
|
|
[ -n "$VIASH_PAR_STRUCTURAL_VARIANTS" ] && ViashError Bad arguments for option \'--structural_variants=*\': \'$VIASH_PAR_STRUCTURAL_VARIANTS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_STRUCTURAL_VARIANTS=$(ViashRemoveFlags "$1")
|
|
shift 1
|
|
;;
|
|
-d)
|
|
[ -n "$VIASH_PAR_STRUCTURAL_VARIANTS" ] && ViashError Bad arguments for option \'-d\': \'$VIASH_PAR_STRUCTURAL_VARIANTS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_STRUCTURAL_VARIANTS="$2"
|
|
[ $# -lt 2 ] && ViashError Not enough arguments passed to -d. Use "--help" to get more information on the parameters. && exit 1
|
|
shift 2
|
|
;;
|
|
--tags)
|
|
[ -n "$VIASH_PAR_TAGS" ] && ViashError Bad arguments for option \'--tags\': \'$VIASH_PAR_TAGS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_TAGS="$2"
|
|
[ $# -lt 2 ] && ViashError Not enough arguments passed to --tags. Use "--help" to get more information on the parameters. && exit 1
|
|
shift 2
|
|
;;
|
|
--tags=*)
|
|
[ -n "$VIASH_PAR_TAGS" ] && ViashError Bad arguments for option \'--tags=*\': \'$VIASH_PAR_TAGS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_TAGS=$(ViashRemoveFlags "$1")
|
|
shift 1
|
|
;;
|
|
-t)
|
|
[ -n "$VIASH_PAR_TAGS" ] && ViashError Bad arguments for option \'-t\': \'$VIASH_PAR_TAGS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_TAGS="$2"
|
|
[ $# -lt 2 ] && ViashError Not enough arguments passed to -t. Use "--help" to get more information on the parameters. && exit 1
|
|
shift 2
|
|
;;
|
|
--protein_domains)
|
|
[ -n "$VIASH_PAR_PROTEIN_DOMAINS" ] && ViashError Bad arguments for option \'--protein_domains\': \'$VIASH_PAR_PROTEIN_DOMAINS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_PROTEIN_DOMAINS="$2"
|
|
[ $# -lt 2 ] && ViashError Not enough arguments passed to --protein_domains. Use "--help" to get more information on the parameters. && exit 1
|
|
shift 2
|
|
;;
|
|
--protein_domains=*)
|
|
[ -n "$VIASH_PAR_PROTEIN_DOMAINS" ] && ViashError Bad arguments for option \'--protein_domains=*\': \'$VIASH_PAR_PROTEIN_DOMAINS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_PROTEIN_DOMAINS=$(ViashRemoveFlags "$1")
|
|
shift 1
|
|
;;
|
|
-p)
|
|
[ -n "$VIASH_PAR_PROTEIN_DOMAINS" ] && ViashError Bad arguments for option \'-p\': \'$VIASH_PAR_PROTEIN_DOMAINS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_PROTEIN_DOMAINS="$2"
|
|
[ $# -lt 2 ] && ViashError Not enough arguments passed to -p. Use "--help" to get more information on the parameters. && exit 1
|
|
shift 2
|
|
;;
|
|
--fusions)
|
|
[ -n "$VIASH_PAR_FUSIONS" ] && ViashError Bad arguments for option \'--fusions\': \'$VIASH_PAR_FUSIONS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_FUSIONS="$2"
|
|
[ $# -lt 2 ] && ViashError Not enough arguments passed to --fusions. Use "--help" to get more information on the parameters. && exit 1
|
|
shift 2
|
|
;;
|
|
--fusions=*)
|
|
[ -n "$VIASH_PAR_FUSIONS" ] && ViashError Bad arguments for option \'--fusions=*\': \'$VIASH_PAR_FUSIONS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_FUSIONS=$(ViashRemoveFlags "$1")
|
|
shift 1
|
|
;;
|
|
-o)
|
|
[ -n "$VIASH_PAR_FUSIONS" ] && ViashError Bad arguments for option \'-o\': \'$VIASH_PAR_FUSIONS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_FUSIONS="$2"
|
|
[ $# -lt 2 ] && ViashError Not enough arguments passed to -o. Use "--help" to get more information on the parameters. && exit 1
|
|
shift 2
|
|
;;
|
|
--fusions_discarded)
|
|
[ -n "$VIASH_PAR_FUSIONS_DISCARDED" ] && ViashError Bad arguments for option \'--fusions_discarded\': \'$VIASH_PAR_FUSIONS_DISCARDED\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_FUSIONS_DISCARDED="$2"
|
|
[ $# -lt 2 ] && ViashError Not enough arguments passed to --fusions_discarded. Use "--help" to get more information on the parameters. && exit 1
|
|
shift 2
|
|
;;
|
|
--fusions_discarded=*)
|
|
[ -n "$VIASH_PAR_FUSIONS_DISCARDED" ] && ViashError Bad arguments for option \'--fusions_discarded=*\': \'$VIASH_PAR_FUSIONS_DISCARDED\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_FUSIONS_DISCARDED=$(ViashRemoveFlags "$1")
|
|
shift 1
|
|
;;
|
|
-O)
|
|
[ -n "$VIASH_PAR_FUSIONS_DISCARDED" ] && ViashError Bad arguments for option \'-O\': \'$VIASH_PAR_FUSIONS_DISCARDED\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_FUSIONS_DISCARDED="$2"
|
|
[ $# -lt 2 ] && ViashError Not enough arguments passed to -O. Use "--help" to get more information on the parameters. && exit 1
|
|
shift 2
|
|
;;
|
|
--max_genomic_breakpoint_distance)
|
|
[ -n "$VIASH_PAR_MAX_GENOMIC_BREAKPOINT_DISTANCE" ] && ViashError Bad arguments for option \'--max_genomic_breakpoint_distance\': \'$VIASH_PAR_MAX_GENOMIC_BREAKPOINT_DISTANCE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_MAX_GENOMIC_BREAKPOINT_DISTANCE="$2"
|
|
[ $# -lt 2 ] && ViashError Not enough arguments passed to --max_genomic_breakpoint_distance. Use "--help" to get more information on the parameters. && exit 1
|
|
shift 2
|
|
;;
|
|
--max_genomic_breakpoint_distance=*)
|
|
[ -n "$VIASH_PAR_MAX_GENOMIC_BREAKPOINT_DISTANCE" ] && ViashError Bad arguments for option \'--max_genomic_breakpoint_distance=*\': \'$VIASH_PAR_MAX_GENOMIC_BREAKPOINT_DISTANCE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_MAX_GENOMIC_BREAKPOINT_DISTANCE=$(ViashRemoveFlags "$1")
|
|
shift 1
|
|
;;
|
|
-D)
|
|
[ -n "$VIASH_PAR_MAX_GENOMIC_BREAKPOINT_DISTANCE" ] && ViashError Bad arguments for option \'-D\': \'$VIASH_PAR_MAX_GENOMIC_BREAKPOINT_DISTANCE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_MAX_GENOMIC_BREAKPOINT_DISTANCE="$2"
|
|
[ $# -lt 2 ] && ViashError Not enough arguments passed to -D. Use "--help" to get more information on the parameters. && exit 1
|
|
shift 2
|
|
;;
|
|
--strandedness)
|
|
[ -n "$VIASH_PAR_STRANDEDNESS" ] && ViashError Bad arguments for option \'--strandedness\': \'$VIASH_PAR_STRANDEDNESS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_STRANDEDNESS="$2"
|
|
[ $# -lt 2 ] && ViashError Not enough arguments passed to --strandedness. Use "--help" to get more information on the parameters. && exit 1
|
|
shift 2
|
|
;;
|
|
--strandedness=*)
|
|
[ -n "$VIASH_PAR_STRANDEDNESS" ] && ViashError Bad arguments for option \'--strandedness=*\': \'$VIASH_PAR_STRANDEDNESS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_STRANDEDNESS=$(ViashRemoveFlags "$1")
|
|
shift 1
|
|
;;
|
|
-s)
|
|
[ -n "$VIASH_PAR_STRANDEDNESS" ] && ViashError Bad arguments for option \'-s\': \'$VIASH_PAR_STRANDEDNESS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_STRANDEDNESS="$2"
|
|
[ $# -lt 2 ] && ViashError Not enough arguments passed to -s. Use "--help" to get more information on the parameters. && exit 1
|
|
shift 2
|
|
;;
|
|
--interesting_contigs)
|
|
if [ -z "$VIASH_PAR_INTERESTING_CONTIGS" ]; then
|
|
VIASH_PAR_INTERESTING_CONTIGS="$2"
|
|
else
|
|
VIASH_PAR_INTERESTING_CONTIGS="$VIASH_PAR_INTERESTING_CONTIGS;""$2"
|
|
fi
|
|
[ $# -lt 2 ] && ViashError Not enough arguments passed to --interesting_contigs. Use "--help" to get more information on the parameters. && exit 1
|
|
shift 2
|
|
;;
|
|
--interesting_contigs=*)
|
|
if [ -z "$VIASH_PAR_INTERESTING_CONTIGS" ]; then
|
|
VIASH_PAR_INTERESTING_CONTIGS=$(ViashRemoveFlags "$1")
|
|
else
|
|
VIASH_PAR_INTERESTING_CONTIGS="$VIASH_PAR_INTERESTING_CONTIGS;"$(ViashRemoveFlags "$1")
|
|
fi
|
|
shift 1
|
|
;;
|
|
-i)
|
|
if [ -z "$VIASH_PAR_INTERESTING_CONTIGS" ]; then
|
|
VIASH_PAR_INTERESTING_CONTIGS="$2"
|
|
else
|
|
VIASH_PAR_INTERESTING_CONTIGS="$VIASH_PAR_INTERESTING_CONTIGS;""$2"
|
|
fi
|
|
[ $# -lt 2 ] && ViashError Not enough arguments passed to -i. Use "--help" to get more information on the parameters. && exit 1
|
|
shift 2
|
|
;;
|
|
--viral_contigs)
|
|
if [ -z "$VIASH_PAR_VIRAL_CONTIGS" ]; then
