CI
af7bcfffa4
Build pipeline: viash-hub.biobox.main-lltcw
Source commit: c733de2e4c
Source message: Bump viash to 0.9.4 (#175)
* Bump viash to 0.9.4
* Add CHANGELOG entry
* Add PR number
2470 lines
114 KiB
Bash
Executable File
2470 lines
114 KiB
Bash
Executable File
#!/usr/bin/env bash
|
|
|
|
# featurecounts main
|
|
#
|
|
# This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
|
|
# work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
|
|
# Intuitive.
|
|
#
|
|
# The component may contain files which fall under a different license. The
|
|
# authors of this component should specify the license in the header of such
|
|
# files, or include a separate license file detailing the licenses of all included
|
|
# files.
|
|
#
|
|
# Component authors:
|
|
# * Sai Nirmayi Yasa (author, maintainer)
|
|
|
|
set -e
|
|
|
|
if [ -z "$VIASH_TEMP" ]; then
|
|
VIASH_TEMP=${VIASH_TEMP:-$VIASH_TMPDIR}
|
|
VIASH_TEMP=${VIASH_TEMP:-$VIASH_TEMPDIR}
|
|
VIASH_TEMP=${VIASH_TEMP:-$VIASH_TMP}
|
|
VIASH_TEMP=${VIASH_TEMP:-$TMPDIR}
|
|
VIASH_TEMP=${VIASH_TEMP:-$TMP}
|
|
VIASH_TEMP=${VIASH_TEMP:-$TEMPDIR}
|
|
VIASH_TEMP=${VIASH_TEMP:-$TEMP}
|
|
VIASH_TEMP=${VIASH_TEMP:-/tmp}
|
|
fi
|
|
|
|
# define helper functions
|
|
# ViashQuote: put quotes around non flag values
|
|
# $1 : unquoted string
|
|
# return : possibly quoted string
|
|
# examples:
|
|
# ViashQuote --foo # returns --foo
|
|
# ViashQuote bar # returns 'bar'
|
|
# Viashquote --foo=bar # returns --foo='bar'
|
|
function ViashQuote {
|
|
if [[ "$1" =~ ^-+[a-zA-Z0-9_\-]+=.+$ ]]; then
|
|
echo "$1" | sed "s#=\(.*\)#='\1'#"
|
|
elif [[ "$1" =~ ^-+[a-zA-Z0-9_\-]+$ ]]; then
|
|
echo "$1"
|
|
else
|
|
echo "'$1'"
|
|
fi
|
|
}
|
|
# ViashRemoveFlags: Remove leading flag
|
|
# $1 : string with a possible leading flag
|
|
# return : string without possible leading flag
|
|
# examples:
|
|
# ViashRemoveFlags --foo=bar # returns bar
|
|
function ViashRemoveFlags {
|
|
echo "$1" | sed 's/^--*[a-zA-Z0-9_\-]*=//'
|
|
}
|
|
# ViashSourceDir: return the path of a bash file, following symlinks
|
|
# usage : ViashSourceDir ${BASH_SOURCE[0]}
|
|
# $1 : Should always be set to ${BASH_SOURCE[0]}
|
|
# returns : The absolute path of the bash file
|
|
function ViashSourceDir {
|
|
local source="$1"
|
|
while [ -h "$source" ]; do
|
|
local dir="$( cd -P "$( dirname "$source" )" >/dev/null 2>&1 && pwd )"
|
|
source="$(readlink "$source")"
|
|
[[ $source != /* ]] && source="$dir/$source"
|
|
done
|
|
cd -P "$( dirname "$source" )" >/dev/null 2>&1 && pwd
|
|
}
|
|
# ViashFindTargetDir: return the path of the '.build.yaml' file, following symlinks
|
|
# usage : ViashFindTargetDir 'ScriptPath'
|
|
# $1 : The location from where to start the upward search
|
|
# returns : The absolute path of the '.build.yaml' file
|
|
function ViashFindTargetDir {
|
|
local source="$1"
|
|
while [[ "$source" != "" && ! -e "$source/.build.yaml" ]]; do
|
|
source=${source%/*}
|
|
done
|
|
echo $source
|
|
}
|
|
# see https://en.wikipedia.org/wiki/Syslog#Severity_level
|
|
VIASH_LOGCODE_EMERGENCY=0
|
|
VIASH_LOGCODE_ALERT=1
|
|
VIASH_LOGCODE_CRITICAL=2
|
|
VIASH_LOGCODE_ERROR=3
|
|
VIASH_LOGCODE_WARNING=4
|
|
VIASH_LOGCODE_NOTICE=5
|
|
VIASH_LOGCODE_INFO=6
|
|
VIASH_LOGCODE_DEBUG=7
|
|
VIASH_VERBOSITY=$VIASH_LOGCODE_NOTICE
|
|
|
|
# ViashLog: Log events depending on the verbosity level
|
|
# usage: ViashLog 1 alert Oh no something went wrong!
|
|
# $1: required verbosity level
|
|
# $2: display tag
|
|
# $3+: messages to display
|
|
# stdout: Your input, prepended by '[$2] '.
|
|
function ViashLog {
|
|
local required_level="$1"
|
|
local display_tag="$2"
|
|
shift 2
|
|
if [ $VIASH_VERBOSITY -ge $required_level ]; then
|
|
>&2 echo "[$display_tag]" "$@"
|
|
fi
|
|
}
|
|
|
|
# ViashEmergency: log events when the system is unstable
|
|
# usage: ViashEmergency Oh no something went wrong.
|
|
# stdout: Your input, prepended by '[emergency] '.
|
|
function ViashEmergency {
|
|
ViashLog $VIASH_LOGCODE_EMERGENCY emergency "$@"
|
|
}
|
|
|
|
# ViashAlert: log events when actions must be taken immediately (e.g. corrupted system database)
|
|
# usage: ViashAlert Oh no something went wrong.
|
|
# stdout: Your input, prepended by '[alert] '.
|
|
function ViashAlert {
|
|
ViashLog $VIASH_LOGCODE_ALERT alert "$@"
|
|
}
|
|
|
|
# ViashCritical: log events when a critical condition occurs
|
|
# usage: ViashCritical Oh no something went wrong.
|
|
# stdout: Your input, prepended by '[critical] '.
|
|
function ViashCritical {
|
|
ViashLog $VIASH_LOGCODE_CRITICAL critical "$@"
|
|
}
|
|
|
|
# ViashError: log events when an error condition occurs
|
|
# usage: ViashError Oh no something went wrong.
|
|
# stdout: Your input, prepended by '[error] '.
|
|
function ViashError {
|
|
ViashLog $VIASH_LOGCODE_ERROR error "$@"
|
|
}
|
|
|
|
# ViashWarning: log potentially abnormal events
|
|
# usage: ViashWarning Something may have gone wrong.
|
|
# stdout: Your input, prepended by '[warning] '.
|
|
function ViashWarning {
|
|
ViashLog $VIASH_LOGCODE_WARNING warning "$@"
|
|
}
|
|
|
|
# ViashNotice: log significant but normal events
|
|
# usage: ViashNotice This just happened.
|
|
# stdout: Your input, prepended by '[notice] '.
|
|
function ViashNotice {
|
|
ViashLog $VIASH_LOGCODE_NOTICE notice "$@"
|
|
}
|
|
|
|
# ViashInfo: log normal events
|
|
# usage: ViashInfo This just happened.
|
|
# stdout: Your input, prepended by '[info] '.
|
|
function ViashInfo {
|
|
ViashLog $VIASH_LOGCODE_INFO info "$@"