|
|
VIASH_PAR_VIRAL_CONTIGS="$2"
|
|
else
|
|
VIASH_PAR_VIRAL_CONTIGS="$VIASH_PAR_VIRAL_CONTIGS;""$2"
|
|
fi
|
|
[ $# -lt 2 ] && ViashError Not enough arguments passed to --viral_contigs. Use "--help" to get more information on the parameters. && exit 1
|
|
shift 2
|
|
;;
|
|
--viral_contigs=*)
|
|
if [ -z "$VIASH_PAR_VIRAL_CONTIGS" ]; then
|
|
VIASH_PAR_VIRAL_CONTIGS=$(ViashRemoveFlags "$1")
|
|
else
|
|
VIASH_PAR_VIRAL_CONTIGS="$VIASH_PAR_VIRAL_CONTIGS;"$(ViashRemoveFlags "$1")
|
|
fi
|
|
shift 1
|
|
;;
|
|
-v)
|
|
if [ -z "$VIASH_PAR_VIRAL_CONTIGS" ]; then
|
|
VIASH_PAR_VIRAL_CONTIGS="$2"
|
|
else
|
|
VIASH_PAR_VIRAL_CONTIGS="$VIASH_PAR_VIRAL_CONTIGS;""$2"
|
|
fi
|
|
[ $# -lt 2 ] && ViashError Not enough arguments passed to -v. Use "--help" to get more information on the parameters. && exit 1
|
|
shift 2
|
|
;;
|
|
--disable_filters)
|
|
if [ -z "$VIASH_PAR_DISABLE_FILTERS" ]; then
|
|
VIASH_PAR_DISABLE_FILTERS="$2"
|
|
else
|
|
VIASH_PAR_DISABLE_FILTERS="$VIASH_PAR_DISABLE_FILTERS;""$2"
|
|
fi
|
|
[ $# -lt 2 ] && ViashError Not enough arguments passed to --disable_filters. Use "--help" to get more information on the parameters. && exit 1
|
|
shift 2
|
|
;;
|
|
--disable_filters=*)
|
|
if [ -z "$VIASH_PAR_DISABLE_FILTERS" ]; then
|
|
VIASH_PAR_DISABLE_FILTERS=$(ViashRemoveFlags "$1")
|
|
else
|
|
VIASH_PAR_DISABLE_FILTERS="$VIASH_PAR_DISABLE_FILTERS;"$(ViashRemoveFlags "$1")
|
|
fi
|
|
shift 1
|
|
;;
|
|
-f)
|
|
if [ -z "$VIASH_PAR_DISABLE_FILTERS" ]; then
|
|
VIASH_PAR_DISABLE_FILTERS="$2"
|
|
else
|
|
VIASH_PAR_DISABLE_FILTERS="$VIASH_PAR_DISABLE_FILTERS;""$2"
|
|
fi
|
|
[ $# -lt 2 ] && ViashError Not enough arguments passed to -f. Use "--help" to get more information on the parameters. && exit 1
|
|
shift 2
|
|
;;
|
|
--max_e_value)
|
|
[ -n "$VIASH_PAR_MAX_E_VALUE" ] && ViashError Bad arguments for option \'--max_e_value\': \'$VIASH_PAR_MAX_E_VALUE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_MAX_E_VALUE="$2"
|
|
[ $# -lt 2 ] && ViashError Not enough arguments passed to --max_e_value. Use "--help" to get more information on the parameters. && exit 1
|
|
shift 2
|
|
;;
|
|
--max_e_value=*)
|
|
[ -n "$VIASH_PAR_MAX_E_VALUE" ] && ViashError Bad arguments for option \'--max_e_value=*\': \'$VIASH_PAR_MAX_E_VALUE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_MAX_E_VALUE=$(ViashRemoveFlags "$1")
|
|
shift 1
|
|
;;
|
|
-E)
|
|
[ -n "$VIASH_PAR_MAX_E_VALUE" ] && ViashError Bad arguments for option \'-E\': \'$VIASH_PAR_MAX_E_VALUE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_MAX_E_VALUE="$2"
|
|
[ $# -lt 2 ] && ViashError Not enough arguments passed to -E. Use "--help" to get more information on the parameters. && exit 1
|
|
shift 2
|
|
;;
|
|
--min_supporting_reads)
|
|
[ -n "$VIASH_PAR_MIN_SUPPORTING_READS" ] && ViashError Bad arguments for option \'--min_supporting_reads\': \'$VIASH_PAR_MIN_SUPPORTING_READS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_MIN_SUPPORTING_READS="$2"
|
|
[ $# -lt 2 ] && ViashError Not enough arguments passed to --min_supporting_reads. Use "--help" to get more information on the parameters. && exit 1
|
|
shift 2
|
|
;;
|
|
--min_supporting_reads=*)
|
|
[ -n "$VIASH_PAR_MIN_SUPPORTING_READS" ] && ViashError Bad arguments for option \'--min_supporting_reads=*\': \'$VIASH_PAR_MIN_SUPPORTING_READS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_MIN_SUPPORTING_READS=$(ViashRemoveFlags "$1")
|
|
shift 1
|
|
;;
|
|
-S)
|
|
[ -n "$VIASH_PAR_MIN_SUPPORTING_READS" ] && ViashError Bad arguments for option \'-S\': \'$VIASH_PAR_MIN_SUPPORTING_READS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_MIN_SUPPORTING_READS="$2"
|
|
[ $# -lt 2 ] && ViashError Not enough arguments passed to -S. Use "--help" to get more information on the parameters. && exit 1
|
|
shift 2
|
|
;;
|
|
--max_mismappers)
|
|
[ -n "$VIASH_PAR_MAX_MISMAPPERS" ] && ViashError Bad arguments for option \'--max_mismappers\': \'$VIASH_PAR_MAX_MISMAPPERS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_MAX_MISMAPPERS="$2"
|
|
[ $# -lt 2 ] && ViashError Not enough arguments passed to --max_mismappers. Use "--help" to get more information on the parameters. && exit 1
|
|
shift 2
|
|
;;
|
|
--max_mismappers=*)
|
|
[ -n "$VIASH_PAR_MAX_MISMAPPERS" ] && ViashError Bad arguments for option \'--max_mismappers=*\': \'$VIASH_PAR_MAX_MISMAPPERS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_MAX_MISMAPPERS=$(ViashRemoveFlags "$1")
|
|
shift 1
|
|
;;
|
|
-m)
|
|
[ -n "$VIASH_PAR_MAX_MISMAPPERS" ] && ViashError Bad arguments for option \'-m\': \'$VIASH_PAR_MAX_MISMAPPERS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_MAX_MISMAPPERS="$2"
|
|
[ $# -lt 2 ] && ViashError Not enough arguments passed to -m. Use "--help" to get more information on the parameters. && exit 1
|
|
shift 2
|
|
;;
|
|
--max_homolog_identity)
|
|
[ -n "$VIASH_PAR_MAX_HOMOLOG_IDENTITY" ] && ViashError Bad arguments for option \'--max_homolog_identity\': \'$VIASH_PAR_MAX_HOMOLOG_IDENTITY\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_MAX_HOMOLOG_IDENTITY="$2"
|
|
[ $# -lt 2 ] && ViashError Not enough arguments passed to --max_homolog_identity. Use "--help" to get more information on the parameters. && exit 1
|
|
shift 2
|
|
;;
|
|
--max_homolog_identity=*)
|
|
[ -n "$VIASH_PAR_MAX_HOMOLOG_IDENTITY" ] && ViashError Bad arguments for option \'--max_homolog_identity=*\': \'$VIASH_PAR_MAX_HOMOLOG_IDENTITY\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_MAX_HOMOLOG_IDENTITY=$(ViashRemoveFlags "$1")
|
|
shift 1
|
|
;;
|
|
-L)
|
|
[ -n "$VIASH_PAR_MAX_HOMOLOG_IDENTITY" ] && ViashError Bad arguments for option \'-L\': \'$VIASH_PAR_MAX_HOMOLOG_IDENTITY\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_MAX_HOMOLOG_IDENTITY="$2"
|
|
[ $# -lt 2 ] && ViashError Not enough arguments passed to -L. Use "--help" to get more information on the parameters. && exit 1
|
|
shift 2
|
|
;;
|
|
--homopolymer_length)
|
|
[ -n "$VIASH_PAR_HOMOPOLYMER_LENGTH" ] && ViashError Bad arguments for option \'--homopolymer_length\': \'$VIASH_PAR_HOMOPOLYMER_LENGTH\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_HOMOPOLYMER_LENGTH="$2"
|
|
[ $# -lt 2 ] && ViashError Not enough arguments passed to --homopolymer_length. Use "--help" to get more information on the parameters. && exit 1
|
|
shift 2
|
|
;;
|
|
--homopolymer_length=*)
|
|
[ -n "$VIASH_PAR_HOMOPOLYMER_LENGTH" ] && ViashError Bad arguments for option \'--homopolymer_length=*\': \'$VIASH_PAR_HOMOPOLYMER_LENGTH\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_HOMOPOLYMER_LENGTH=$(ViashRemoveFlags "$1")
|
|
shift 1
|
|
;;
|
|
-H)
|
|
[ -n "$VIASH_PAR_HOMOPOLYMER_LENGTH" ] && ViashError Bad arguments for option \'-H\': \'$VIASH_PAR_HOMOPOLYMER_LENGTH\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_HOMOPOLYMER_LENGTH="$2"
|
|
[ $# -lt 2 ] && ViashError Not enough arguments passed to -H. Use "--help" to get more information on the parameters. && exit 1
|
|
shift 2
|
|
;;
|
|
--read_through_distance)
|
|
[ -n "$VIASH_PAR_READ_THROUGH_DISTANCE" ] && ViashError Bad arguments for option \'--read_through_distance\': \'$VIASH_PAR_READ_THROUGH_DISTANCE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_READ_THROUGH_DISTANCE="$2"
|
|
[ $# -lt 2 ] && ViashError Not enough arguments passed to --read_through_distance. Use "--help" to get more information on the parameters. && exit 1
|
|
shift 2
|
|
;;
|
|
--read_through_distance=*)
|
|
[ -n "$VIASH_PAR_READ_THROUGH_DISTANCE" ] && ViashError Bad arguments for option \'--read_through_distance=*\': \'$VIASH_PAR_READ_THROUGH_DISTANCE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_READ_THROUGH_DISTANCE=$(ViashRemoveFlags "$1")
|
|
shift 1
|
|
;;
|
|
-R)
|
|
[ -n "$VIASH_PAR_READ_THROUGH_DISTANCE" ] && ViashError Bad arguments for option \'-R\': \'$VIASH_PAR_READ_THROUGH_DISTANCE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_READ_THROUGH_DISTANCE="$2"
|
|
[ $# -lt 2 ] && ViashError Not enough arguments passed to -R. Use "--help" to get more information on the parameters. && exit 1
|
|
shift 2
|
|
;;
|
|
--min_anchor_length)
|
|
[ -n "$VIASH_PAR_MIN_ANCHOR_LENGTH" ] && ViashError Bad arguments for option \'--min_anchor_length\': \'$VIASH_PAR_MIN_ANCHOR_LENGTH\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_MIN_ANCHOR_LENGTH="$2"
|
|
[ $# -lt 2 ] && ViashError Not enough arguments passed to --min_anchor_length. Use "--help" to get more information on the parameters. && exit 1
|
|
shift 2
|
|
;;
|
|
--min_anchor_length=*)
|
|
[ -n "$VIASH_PAR_MIN_ANCHOR_LENGTH" ] && ViashError Bad arguments for option \'--min_anchor_length=*\': \'$VIASH_PAR_MIN_ANCHOR_LENGTH\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_MIN_ANCHOR_LENGTH=$(ViashRemoveFlags "$1")
|
|
shift 1
|
|
;;
|
|
-A)
|
|
[ -n "$VIASH_PAR_MIN_ANCHOR_LENGTH" ] && ViashError Bad arguments for option \'-A\': \'$VIASH_PAR_MIN_ANCHOR_LENGTH\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_MIN_ANCHOR_LENGTH="$2"
|
|
[ $# -lt 2 ] && ViashError Not enough arguments passed to -A. Use "--help" to get more information on the parameters. && exit 1
|
|
shift 2
|
|
;;
|
|
--many_spliced_events)
|
|
[ -n "$VIASH_PAR_MANY_SPLICED_EVENTS" ] && ViashError Bad arguments for option \'--many_spliced_events\': \'$VIASH_PAR_MANY_SPLICED_EVENTS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_MANY_SPLICED_EVENTS="$2"
|
|
[ $# -lt 2 ] && ViashError Not enough arguments passed to --many_spliced_events. Use "--help" to get more information on the parameters. && exit 1
|
|
shift 2
|
|
;;
|
|
--many_spliced_events=*)
|
|
[ -n "$VIASH_PAR_MANY_SPLICED_EVENTS" ] && ViashError Bad arguments for option \'--many_spliced_events=*\': \'$VIASH_PAR_MANY_SPLICED_EVENTS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_MANY_SPLICED_EVENTS=$(ViashRemoveFlags "$1")
|
|
shift 1
|
|
;;
|
|
-M)
|
|
[ -n "$VIASH_PAR_MANY_SPLICED_EVENTS" ] && ViashError Bad arguments for option \'-M\': \'$VIASH_PAR_MANY_SPLICED_EVENTS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_MANY_SPLICED_EVENTS="$2"
|
|
[ $# -lt 2 ] && ViashError Not enough arguments passed to -M. Use "--help" to get more information on the parameters. && exit 1
|
|
shift 2
|
|
;;
|
|
--max_kmer_content)
|
|
[ -n "$VIASH_PAR_MAX_KMER_CONTENT" ] && ViashError Bad arguments for option \'--max_kmer_content\': \'$VIASH_PAR_MAX_KMER_CONTENT\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_MAX_KMER_CONTENT="$2"
|
|
[ $# -lt 2 ] && ViashError Not enough arguments passed to --max_kmer_content. Use "--help" to get more information on the parameters. && exit 1
|
|
shift 2
|
|
;;
|
|
--max_kmer_content=*)
|
|
[ -n "$VIASH_PAR_MAX_KMER_CONTENT" ] && ViashError Bad arguments for option \'--max_kmer_content=*\': \'$VIASH_PAR_MAX_KMER_CONTENT\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_MAX_KMER_CONTENT=$(ViashRemoveFlags "$1")
|
|
shift 1
|
|
;;
|
|
-K)
|
|
[ -n "$VIASH_PAR_MAX_KMER_CONTENT" ] && ViashError Bad arguments for option \'-K\': \'$VIASH_PAR_MAX_KMER_CONTENT\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_MAX_KMER_CONTENT="$2"
|
|
[ $# -lt 2 ] && ViashError Not enough arguments passed to -K. Use "--help" to get more information on the parameters. && exit 1
|
|
shift 2
|
|
;;
|
|
--max_mismatch_pvalue)
|
|
[ -n "$VIASH_PAR_MAX_MISMATCH_PVALUE" ] && ViashError Bad arguments for option \'--max_mismatch_pvalue\': \'$VIASH_PAR_MAX_MISMATCH_PVALUE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_MAX_MISMATCH_PVALUE="$2"
|
|
[ $# -lt 2 ] && ViashError Not enough arguments passed to --max_mismatch_pvalue. Use "--help" to get more information on the parameters. && exit 1
|
|
shift 2
|
|
;;
|
|
--max_mismatch_pvalue=*)
|
|
[ -n "$VIASH_PAR_MAX_MISMATCH_PVALUE" ] && ViashError Bad arguments for option \'--max_mismatch_pvalue=*\': \'$VIASH_PAR_MAX_MISMATCH_PVALUE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_MAX_MISMATCH_PVALUE=$(ViashRemoveFlags "$1")
|
|
shift 1
|
|
;;
|
|
-V)
|
|
[ -n "$VIASH_PAR_MAX_MISMATCH_PVALUE" ] && ViashError Bad arguments for option \'-V\': \'$VIASH_PAR_MAX_MISMATCH_PVALUE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_MAX_MISMATCH_PVALUE="$2"
|
|
[ $# -lt 2 ] && ViashError Not enough arguments passed to -V. Use "--help" to get more information on the parameters. && exit 1
|
|
shift 2
|
|
;;
|
|
--fragment_length)
|
|
[ -n "$VIASH_PAR_FRAGMENT_LENGTH" ] && ViashError Bad arguments for option \'--fragment_length\': \'$VIASH_PAR_FRAGMENT_LENGTH\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_FRAGMENT_LENGTH="$2"
|
|
[ $# -lt 2 ] && ViashError Not enough arguments passed to --fragment_length. Use "--help" to get more information on the parameters. && exit 1
|
|
shift 2
|
|
;;
|
|
--fragment_length=*)
|
|
[ -n "$VIASH_PAR_FRAGMENT_LENGTH" ] && ViashError Bad arguments for option \'--fragment_length=*\': \'$VIASH_PAR_FRAGMENT_LENGTH\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_FRAGMENT_LENGTH=$(ViashRemoveFlags "$1")
|
|
shift 1
|
|
;;
|
|
-F)
|
|
[ -n "$VIASH_PAR_FRAGMENT_LENGTH" ] && ViashError Bad arguments for option \'-F\': \'$VIASH_PAR_FRAGMENT_LENGTH\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_FRAGMENT_LENGTH="$2"
|
|
[ $# -lt 2 ] && ViashError Not enough arguments passed to -F. Use "--help" to get more information on the parameters. && exit 1
|
|
shift 2
|
|
;;
|
|
--max_reads)
|
|
[ -n "$VIASH_PAR_MAX_READS" ] && ViashError Bad arguments for option \'--max_reads\': \'$VIASH_PAR_MAX_READS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_MAX_READS="$2"
|
|
[ $# -lt 2 ] && ViashError Not enough arguments passed to --max_reads. Use "--help" to get more information on the parameters. && exit 1
|
|
shift 2
|
|
;;
|
|
--max_reads=*)
|
|
[ -n "$VIASH_PAR_MAX_READS" ] && ViashError Bad arguments for option \'--max_reads=*\': \'$VIASH_PAR_MAX_READS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_MAX_READS=$(ViashRemoveFlags "$1")
|
|
shift 1
|
|
;;
|
|
-U)
|
|
[ -n "$VIASH_PAR_MAX_READS" ] && ViashError Bad arguments for option \'-U\': \'$VIASH_PAR_MAX_READS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_MAX_READS="$2"
|
|
[ $# -lt 2 ] && ViashError Not enough arguments passed to -U. Use "--help" to get more information on the parameters. && exit 1
|
|
shift 2
|
|
;;
|
|
--quantile)
|
|
[ -n "$VIASH_PAR_QUANTILE" ] && ViashError Bad arguments for option \'--quantile\': \'$VIASH_PAR_QUANTILE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_QUANTILE="$2"
|
|
[ $# -lt 2 ] && ViashError Not enough arguments passed to --quantile. Use "--help" to get more information on the parameters. && exit 1
|
|
shift 2
|
|
;;
|
|
--quantile=*)
|
|
[ -n "$VIASH_PAR_QUANTILE" ] && ViashError Bad arguments for option \'--quantile=*\': \'$VIASH_PAR_QUANTILE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_QUANTILE=$(ViashRemoveFlags "$1")
|
|
shift 1
|
|
;;
|
|
-Q)
|
|
[ -n "$VIASH_PAR_QUANTILE" ] && ViashError Bad arguments for option \'-Q\': \'$VIASH_PAR_QUANTILE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_QUANTILE="$2"
|
|
[ $# -lt 2 ] && ViashError Not enough arguments passed to -Q. Use "--help" to get more information on the parameters. && exit 1
|
|
shift 2
|
|
;;
|
|
--exonic_fraction)
|
|
[ -n "$VIASH_PAR_EXONIC_FRACTION" ] && ViashError Bad arguments for option \'--exonic_fraction\': \'$VIASH_PAR_EXONIC_FRACTION\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_EXONIC_FRACTION="$2"
|
|