|
|
}
|
|
|
|
# ViashDebug: log all events, for debugging purposes
|
|
# usage: ViashDebug This just happened.
|
|
# stdout: Your input, prepended by '[debug] '.
|
|
function ViashDebug {
|
|
ViashLog $VIASH_LOGCODE_DEBUG debug "$@"
|
|
}
|
|
|
|
# find source folder of this component
|
|
VIASH_META_RESOURCES_DIR=`ViashSourceDir ${BASH_SOURCE[0]}`
|
|
|
|
# find the root of the built components & dependencies
|
|
VIASH_TARGET_DIR=`ViashFindTargetDir $VIASH_META_RESOURCES_DIR`
|
|
|
|
# define meta fields
|
|
VIASH_META_NAME="featurecounts"
|
|
VIASH_META_FUNCTIONALITY_NAME="featurecounts"
|
|
VIASH_META_EXECUTABLE="$VIASH_META_RESOURCES_DIR/$VIASH_META_NAME"
|
|
VIASH_META_CONFIG="$VIASH_META_RESOURCES_DIR/.config.vsh.yaml"
|
|
VIASH_META_TEMP_DIR="$VIASH_TEMP"
|
|
|
|
|
|
|
|
# initialise variables
|
|
VIASH_MODE='run'
|
|
VIASH_ENGINE_ID='docker'
|
|
|
|
######## Helper functions for setting up Docker images for viash ########
|
|
# expects: ViashDockerBuild
|
|
|
|
# ViashDockerInstallationCheck: check whether Docker is installed correctly
|
|
#
|
|
# examples:
|
|
# ViashDockerInstallationCheck
|
|
function ViashDockerInstallationCheck {
|
|
ViashDebug "Checking whether Docker is installed"
|
|
if [ ! command -v docker &> /dev/null ]; then
|
|
ViashCritical "Docker doesn't seem to be installed. See 'https://docs.docker.com/get-docker/' for instructions."
|
|
exit 1
|
|
fi
|
|
|
|
ViashDebug "Checking whether the Docker daemon is running"
|
|
local save=$-; set +e
|
|
local docker_version=$(docker version --format '{{.Client.APIVersion}}' 2> /dev/null)
|
|
local out=$?
|
|
[[ $save =~ e ]] && set -e
|
|
if [ $out -ne 0 ]; then
|
|
ViashCritical "Docker daemon does not seem to be running. Try one of the following:"
|
|
ViashCritical "- Try running 'dockerd' in the command line"
|
|
ViashCritical "- See https://docs.docker.com/config/daemon/"
|
|
exit 1
|
|
fi
|
|
}
|
|
|
|
# ViashDockerRemoteTagCheck: check whether a Docker image is available
|
|
# on a remote. Assumes `docker login` has been performed, if relevant.
|
|
#
|
|
# $1 : image identifier with format `[registry/]image[:tag]`
|
|
# exit code $? : whether or not the image was found
|
|
# examples:
|
|
# ViashDockerRemoteTagCheck python:latest
|
|
# echo $? # returns '0'
|
|
# ViashDockerRemoteTagCheck sdaizudceahifu
|
|
# echo $? # returns '1'
|
|
function ViashDockerRemoteTagCheck {
|
|
docker manifest inspect $1 > /dev/null 2> /dev/null
|
|
}
|
|
|
|
# ViashDockerLocalTagCheck: check whether a Docker image is available locally
|
|
#
|
|
# $1 : image identifier with format `[registry/]image[:tag]`
|
|
# exit code $? : whether or not the image was found
|
|
# examples:
|
|
# docker pull python:latest
|
|
# ViashDockerLocalTagCheck python:latest
|
|
# echo $? # returns '0'
|
|
# ViashDockerLocalTagCheck sdaizudceahifu
|
|
# echo $? # returns '1'
|
|
function ViashDockerLocalTagCheck {
|
|
[ -n "$(docker images -q $1)" ]
|
|
}
|
|
|
|
# ViashDockerPull: pull a Docker image
|
|
#
|
|
# $1 : image identifier with format `[registry/]image[:tag]`
|
|
# exit code $? : whether or not the image was found
|
|
# examples:
|
|
# ViashDockerPull python:latest
|
|
# echo $? # returns '0'
|
|
# ViashDockerPull sdaizudceahifu
|
|
# echo $? # returns '1'
|
|
function ViashDockerPull {
|
|
ViashNotice "Checking if Docker image is available at '$1'"
|
|
if [ $VIASH_VERBOSITY -ge $VIASH_LOGCODE_INFO ]; then
|
|
docker pull $1 && return 0 || return 1
|
|
else
|
|
local save=$-; set +e
|
|
docker pull $1 2> /dev/null > /dev/null
|
|
local out=$?
|
|
[[ $save =~ e ]] && set -e
|
|
if [ $out -ne 0 ]; then
|
|
ViashWarning "Could not pull from '$1'. Docker image doesn't exist or is not accessible."