[ $# -lt 2 ] && ViashError Not enough arguments passed to --exonic_fraction. Use "--help" to get more information on the parameters. && exit 1
|
|
shift 2
|
|
;;
|
|
--exonic_fraction=*)
|
|
[ -n "$VIASH_PAR_EXONIC_FRACTION" ] && ViashError Bad arguments for option \'--exonic_fraction=*\': \'$VIASH_PAR_EXONIC_FRACTION\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_EXONIC_FRACTION=$(ViashRemoveFlags "$1")
|
|
shift 1
|
|
;;
|
|
-e)
|
|
[ -n "$VIASH_PAR_EXONIC_FRACTION" ] && ViashError Bad arguments for option \'-e\': \'$VIASH_PAR_EXONIC_FRACTION\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_EXONIC_FRACTION="$2"
|
|
[ $# -lt 2 ] && ViashError Not enough arguments passed to -e. Use "--help" to get more information on the parameters. && exit 1
|
|
shift 2
|
|
;;
|
|
--top_n)
|
|
[ -n "$VIASH_PAR_TOP_N" ] && ViashError Bad arguments for option \'--top_n\': \'$VIASH_PAR_TOP_N\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_TOP_N="$2"
|
|
[ $# -lt 2 ] && ViashError Not enough arguments passed to --top_n. Use "--help" to get more information on the parameters. && exit 1
|
|
shift 2
|
|
;;
|
|
--top_n=*)
|
|
[ -n "$VIASH_PAR_TOP_N" ] && ViashError Bad arguments for option \'--top_n=*\': \'$VIASH_PAR_TOP_N\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_TOP_N=$(ViashRemoveFlags "$1")
|
|
shift 1
|
|
;;
|
|
-T)
|
|
[ -n "$VIASH_PAR_TOP_N" ] && ViashError Bad arguments for option \'-T\': \'$VIASH_PAR_TOP_N\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_TOP_N="$2"
|
|
[ $# -lt 2 ] && ViashError Not enough arguments passed to -T. Use "--help" to get more information on the parameters. && exit 1
|
|
shift 2
|
|
;;
|
|
--covered_fraction)
|
|
[ -n "$VIASH_PAR_COVERED_FRACTION" ] && ViashError Bad arguments for option \'--covered_fraction\': \'$VIASH_PAR_COVERED_FRACTION\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_COVERED_FRACTION="$2"
|
|
[ $# -lt 2 ] && ViashError Not enough arguments passed to --covered_fraction. Use "--help" to get more information on the parameters. && exit 1
|
|
shift 2
|
|
;;
|
|
--covered_fraction=*)
|
|
[ -n "$VIASH_PAR_COVERED_FRACTION" ] && ViashError Bad arguments for option \'--covered_fraction=*\': \'$VIASH_PAR_COVERED_FRACTION\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_COVERED_FRACTION=$(ViashRemoveFlags "$1")
|
|
shift 1
|
|
;;
|
|
-C)
|
|
[ -n "$VIASH_PAR_COVERED_FRACTION" ] && ViashError Bad arguments for option \'-C\': \'$VIASH_PAR_COVERED_FRACTION\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_COVERED_FRACTION="$2"
|
|
[ $# -lt 2 ] && ViashError Not enough arguments passed to -C. Use "--help" to get more information on the parameters. && exit 1
|
|
shift 2
|
|
;;
|
|
--max_itd_length)
|
|
[ -n "$VIASH_PAR_MAX_ITD_LENGTH" ] && ViashError Bad arguments for option \'--max_itd_length\': \'$VIASH_PAR_MAX_ITD_LENGTH\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_MAX_ITD_LENGTH="$2"
|
|
[ $# -lt 2 ] && ViashError Not enough arguments passed to --max_itd_length. Use "--help" to get more information on the parameters. && exit 1
|
|
shift 2
|
|
;;
|
|
--max_itd_length=*)
|
|
[ -n "$VIASH_PAR_MAX_ITD_LENGTH" ] && ViashError Bad arguments for option \'--max_itd_length=*\': \'$VIASH_PAR_MAX_ITD_LENGTH\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_MAX_ITD_LENGTH=$(ViashRemoveFlags "$1")
|
|
shift 1
|
|
;;
|
|
-l)
|
|
[ -n "$VIASH_PAR_MAX_ITD_LENGTH" ] && ViashError Bad arguments for option \'-l\': \'$VIASH_PAR_MAX_ITD_LENGTH\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_MAX_ITD_LENGTH="$2"
|
|
[ $# -lt 2 ] && ViashError Not enough arguments passed to -l. Use "--help" to get more information on the parameters. && exit 1
|
|
shift 2
|
|
;;
|
|
--min_itd_allele_fraction)
|
|
[ -n "$VIASH_PAR_MIN_ITD_ALLELE_FRACTION" ] && ViashError Bad arguments for option \'--min_itd_allele_fraction\': \'$VIASH_PAR_MIN_ITD_ALLELE_FRACTION\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_MIN_ITD_ALLELE_FRACTION="$2"
|
|
[ $# -lt 2 ] && ViashError Not enough arguments passed to --min_itd_allele_fraction. Use "--help" to get more information on the parameters. && exit 1
|
|
shift 2
|
|
;;
|
|
--min_itd_allele_fraction=*)
|
|
[ -n "$VIASH_PAR_MIN_ITD_ALLELE_FRACTION" ] && ViashError Bad arguments for option \'--min_itd_allele_fraction=*\': \'$VIASH_PAR_MIN_ITD_ALLELE_FRACTION\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_MIN_ITD_ALLELE_FRACTION=$(ViashRemoveFlags "$1")
|
|
shift 1
|
|
;;
|
|
-z)
|
|
[ -n "$VIASH_PAR_MIN_ITD_ALLELE_FRACTION" ] && ViashError Bad arguments for option \'-z\': \'$VIASH_PAR_MIN_ITD_ALLELE_FRACTION\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_MIN_ITD_ALLELE_FRACTION="$2"
|
|
[ $# -lt 2 ] && ViashError Not enough arguments passed to -z. Use "--help" to get more information on the parameters. && exit 1
|
|
shift 2
|
|
;;
|
|
--min_itd_supporting_reads)
|
|
[ -n "$VIASH_PAR_MIN_ITD_SUPPORTING_READS" ] && ViashError Bad arguments for option \'--min_itd_supporting_reads\': \'$VIASH_PAR_MIN_ITD_SUPPORTING_READS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_MIN_ITD_SUPPORTING_READS="$2"
|
|
[ $# -lt 2 ] && ViashError Not enough arguments passed to --min_itd_supporting_reads. Use "--help" to get more information on the parameters. && exit 1
|
|
shift 2
|
|
;;
|
|
--min_itd_supporting_reads=*)
|
|
[ -n "$VIASH_PAR_MIN_ITD_SUPPORTING_READS" ] && ViashError Bad arguments for option \'--min_itd_supporting_reads=*\': \'$VIASH_PAR_MIN_ITD_SUPPORTING_READS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_MIN_ITD_SUPPORTING_READS=$(ViashRemoveFlags "$1")
|
|
shift 1
|
|
;;
|
|
-Z)
|
|
[ -n "$VIASH_PAR_MIN_ITD_SUPPORTING_READS" ] && ViashError Bad arguments for option \'-Z\': \'$VIASH_PAR_MIN_ITD_SUPPORTING_READS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_MIN_ITD_SUPPORTING_READS="$2"
|
|
[ $# -lt 2 ] && ViashError Not enough arguments passed to -Z. Use "--help" to get more information on the parameters. && exit 1
|
|
shift 2
|
|
;;
|
|
--skip_duplicate_marking)
|
|
[ -n "$VIASH_PAR_SKIP_DUPLICATE_MARKING" ] && ViashError Bad arguments for option \'--skip_duplicate_marking\': \'$VIASH_PAR_SKIP_DUPLICATE_MARKING\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_SKIP_DUPLICATE_MARKING=true
|
|
shift 1
|
|
;;
|
|
-u)
|
|
[ -n "$VIASH_PAR_SKIP_DUPLICATE_MARKING" ] && ViashError Bad arguments for option \'-u\': \'$VIASH_PAR_SKIP_DUPLICATE_MARKING\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_SKIP_DUPLICATE_MARKING=true
|
|
shift 1
|
|
;;
|
|
--extra_information)
|
|
[ -n "$VIASH_PAR_EXTRA_INFORMATION" ] && ViashError Bad arguments for option \'--extra_information\': \'$VIASH_PAR_EXTRA_INFORMATION\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_EXTRA_INFORMATION=true
|
|
shift 1
|
|
;;
|
|
-X)
|
|
[ -n "$VIASH_PAR_EXTRA_INFORMATION" ] && ViashError Bad arguments for option \'-X\': \'$VIASH_PAR_EXTRA_INFORMATION\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_EXTRA_INFORMATION=true
|
|
shift 1
|
|
;;
|
|
--fill_gaps)
|
|
[ -n "$VIASH_PAR_FILL_GAPS" ] && ViashError Bad arguments for option \'--fill_gaps\': \'$VIASH_PAR_FILL_GAPS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_FILL_GAPS=true
|
|
shift 1
|
|
;;
|
|
-I)
|
|
[ -n "$VIASH_PAR_FILL_GAPS" ] && ViashError Bad arguments for option \'-I\': \'$VIASH_PAR_FILL_GAPS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_FILL_GAPS=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/arriba: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
|
|
if [ -z ${VIASH_META_CPUS+x} ]; then
|
|
VIASH_META_CPUS="1"
|
|
fi
|
|
|
|
# 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_BAM+x} ]; then
|
|
ViashError '--bam' is a required argument. Use "--help" to get more information on the parameters.
|
|
exit 1
|
|
fi
|
|
if [ -z ${VIASH_PAR_GENOME+x} ]; then
|
|
ViashError '--genome' is a required argument. Use "--help" to get more information on the parameters.
|
|
exit 1
|
|
fi
|
|
if [ -z ${VIASH_PAR_GENE_ANNOTATION+x} ]; then
|
|
ViashError '--gene_annotation' is a required argument. Use "--help" to get more information on the parameters.
|
|
exit 1
|
|
fi
|
|
if [ -z ${VIASH_PAR_FUSIONS+x} ]; then
|
|
ViashError '--fusions' 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_SKIP_DUPLICATE_MARKING+x} ]; then
|
|
VIASH_PAR_SKIP_DUPLICATE_MARKING="false"
|
|
fi
|
|
if [ -z ${VIASH_PAR_EXTRA_INFORMATION+x} ]; then
|
|
VIASH_PAR_EXTRA_INFORMATION="false"
|
|
fi
|
|
if [ -z ${VIASH_PAR_FILL_GAPS+x} ]; then
|
|
VIASH_PAR_FILL_GAPS="false"
|
|
fi
|
|
|
|
# check whether required files exist
|
|
if [ ! -z "$VIASH_PAR_BAM" ] && [ ! -e "$VIASH_PAR_BAM" ]; then
|
|
ViashError "Input file '$VIASH_PAR_BAM' does not exist."
|
|
exit 1
|
|
fi
|
|
if [ ! -z "$VIASH_PAR_GENOME" ] && [ ! -e "$VIASH_PAR_GENOME" ]; then
|
|
ViashError "Input file '$VIASH_PAR_GENOME' does not exist."
|
|
exit 1
|
|
fi
|
|
if [ ! -z "$VIASH_PAR_GENE_ANNOTATION" ] && [ ! -e "$VIASH_PAR_GENE_ANNOTATION" ]; then
|
|
ViashError "Input file '$VIASH_PAR_GENE_ANNOTATION' does not exist."
|
|
exit 1
|
|
fi
|
|
if [ ! -z "$VIASH_PAR_KNOWN_FUSIONS" ] && [ ! -e "$VIASH_PAR_KNOWN_FUSIONS" ]; then
|
|
ViashError "Input file '$VIASH_PAR_KNOWN_FUSIONS' does not exist."
|
|
exit 1
|
|
fi
|
|
if [ ! -z "$VIASH_PAR_BLACKLIST" ] && [ ! -e "$VIASH_PAR_BLACKLIST" ]; then
|
|
ViashError "Input file '$VIASH_PAR_BLACKLIST' does not exist."
|
|
exit 1
|
|
fi
|
|
if [ ! -z "$VIASH_PAR_STRUCTURAL_VARIANTS" ] && [ ! -e "$VIASH_PAR_STRUCTURAL_VARIANTS" ]; then
|
|
ViashError "Input file '$VIASH_PAR_STRUCTURAL_VARIANTS' does not exist."
|
|
exit 1
|
|
fi
|
|
if [ ! -z "$VIASH_PAR_TAGS" ] && [ ! -e "$VIASH_PAR_TAGS" ]; then
|
|
ViashError "Input file '$VIASH_PAR_TAGS' does not exist."
|
|
exit 1
|
|
fi
|
|
if [ ! -z "$VIASH_PAR_PROTEIN_DOMAINS" ] && [ ! -e "$VIASH_PAR_PROTEIN_DOMAINS" ]; then
|
|
ViashError "Input file '$VIASH_PAR_PROTEIN_DOMAINS' does not exist."
|
|
exit 1
|
|
fi
|
|
|
|
# check whether parameters values are of the right type
|
|
if [[ -n "$VIASH_PAR_MAX_GENOMIC_BREAKPOINT_DISTANCE" ]]; then
|
|
if ! [[ "$VIASH_PAR_MAX_GENOMIC_BREAKPOINT_DISTANCE" =~ ^[-+]?[0-9]+$ ]]; then
|
|
ViashError '--max_genomic_breakpoint_distance' has to be a long. Use "--help" to get more information on the parameters.
|
|
exit 1
|
|
fi
|
|
fi
|
|
if [[ -n "$VIASH_PAR_MAX_E_VALUE" ]]; then
|
|
if ! [[ "$VIASH_PAR_MAX_E_VALUE" =~ ^[-+]?(\.[0-9]+|[0-9]+(\.[0-9]*)?)([eE][-+]?[0-9]+)?$ ]]; then
|
|
ViashError '--max_e_value' has to be a double. Use "--help" to get more information on the parameters.
|
|
exit 1
|
|
fi
|
|
fi
|
|
if [[ -n "$VIASH_PAR_MIN_SUPPORTING_READS" ]]; then
|
|
if ! [[ "$VIASH_PAR_MIN_SUPPORTING_READS" =~ ^[-+]?[0-9]+$ ]]; then
|
|
ViashError '--min_supporting_reads' has to be an integer. Use "--help" to get more information on the parameters.
|
|
exit 1
|
|
fi
|
|
fi
|
|
if [[ -n "$VIASH_PAR_MAX_MISMAPPERS" ]]; then
|
|
if ! [[ "$VIASH_PAR_MAX_MISMAPPERS" =~ ^[-+]?(\.[0-9]+|[0-9]+(\.[0-9]*)?)([eE][-+]?[0-9]+)?$ ]]; then
|
|
ViashError '--max_mismappers' has to be a double. Use "--help" to get more information on the parameters.
|
|
exit 1
|
|
fi
|
|
fi
|
|
if [[ -n "$VIASH_PAR_MAX_HOMOLOG_IDENTITY" ]]; then
|
|
if ! [[ "$VIASH_PAR_MAX_HOMOLOG_IDENTITY" =~ ^[-+]?(\.[0-9]+|[0-9]+(\.[0-9]*)?)([eE][-+]?[0-9]+)?$ ]]; then
|
|
ViashError '--max_homolog_identity' has to be a double. Use "--help" to get more information on the parameters.
|
|
exit 1
|
|
fi
|
|
fi
|
|
if [[ -n "$VIASH_PAR_HOMOPOLYMER_LENGTH" ]]; then
|
|
if ! [[ "$VIASH_PAR_HOMOPOLYMER_LENGTH" =~ ^[-+]?[0-9]+$ ]]; then
|
|
ViashError '--homopolymer_length' has to be an integer. Use "--help" to get more information on the parameters.
|
|
exit 1
|
|
fi
|
|
fi
|
|
if [[ -n "$VIASH_PAR_READ_THROUGH_DISTANCE" ]]; then
|
|
if ! [[ "$VIASH_PAR_READ_THROUGH_DISTANCE" =~ ^[-+]?[0-9]+$ ]]; then
|
|
ViashError '--read_through_distance' has to be an integer. Use "--help" to get more information on the parameters.
|
|
exit 1
|
|
fi
|
|
fi
|
|
if [[ -n "$VIASH_PAR_MIN_ANCHOR_LENGTH" ]]; then
|
|
if ! [[ "$VIASH_PAR_MIN_ANCHOR_LENGTH" =~ ^[-+]?[0-9]+$ ]]; then
|
|
ViashError '--min_anchor_length' has to be an integer. Use "--help" to get more information on the parameters.
|
|
exit 1
|
|
fi
|
|
fi
|
|
if [[ -n "$VIASH_PAR_MANY_SPLICED_EVENTS" ]]; then
|
|
if ! [[ "$VIASH_PAR_MANY_SPLICED_EVENTS" =~ ^[-+]?[0-9]+$ ]]; then
|
|
ViashError '--many_spliced_events' has to be an integer. Use "--help" to get more information on the parameters.
|
|
exit 1
|
|
fi
|
|
fi
|
|
if [[ -n "$VIASH_PAR_MAX_KMER_CONTENT" ]]; then
|
|
if ! [[ "$VIASH_PAR_MAX_KMER_CONTENT" =~ ^[-+]?(\.[0-9]+|[0-9]+(\.[0-9]*)?)([eE][-+]?[0-9]+)?$ ]]; then
|
|
ViashError '--max_kmer_content' has to be a double. Use "--help" to get more information on the parameters.
|
|
exit 1
|
|
fi
|
|
fi
|
|
if [[ -n "$VIASH_PAR_MAX_MISMATCH_PVALUE" ]]; then
|
|
if ! [[ "$VIASH_PAR_MAX_MISMATCH_PVALUE" =~ ^[-+]?(\.[0-9]+|[0-9]+(\.[0-9]*)?)([eE][-+]?[0-9]+)?$ ]]; then
|
|
ViashError '--max_mismatch_pvalue' has to be a double. Use "--help" to get more information on the parameters.
|
|
exit 1
|
|
fi
|
|
fi
|
|
if [[ -n "$VIASH_PAR_FRAGMENT_LENGTH" ]]; then
|
|
if ! [[ "$VIASH_PAR_FRAGMENT_LENGTH" =~ ^[-+]?[0-9]+$ ]]; then
|
|
ViashError '--fragment_length' has to be an integer. Use "--help" to get more information on the parameters.