|
|
fi
|
|
return $out
|
|
fi
|
|
}
|
|
|
|
# ViashDockerPush: push a Docker image
|
|
#
|
|
# $1 : image identifier with format `[registry/]image[:tag]`
|
|
# exit code $? : whether or not the image was found
|
|
# examples:
|
|
# ViashDockerPush python:latest
|
|
# echo $? # returns '0'
|
|
# ViashDockerPush sdaizudceahifu
|
|
# echo $? # returns '1'
|
|
function ViashDockerPush {
|
|
ViashNotice "Pushing image to '$1'"
|
|
local save=$-; set +e
|
|
local out
|
|
if [ $VIASH_VERBOSITY -ge $VIASH_LOGCODE_INFO ]; then
|
|
docker push $1
|
|
out=$?
|
|
else
|
|
docker push $1 2> /dev/null > /dev/null
|
|
out=$?
|
|
fi
|
|
[[ $save =~ e ]] && set -e
|
|
if [ $out -eq 0 ]; then
|
|
ViashNotice "Container '$1' push succeeded."
|
|
else
|
|
ViashError "Container '$1' push errored. You might not be logged in or have the necessary permissions."
|
|
fi
|
|
return $out
|
|
}
|
|
|
|
# ViashDockerPullElseBuild: pull a Docker image, else build it
|
|
#
|
|
# $1 : image identifier with format `[registry/]image[:tag]`
|
|
# ViashDockerBuild : a Bash function which builds a docker image, takes image identifier as argument.
|
|
# examples:
|
|
# ViashDockerPullElseBuild mynewcomponent
|
|
function ViashDockerPullElseBuild {
|
|
local save=$-; set +e
|
|
ViashDockerPull $1
|
|
local out=$?
|
|
[[ $save =~ e ]] && set -e
|
|
if [ $out -ne 0 ]; then
|
|
ViashDockerBuild $@
|
|
fi
|
|
}
|
|
|
|
# ViashDockerSetup: create a Docker image, according to specified docker setup strategy
|
|
#
|
|
# $1 : image identifier with format `[registry/]image[:tag]`
|
|
# $2 : docker setup strategy, see DockerSetupStrategy.scala
|
|
# examples:
|
|
# ViashDockerSetup mynewcomponent alwaysbuild
|
|
function ViashDockerSetup {
|
|
local image_id="$1"
|
|
local setup_strategy="$2"
|
|
if [ "$setup_strategy" == "alwaysbuild" -o "$setup_strategy" == "build" -o "$setup_strategy" == "b" ]; then
|
|
ViashDockerBuild $image_id --no-cache $(ViashDockerBuildArgs "$engine_id")
|
|
elif [ "$setup_strategy" == "alwayspull" -o "$setup_strategy" == "pull" -o "$setup_strategy" == "p" ]; then
|
|
ViashDockerPull $image_id
|
|
elif [ "$setup_strategy" == "alwayspullelsebuild" -o "$setup_strategy" == "pullelsebuild" ]; then
|
|
ViashDockerPullElseBuild $image_id --no-cache $(ViashDockerBuildArgs "$engine_id")
|
|
elif [ "$setup_strategy" == "alwayspullelsecachedbuild" -o "$setup_strategy" == "pullelsecachedbuild" ]; then
|
|
ViashDockerPullElseBuild $image_id $(ViashDockerBuildArgs "$engine_id")
|
|
elif [ "$setup_strategy" == "alwayscachedbuild" -o "$setup_strategy" == "cachedbuild" -o "$setup_strategy" == "cb" ]; then
|
|
ViashDockerBuild $image_id $(ViashDockerBuildArgs "$engine_id")
|
|
elif [[ "$setup_strategy" =~ ^ifneedbe ]]; then
|
|
local save=$-; set +e
|
|
ViashDockerLocalTagCheck $image_id
|
|
local outCheck=$?
|
|
[[ $save =~ e ]] && set -e
|
|
if [ $outCheck -eq 0 ]; then
|
|
ViashInfo "Image $image_id already exists"
|
|
elif [ "$setup_strategy" == "ifneedbebuild" ]; then
|
|
ViashDockerBuild $image_id --no-cache $(ViashDockerBuildArgs "$engine_id")
|
|
elif [ "$setup_strategy" == "ifneedbecachedbuild" ]; then
|
|
ViashDockerBuild $image_id $(ViashDockerBuildArgs "$engine_id")
|
|
elif [ "$setup_strategy" == "ifneedbepull" ]; then
|
|
ViashDockerPull $image_id
|
|
elif [ "$setup_strategy" == "ifneedbepullelsebuild" ]; then
|
|
ViashDockerPullElseBuild $image_id --no-cache $(ViashDockerBuildArgs "$engine_id")
|
|
elif [ "$setup_strategy" == "ifneedbepullelsecachedbuild" ]; then
|
|
ViashDockerPullElseBuild $image_id $(ViashDockerBuildArgs "$engine_id")
|
|
else
|
|
ViashError "Unrecognised Docker strategy: $setup_strategy"
|
|
exit 1
|
|
fi
|
|
elif [ "$setup_strategy" == "push" -o "$setup_strategy" == "forcepush" -o "$setup_strategy" == "alwayspush" ]; then
|
|
ViashDockerPush "$image_id"
|
|
elif [ "$setup_strategy" == "pushifnotpresent" -o "$setup_strategy" == "gentlepush" -o "$setup_strategy" == "maybepush" ]; then
|
|
local save=$-; set +e
|
|
ViashDockerRemoteTagCheck $image_id
|
|
local outCheck=$?
|
|
[[ $save =~ e ]] && set -e
|
|
if [ $outCheck -eq 0 ]; then
|
|
ViashNotice "Container '$image_id' exists, doing nothing."
|
|
else
|
|
ViashNotice "Container '$image_id' does not yet exist."
|
|
ViashDockerPush "$image_id"
|
|
fi
|
|
elif [ "$setup_strategy" == "donothing" -o "$setup_strategy" == "meh" ]; then
|
|
ViashNotice "Skipping setup."
|
|
else
|
|
ViashError "Unrecognised Docker strategy: $setup_strategy"
|
|
exit 1
|
|
fi
|
|
}
|
|
|
|
# ViashDockerCheckCommands: Check whether a docker container has the required commands
|
|
#
|
|
# $1 : image identifier with format `[registry/]image[:tag]`
|
|
# $@ : commands to verify being present
|
|
# examples:
|
|
# ViashDockerCheckCommands bash:4.0 bash ps foo
|
|
function ViashDockerCheckCommands {
|
|
local image_id="$1"
|
|
shift 1
|
|
local commands="$@"
|
|
local save=$-; set +e
|
|
local missing # mark 'missing' as local in advance, otherwise the exit code of the command will be missing and always be '0'
|
|
missing=$(docker run --rm --entrypoint=sh "$image_id" -c "for command in $commands; do command -v \$command >/dev/null 2>&1; if [ \$? -ne 0 ]; then echo \$command; exit 1; fi; done")
|
|
local outCheck=$?
|
|
[[ $save =~ e ]] && set -e
|
|
if [ $outCheck -ne 0 ]; then
|
|
ViashError "Docker container '$image_id' does not contain command '$missing'."
|
|
exit 1
|
|
fi
|
|
}
|
|
|
|
# ViashDockerBuild: build a docker image
|
|
# $1 : image identifier with format `[registry/]image[:tag]`
|
|
# $... : additional arguments to pass to docker build
|
|
# $VIASH_META_TEMP_DIR : temporary directory to store dockerfile & optional resources in
|
|
# $VIASH_META_NAME : name of the component
|
|
# $VIASH_META_RESOURCES_DIR : directory containing the resources
|
|
# $VIASH_VERBOSITY : verbosity level
|
|
# exit code $? : whether or not the image was built successfully
|
|
function ViashDockerBuild {
|
|
local image_id="$1"
|
|
shift 1
|
|
|
|
# create temporary directory to store dockerfile & optional resources in
|
|
local tmpdir=$(mktemp -d "$VIASH_META_TEMP_DIR/dockerbuild-$VIASH_META_NAME-XXXXXX")
|
|
local dockerfile="$tmpdir/Dockerfile"
|
|
function clean_up {
|
|
rm -rf "$tmpdir"
|
|
}
|
|
trap clean_up EXIT
|
|
|
|
# store dockerfile and resources
|
|
ViashDockerfile "$VIASH_ENGINE_ID" > "$dockerfile"
|
|
|
|
# generate the build command
|
|
local docker_build_cmd="docker build -t '$image_id' $@ '$VIASH_META_RESOURCES_DIR' -f '$dockerfile'"
|
|
|
|
# build the container
|
|
ViashNotice "Building container '$image_id' with Dockerfile"
|
|
ViashInfo "$docker_build_cmd"
|
|
local save=$-; set +e
|
|
if [ $VIASH_VERBOSITY -ge $VIASH_LOGCODE_INFO ]; then
|
|
eval $docker_build_cmd
|
|
else
|
|
eval $docker_build_cmd &> "$tmpdir/docker_build.log"
|
|
fi
|
|
|
|
# check exit code
|
|
local out=$?