|
|
exit 1
|
|
fi
|
|
fi
|
|
if [[ -n "$VIASH_PAR_MAX_READS" ]]; then
|
|
if ! [[ "$VIASH_PAR_MAX_READS" =~ ^[-+]?[0-9]+$ ]]; then
|
|
ViashError '--max_reads' has to be an integer. Use "--help" to get more information on the parameters.
|
|
exit 1
|
|
fi
|
|
fi
|
|
if [[ -n "$VIASH_PAR_QUANTILE" ]]; then
|
|
if ! [[ "$VIASH_PAR_QUANTILE" =~ ^[-+]?(\.[0-9]+|[0-9]+(\.[0-9]*)?)([eE][-+]?[0-9]+)?$ ]]; then
|
|
ViashError '--quantile' has to be a double. Use "--help" to get more information on the parameters.
|
|
exit 1
|
|
fi
|
|
fi
|
|
if [[ -n "$VIASH_PAR_EXONIC_FRACTION" ]]; then
|
|
if ! [[ "$VIASH_PAR_EXONIC_FRACTION" =~ ^[-+]?(\.[0-9]+|[0-9]+(\.[0-9]*)?)([eE][-+]?[0-9]+)?$ ]]; then
|
|
ViashError '--exonic_fraction' has to be a double. Use "--help" to get more information on the parameters.
|
|
exit 1
|
|
fi
|
|
fi
|
|
if [[ -n "$VIASH_PAR_TOP_N" ]]; then
|
|
if ! [[ "$VIASH_PAR_TOP_N" =~ ^[-+]?[0-9]+$ ]]; then
|
|
ViashError '--top_n' has to be an integer. Use "--help" to get more information on the parameters.
|
|
exit 1
|
|
fi
|
|
fi
|
|
if [[ -n "$VIASH_PAR_COVERED_FRACTION" ]]; then
|
|
if ! [[ "$VIASH_PAR_COVERED_FRACTION" =~ ^[-+]?(\.[0-9]+|[0-9]+(\.[0-9]*)?)([eE][-+]?[0-9]+)?$ ]]; then
|
|
ViashError '--covered_fraction' has to be a double. Use "--help" to get more information on the parameters.
|
|
exit 1
|
|
fi
|
|
fi
|
|
if [[ -n "$VIASH_PAR_MAX_ITD_LENGTH" ]]; then
|
|
if ! [[ "$VIASH_PAR_MAX_ITD_LENGTH" =~ ^[-+]?[0-9]+$ ]]; then
|
|
ViashError '--max_itd_length' has to be an integer. Use "--help" to get more information on the parameters.
|
|
exit 1
|
|
fi
|
|
fi
|
|
if [[ -n "$VIASH_PAR_MIN_ITD_ALLELE_FRACTION" ]]; then
|
|
if ! [[ "$VIASH_PAR_MIN_ITD_ALLELE_FRACTION" =~ ^[-+]?(\.[0-9]+|[0-9]+(\.[0-9]*)?)([eE][-+]?[0-9]+)?$ ]]; then
|
|
ViashError '--min_itd_allele_fraction' has to be a double. Use "--help" to get more information on the parameters.
|
|
exit 1
|
|
fi
|
|
fi
|
|
if [[ -n "$VIASH_PAR_MIN_ITD_SUPPORTING_READS" ]]; then
|
|
if ! [[ "$VIASH_PAR_MIN_ITD_SUPPORTING_READS" =~ ^[-+]?[0-9]+$ ]]; then
|
|
ViashError '--min_itd_supporting_reads' has to be an integer. Use "--help" to get more information on the parameters.
|
|
exit 1
|
|
fi
|
|
fi
|
|
if [[ -n "$VIASH_PAR_SKIP_DUPLICATE_MARKING" ]]; then
|
|
if ! [[ "$VIASH_PAR_SKIP_DUPLICATE_MARKING" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then
|
|
ViashError '--skip_duplicate_marking' has to be a boolean_true. Use "--help" to get more information on the parameters.
|
|
exit 1
|
|
fi
|
|
fi
|
|
if [[ -n "$VIASH_PAR_EXTRA_INFORMATION" ]]; then
|
|
if ! [[ "$VIASH_PAR_EXTRA_INFORMATION" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then
|
|
ViashError '--extra_information' has to be a boolean_true. Use "--help" to get more information on the parameters.
|
|
exit 1
|
|
fi
|
|
fi
|
|
if [[ -n "$VIASH_PAR_FILL_GAPS" ]]; then
|
|
if ! [[ "$VIASH_PAR_FILL_GAPS" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then
|
|
ViashError '--fill_gaps' 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 "$VIASH_PAR_STRANDEDNESS" ]; then
|
|
VIASH_PAR_STRANDEDNESS_CHOICES=("auto;yes;no;reverse")
|
|
IFS=';'
|
|
set -f
|
|
if ! [[ ";${VIASH_PAR_STRANDEDNESS_CHOICES[*]};" =~ ";$VIASH_PAR_STRANDEDNESS;" ]]; then
|
|
ViashError '--strandedness' specified value of \'$VIASH_PAR_STRANDEDNESS\' 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_DISABLE_FILTERS" ]; then
|
|
VIASH_PAR_DISABLE_FILTERS_CHOICES=("homologs;low_entropy;isoforms;top_expressed_viral_contigs;viral_contigs;uninteresting_contigs;non_coding_neighbors;mismatches;duplicates;no_genomic_support;genomic_support;intronic;end_to_end;relative_support;low_coverage_viral_contigs;merge_adjacent;mismappers;multimappers;same_gene;long_gap;internal_tandem_duplication;small_insert_size;read_through;inconsistently_clipped;intragenic_exonic;marginal_read_through;spliced;hairpin;blacklist;min_support;select_best;in_vitro;short_anchor;known_fusions;no_coverage;homopolymer;many_spliced")
|
|
IFS=';'
|
|
set -f
|
|
for val in $VIASH_PAR_DISABLE_FILTERS; do
|
|
if ! [[ ";${VIASH_PAR_DISABLE_FILTERS_CHOICES[*]};" =~ ";${val};" ]]; then
|
|
ViashError '--disable_filters' specified value of \'${val}\' is not in the list of allowed values. Use "--help" to get more information on the parameters.
|
|
exit 1
|
|
fi
|
|
done
|
|
set +f
|
|
unset IFS
|
|
fi
|
|
|
|
# create parent directories of output files, if so desired
|
|
if [ ! -z "$VIASH_PAR_FUSIONS" ] && [ ! -d "$(dirname "$VIASH_PAR_FUSIONS")" ]; then
|
|
mkdir -p "$(dirname "$VIASH_PAR_FUSIONS")"
|
|
fi
|
|
if [ ! -z "$VIASH_PAR_FUSIONS_DISCARDED" ] && [ ! -d "$(dirname "$VIASH_PAR_FUSIONS_DISCARDED")" ]; then
|
|
mkdir -p "$(dirname "$VIASH_PAR_FUSIONS_DISCARDED")"
|
|
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_BAM" ]; then
|
|
VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$VIASH_PAR_BAM")" )
|
|
VIASH_PAR_BAM=$(ViashDockerAutodetectMount "$VIASH_PAR_BAM")
|
|
fi
|
|
if [ ! -z "$VIASH_PAR_GENOME" ]; then
|
|
VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$VIASH_PAR_GENOME")" )
|
|
VIASH_PAR_GENOME=$(ViashDockerAutodetectMount "$VIASH_PAR_GENOME")
|
|
fi
|
|
if [ ! -z "$VIASH_PAR_GENE_ANNOTATION" ]; then
|
|
VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$VIASH_PAR_GENE_ANNOTATION")" )
|
|
VIASH_PAR_GENE_ANNOTATION=$(ViashDockerAutodetectMount "$VIASH_PAR_GENE_ANNOTATION")
|
|
fi
|
|
if [ ! -z "$VIASH_PAR_KNOWN_FUSIONS" ]; then
|
|
VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$VIASH_PAR_KNOWN_FUSIONS")" )
|
|
VIASH_PAR_KNOWN_FUSIONS=$(ViashDockerAutodetectMount "$VIASH_PAR_KNOWN_FUSIONS")
|
|
fi
|
|
if [ ! -z "$VIASH_PAR_BLACKLIST" ]; then
|
|
VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$VIASH_PAR_BLACKLIST")" )
|
|
VIASH_PAR_BLACKLIST=$(ViashDockerAutodetectMount "$VIASH_PAR_BLACKLIST")
|
|
fi
|
|
if [ ! -z "$VIASH_PAR_STRUCTURAL_VARIANTS" ]; then
|
|
VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$VIASH_PAR_STRUCTURAL_VARIANTS")" )
|
|
VIASH_PAR_STRUCTURAL_VARIANTS=$(ViashDockerAutodetectMount "$VIASH_PAR_STRUCTURAL_VARIANTS")
|
|
fi
|
|
if [ ! -z "$VIASH_PAR_TAGS" ]; then
|
|
VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$VIASH_PAR_TAGS")" )
|
|
VIASH_PAR_TAGS=$(ViashDockerAutodetectMount "$VIASH_PAR_TAGS")
|
|
fi
|
|
if [ ! -z "$VIASH_PAR_PROTEIN_DOMAINS" ]; then
|
|
VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$VIASH_PAR_PROTEIN_DOMAINS")" )
|
|
VIASH_PAR_PROTEIN_DOMAINS=$(ViashDockerAutodetectMount "$VIASH_PAR_PROTEIN_DOMAINS")
|
|
fi
|
|
if [ ! -z "$VIASH_PAR_FUSIONS" ]; then
|
|
VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$VIASH_PAR_FUSIONS")" )
|
|
VIASH_PAR_FUSIONS=$(ViashDockerAutodetectMount "$VIASH_PAR_FUSIONS")
|
|
VIASH_CHOWN_VARS+=( "$VIASH_PAR_FUSIONS" )
|
|
fi
|
|
if [ ! -z "$VIASH_PAR_FUSIONS_DISCARDED" ]; then
|
|
VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$VIASH_PAR_FUSIONS_DISCARDED")" )
|
|
VIASH_PAR_FUSIONS_DISCARDED=$(ViashDockerAutodetectMount "$VIASH_PAR_FUSIONS_DISCARDED")
|
|
VIASH_CHOWN_VARS+=( "$VIASH_PAR_FUSIONS_DISCARDED" )
|
|
fi
|
|
if [ ! -z "$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-arriba-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'
|
|
#!/bin/bash
|
|
|
|
## VIASH START
|
|
# The following code has been auto-generated by Viash.
|
|
$( if [ ! -z ${VIASH_PAR_BAM+x} ]; then echo "${VIASH_PAR_BAM}" | sed "s#'#'\"'\"'#g;s#.*#par_bam='&'#" ; else echo "# par_bam="; fi )
|
|
$( if [ ! -z ${VIASH_PAR_GENOME+x} ]; then echo "${VIASH_PAR_GENOME}" | sed "s#'#'\"'\"'#g;s#.*#par_genome='&'#" ; else echo "# par_genome="; fi )
|
|
$( if [ ! -z ${VIASH_PAR_GENE_ANNOTATION+x} ]; then echo "${VIASH_PAR_GENE_ANNOTATION}" | sed "s#'#'\"'\"'#g;s#.*#par_gene_annotation='&'#" ; else echo "# par_gene_annotation="; fi )
|
|
$( if [ ! -z ${VIASH_PAR_KNOWN_FUSIONS+x} ]; then echo "${VIASH_PAR_KNOWN_FUSIONS}" | sed "s#'#'\"'\"'#g;s#.*#par_known_fusions='&'#" ; else echo "# par_known_fusions="; fi )
|
|
$( if [ ! -z ${VIASH_PAR_BLACKLIST+x} ]; then echo "${VIASH_PAR_BLACKLIST}" | sed "s#'#'\"'\"'#g;s#.*#par_blacklist='&'#" ; else echo "# par_blacklist="; fi )
|
|
$( if [ ! -z ${VIASH_PAR_STRUCTURAL_VARIANTS+x} ]; then echo "${VIASH_PAR_STRUCTURAL_VARIANTS}" | sed "s#'#'\"'\"'#g;s#.*#par_structural_variants='&'#" ; else echo "# par_structural_variants="; fi )
|
|
$( if [ ! -z ${VIASH_PAR_TAGS+x} ]; then echo "${VIASH_PAR_TAGS}" | sed "s#'#'\"'\"'#g;s#.*#par_tags='&'#" ; else echo "# par_tags="; fi )
|
|
$( if [ ! -z ${VIASH_PAR_PROTEIN_DOMAINS+x} ]; then echo "${VIASH_PAR_PROTEIN_DOMAINS}" | sed "s#'#'\"'\"'#g;s#.*#par_protein_domains='&'#" ; else echo "# par_protein_domains="; fi )
|
|
$( if [ ! -z ${VIASH_PAR_FUSIONS+x} ]; then echo "${VIASH_PAR_FUSIONS}" | sed "s#'#'\"'\"'#g;s#.*#par_fusions='&'#" ; else echo "# par_fusions="; fi )
|
|
$( if [ ! -z ${VIASH_PAR_FUSIONS_DISCARDED+x} ]; then echo "${VIASH_PAR_FUSIONS_DISCARDED}" | sed "s#'#'\"'\"'#g;s#.*#par_fusions_discarded='&'#" ; else echo "# par_fusions_discarded="; fi )
|
|
$( if [ ! -z ${VIASH_PAR_MAX_GENOMIC_BREAKPOINT_DISTANCE+x} ]; then echo "${VIASH_PAR_MAX_GENOMIC_BREAKPOINT_DISTANCE}" | sed "s#'#'\"'\"'#g;s#.*#par_max_genomic_breakpoint_distance='&'#" ; else echo "# par_max_genomic_breakpoint_distance="; fi )
|
|
$( if [ ! -z ${VIASH_PAR_STRANDEDNESS+x} ]; then echo "${VIASH_PAR_STRANDEDNESS}" | sed "s#'#'\"'\"'#g;s#.*#par_strandedness='&'#" ; else echo "# par_strandedness="; fi )
|
|
$( if [ ! -z ${VIASH_PAR_INTERESTING_CONTIGS+x} ]; then echo "${VIASH_PAR_INTERESTING_CONTIGS}" | sed "s#'#'\"'\"'#g;s#.*#par_interesting_contigs='&'#" ; else echo "# par_interesting_contigs="; fi )
|
|
$( if [ ! -z ${VIASH_PAR_VIRAL_CONTIGS+x} ]; then echo "${VIASH_PAR_VIRAL_CONTIGS}" | sed "s#'#'\"'\"'#g;s#.*#par_viral_contigs='&'#" ; else echo "# par_viral_contigs="; fi )
|
|
$( if [ ! -z ${VIASH_PAR_DISABLE_FILTERS+x} ]; then echo "${VIASH_PAR_DISABLE_FILTERS}" | sed "s#'#'\"'\"'#g;s#.*#par_disable_filters='&'#" ; else echo "# par_disable_filters="; fi )
|
|
$( if [ ! -z ${VIASH_PAR_MAX_E_VALUE+x} ]; then echo "${VIASH_PAR_MAX_E_VALUE}" | sed "s#'#'\"'\"'#g;s#.*#par_max_e_value='&'#" ; else echo "# par_max_e_value="; fi )
|
|
$( if [ ! -z ${VIASH_PAR_MIN_SUPPORTING_READS+x} ]; then echo "${VIASH_PAR_MIN_SUPPORTING_READS}" | sed "s#'#'\"'\"'#g;s#.*#par_min_supporting_reads='&'#" ; else echo "# par_min_supporting_reads="; fi )
|
|
$( if [ ! -z ${VIASH_PAR_MAX_MISMAPPERS+x} ]; then echo "${VIASH_PAR_MAX_MISMAPPERS}" | sed "s#'#'\"'\"'#g;s#.*#par_max_mismappers='&'#" ; else echo "# par_max_mismappers="; fi )
|
|
$( if [ ! -z ${VIASH_PAR_MAX_HOMOLOG_IDENTITY+x} ]; then echo "${VIASH_PAR_MAX_HOMOLOG_IDENTITY}" | sed "s#'#'\"'\"'#g;s#.*#par_max_homolog_identity='&'#" ; else echo "# par_max_homolog_identity="; fi )
|
|
$( if [ ! -z ${VIASH_PAR_HOMOPOLYMER_LENGTH+x} ]; then echo "${VIASH_PAR_HOMOPOLYMER_LENGTH}" | sed "s#'#'\"'\"'#g;s#.*#par_homopolymer_length='&'#" ; else echo "# par_homopolymer_length="; fi )
|
|
$( if [ ! -z ${VIASH_PAR_READ_THROUGH_DISTANCE+x} ]; then echo "${VIASH_PAR_READ_THROUGH_DISTANCE}" | sed "s#'#'\"'\"'#g;s#.*#par_read_through_distance='&'#" ; else echo "# par_read_through_distance="; fi )
|
|
$( if [ ! -z ${VIASH_PAR_MIN_ANCHOR_LENGTH+x} ]; then echo "${VIASH_PAR_MIN_ANCHOR_LENGTH}" | sed "s#'#'\"'\"'#g;s#.*#par_min_anchor_length='&'#" ; else echo "# par_min_anchor_length="; fi )
|
|
$( if [ ! -z ${VIASH_PAR_MANY_SPLICED_EVENTS+x} ]; then echo "${VIASH_PAR_MANY_SPLICED_EVENTS}" | sed "s#'#'\"'\"'#g;s#.*#par_many_spliced_events='&'#" ; else echo "# par_many_spliced_events="; fi )
|
|
$( if [ ! -z ${VIASH_PAR_MAX_KMER_CONTENT+x} ]; then echo "${VIASH_PAR_MAX_KMER_CONTENT}" | sed "s#'#'\"'\"'#g;s#.*#par_max_kmer_content='&'#" ; else echo "# par_max_kmer_content="; fi )
|
|
$( if [ ! -z ${VIASH_PAR_MAX_MISMATCH_PVALUE+x} ]; then echo "${VIASH_PAR_MAX_MISMATCH_PVALUE}" | sed "s#'#'\"'\"'#g;s#.*#par_max_mismatch_pvalue='&'#" ; else echo "# par_max_mismatch_pvalue="; fi )
|
|
$( if [ ! -z ${VIASH_PAR_FRAGMENT_LENGTH+x} ]; then echo "${VIASH_PAR_FRAGMENT_LENGTH}" | sed "s#'#'\"'\"'#g;s#.*#par_fragment_length='&'#" ; else echo "# par_fragment_length="; fi )
|
|
$( if [ ! -z ${VIASH_PAR_MAX_READS+x} ]; then echo "${VIASH_PAR_MAX_READS}" | sed "s#'#'\"'\"'#g;s#.*#par_max_reads='&'#" ; else echo "# par_max_reads="; fi )
|
|
$( if [ ! -z ${VIASH_PAR_QUANTILE+x} ]; then echo "${VIASH_PAR_QUANTILE}" | sed "s#'#'\"'\"'#g;s#.*#par_quantile='&'#" ; else echo "# par_quantile="; fi )
|
|
$( if [ ! -z ${VIASH_PAR_EXONIC_FRACTION+x} ]; then echo "${VIASH_PAR_EXONIC_FRACTION}" | sed "s#'#'\"'\"'#g;s#.*#par_exonic_fraction='&'#" ; else echo "# par_exonic_fraction="; fi )
|
|
$( if [ ! -z ${VIASH_PAR_TOP_N+x} ]; then echo "${VIASH_PAR_TOP_N}" | sed "s#'#'\"'\"'#g;s#.*#par_top_n='&'#" ; else echo "# par_top_n="; fi )
|
|
$( if [ ! -z ${VIASH_PAR_COVERED_FRACTION+x} ]; then echo "${VIASH_PAR_COVERED_FRACTION}" | sed "s#'#'\"'\"'#g;s#.*#par_covered_fraction='&'#" ; else echo "# par_covered_fraction="; fi )
|
|
$( if [ ! -z ${VIASH_PAR_MAX_ITD_LENGTH+x} ]; then echo "${VIASH_PAR_MAX_ITD_LENGTH}" | sed "s#'#'\"'\"'#g;s#.*#par_max_itd_length='&'#" ; else echo "# par_max_itd_length="; fi )
|
|
$( if [ ! -z ${VIASH_PAR_MIN_ITD_ALLELE_FRACTION+x} ]; then echo "${VIASH_PAR_MIN_ITD_ALLELE_FRACTION}" | sed "s#'#'\"'\"'#g;s#.*#par_min_itd_allele_fraction='&'#" ; else echo "# par_min_itd_allele_fraction="; fi )
|
|
$( if [ ! -z ${VIASH_PAR_MIN_ITD_SUPPORTING_READS+x} ]; then echo "${VIASH_PAR_MIN_ITD_SUPPORTING_READS}" | sed "s#'#'\"'\"'#g;s#.*#par_min_itd_supporting_reads='&'#" ; else echo "# par_min_itd_supporting_reads="; fi )
|
|
$( if [ ! -z ${VIASH_PAR_SKIP_DUPLICATE_MARKING+x} ]; then echo "${VIASH_PAR_SKIP_DUPLICATE_MARKING}" | sed "s#'#'\"'\"'#g;s#.*#par_skip_duplicate_marking='&'#" ; else echo "# par_skip_duplicate_marking="; fi )
|
|
$( if [ ! -z ${VIASH_PAR_EXTRA_INFORMATION+x} ]; then echo "${VIASH_PAR_EXTRA_INFORMATION}" | sed "s#'#'\"'\"'#g;s#.*#par_extra_information='&'#" ; else echo "# par_extra_information="; fi )
|
|
$( if [ ! -z ${VIASH_PAR_FILL_GAPS+x} ]; then echo "${VIASH_PAR_FILL_GAPS}" | sed "s#'#'\"'\"'#g;s#.*#par_fill_gaps='&'#" ; else echo "# par_fill_gaps="; 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
|
|
|
|
# unset flags
|
|
[[ "\$par_skip_duplicate_marking" == "false" ]] && unset par_skip_duplicate_marking
|
|
[[ "\$par_extra_information" == "false" ]] && unset par_extra_information
|
|
[[ "\$par_fill_gaps" == "false" ]] && unset par_fill_gaps
|
|
|
|
# replace ';' with ','
|
|
par_interesting_contigs=\$(echo \$par_interesting_contigs | tr ';' ',')
|
|
par_viral_contigs=\$(echo \$par_viral_contigs | tr ';' ',')
|
|
par_disable_filters=\$(echo \$par_disable_filters | tr ';' ',')
|
|
|
|
# run arriba
|
|
arriba \\
|
|
-x "\$par_bam" \\
|
|
-a "\$par_genome" \\
|
|
-g "\$par_gene_annotation" \\
|
|
-o "\$par_fusions" \\
|
|
\${par_known_fusions:+-k "\${par_known_fusions}"} \\
|
|
\${par_blacklist:+-b "\${par_blacklist}"} \\
|
|
\${par_structural_variants:+-d "\${par_structural_variants}"} \\
|
|
\${par_tags:+-t "\${par_tags}"} \\
|
|
\${par_protein_domains:+-p "\${par_protein_domains}"} \\
|
|
\${par_fusions_discarded:+-O "\${par_fusions_discarded}"} \\
|
|
\${par_max_genomic_breakpoint_distance:+-D "\${par_max_genomic_breakpoint_distance}"} \\
|
|
\${par_strandedness:+-s "\${par_strandedness}"} \\
|
|
\${par_interesting_contigs:+-i "\${par_interesting_contigs}"} \\
|
|
\${par_viral_contigs:+-v "\${par_viral_contigs}"} \\
|
|
\${par_disable_filters:+-f "\${par_disable_filters}"} \\
|
|
\${par_max_e_value:+-E "\${par_max_e_value}"} \\
|
|
\${par_min_supporting_reads:+-S "\${par_min_supporting_reads}"} \\
|
|
\${par_max_mismappers:+-m "\${par_max_mismappers}"} \\
|
|
\${par_max_homolog_identity:+-L "\${par_max_homolog_identity}"} \\
|
|
\${par_homopolymer_length:+-H "\${par_homopolymer_length}"} \\
|
|
\${par_read_through_distance:+-R "\${par_read_through_distance}"} \\
|
|
\${par_min_anchor_length:+-A "\${par_min_anchor_length}"} \\
|
|
\${par_many_spliced_events:+-M "\${par_many_spliced_events}"} \\
|
|
\${par_max_kmer_content:+-K "\${par_max_kmer_content}"} \\
|
|
\${par_max_mismatch_pvalue:+-V "\${par_max_mismatch_pvalue}"} \\
|
|
\${par_fragment_length:+-F "\${par_fragment_length}"} \\
|
|
\${par_max_reads:+-U "\${par_max_reads}"} \\
|
|
\${par_quantile:+-Q "\${par_quantile}"} \\
|
|
\${par_exonic_fraction:+-e "\${par_exonic_fraction}"} \\
|
|
\${par_top_n:+-T "\${par_top_n}"} \\
|
|
\${par_covered_fraction:+-C "\${par_covered_fraction}"} \\
|
|
\${par_max_itd_length:+-l "\${par_max_itd_length}"} \\
|
|
\${par_min_itd_allele_fraction:+-z "\${par_min_itd_allele_fraction}"} \\
|
|
\${par_min_itd_supporting_reads:+-Z "\${par_min_itd_supporting_reads}"} \\
|
|
\${par_skip_duplicate_marking:+-u} \\
|
|
\${par_extra_information:+-X} \\
|
|
\${par_fill_gaps:+-I}
|
|
VIASHMAIN
|
|
bash "\$tempscript" &
|
|
wait "\$!"
|
|
|
|
VIASHEOF
|
|
|
|
|
|
if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then
|
|
# strip viash automount from file paths
|
|
|
|
if [ ! -z "$VIASH_PAR_BAM" ]; then
|
|
VIASH_PAR_BAM=$(ViashDockerStripAutomount "$VIASH_PAR_BAM")
|
|
fi
|
|
if [ ! -z "$VIASH_PAR_GENOME" ]; then
|
|
VIASH_PAR_GENOME=$(ViashDockerStripAutomount "$VIASH_PAR_GENOME")
|
|
fi
|
|
if [ ! -z "$VIASH_PAR_GENE_ANNOTATION" ]; then
|
|
VIASH_PAR_GENE_ANNOTATION=$(ViashDockerStripAutomount "$VIASH_PAR_GENE_ANNOTATION")
|
|
fi
|
|
if [ ! -z "$VIASH_PAR_KNOWN_FUSIONS" ]; then
|
|
VIASH_PAR_KNOWN_FUSIONS=$(ViashDockerStripAutomount "$VIASH_PAR_KNOWN_FUSIONS")
|
|
fi
|
|
if [ ! -z "$VIASH_PAR_BLACKLIST" ]; then
|
|
VIASH_PAR_BLACKLIST=$(ViashDockerStripAutomount "$VIASH_PAR_BLACKLIST")
|
|
fi
|
|
if [ ! -z "$VIASH_PAR_STRUCTURAL_VARIANTS" ]; then
|
|
VIASH_PAR_STRUCTURAL_VARIANTS=$(ViashDockerStripAutomount "$VIASH_PAR_STRUCTURAL_VARIANTS")
|
|
fi
|
|
if [ ! -z "$VIASH_PAR_TAGS" ]; then
|
|
VIASH_PAR_TAGS=$(ViashDockerStripAutomount "$VIASH_PAR_TAGS")
|
|
fi
|
|
if [ ! -z "$VIASH_PAR_PROTEIN_DOMAINS" ]; then
|
|
VIASH_PAR_PROTEIN_DOMAINS=$(ViashDockerStripAutomount "$VIASH_PAR_PROTEIN_DOMAINS")
|
|
fi
|
|
if [ ! -z "$VIASH_PAR_FUSIONS" ]; then
|
|
VIASH_PAR_FUSIONS=$(ViashDockerStripAutomount "$VIASH_PAR_FUSIONS")
|
|
fi
|
|
if [ ! -z "$VIASH_PAR_FUSIONS_DISCARDED" ]; then
|
|
VIASH_PAR_FUSIONS_DISCARDED=$(ViashDockerStripAutomount "$VIASH_PAR_FUSIONS_DISCARDED")
|
|
fi
|
|
if [ ! -z "$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_FUSIONS" ] && [ ! -e "$VIASH_PAR_FUSIONS" ]; then
|
|
ViashError "Output file '$VIASH_PAR_FUSIONS' does not exist."
|
|
exit 1
|
|
fi
|
|
if [ ! -z "$VIASH_PAR_FUSIONS_DISCARDED" ] && [ ! -e "$VIASH_PAR_FUSIONS_DISCARDED" ]; then
|
|
ViashError "Output file '$VIASH_PAR_FUSIONS_DISCARDED' does not exist."
|
|
exit 1
|
|
fi
|
|
|
|
|
|
exit 0
|