|
|
[[ $save =~ e ]] && set -e
|
|
if [ $out -ne 0 ]; then
|
|
ViashError "Error occurred while building container '$image_id'"
|
|
if [ $VIASH_VERBOSITY -lt $VIASH_LOGCODE_INFO ]; then
|
|
ViashError "Transcript: --------------------------------"
|
|
cat "$tmpdir/docker_build.log"
|
|
ViashError "End of transcript --------------------------"
|
|
fi
|
|
exit 1
|
|
fi
|
|
}
|
|
|
|
######## End of helper functions for setting up Docker images for viash ########
|
|
|
|
# ViashDockerFile: print the dockerfile to stdout
|
|
# $1 : engine identifier
|
|
# return : dockerfile required to run this component
|
|
# examples:
|
|
# ViashDockerFile
|
|
function ViashDockerfile {
|
|
local engine_id="$1"
|
|
|
|
if [[ "$engine_id" == "docker" ]]; then
|
|
cat << 'VIASHDOCKER'
|
|
FROM quay.io/biocontainers/subread:2.0.6--he4a0461_0
|
|
ENTRYPOINT []
|
|
RUN featureCounts -v 2>&1 | sed 's/featureCounts v\([0-9.]*\)/featureCounts: \1/' > /var/software_versions.txt
|
|
|
|
LABEL org.opencontainers.image.authors="Sai Nirmayi Yasa"
|
|
LABEL org.opencontainers.image.description="Companion container for running component featurecounts"
|
|
LABEL org.opencontainers.image.created="2025-04-29T10:54:46Z"
|
|
LABEL org.opencontainers.image.source="https://github.com/ShiLab-Bioinformatics/subread"
|
|
LABEL org.opencontainers.image.revision="c733de2e4cc21eccb241060f82bce0b332f79d81"
|
|
LABEL org.opencontainers.image.version="main"
|
|
|
|
VIASHDOCKER
|
|
fi
|
|
}
|
|
|
|
# ViashDockerBuildArgs: return the arguments to pass to docker build
|
|
# $1 : engine identifier
|
|
# return : arguments to pass to docker build
|
|
function ViashDockerBuildArgs {
|
|
local engine_id="$1"
|
|
|
|
if [[ "$engine_id" == "docker" ]]; then
|
|
echo ""
|
|
fi
|
|
}
|
|
|
|
# ViashAbsolutePath: generate absolute path from relative path
|
|
# borrowed from https://stackoverflow.com/a/21951256
|
|
# $1 : relative filename
|
|
# return : absolute path
|
|
# examples:
|
|
# ViashAbsolutePath some_file.txt # returns /path/to/some_file.txt
|
|
# ViashAbsolutePath /foo/bar/.. # returns /foo
|
|
function ViashAbsolutePath {
|
|
local thePath
|
|
local parr
|
|
local outp
|
|
local len
|
|
if [[ ! "$1" =~ ^/ ]]; then
|
|
thePath="$PWD/$1"
|
|
else
|
|
thePath="$1"
|
|
fi
|
|
echo "$thePath" | (
|
|
IFS=/
|
|
read -a parr
|
|
declare -a outp
|
|
for i in "${parr[@]}"; do
|
|
case "$i" in
|
|
''|.) continue ;;
|
|
..)
|
|
len=${#outp[@]}
|
|
if ((len==0)); then
|
|
continue
|
|
else
|
|
unset outp[$((len-1))]
|
|
fi
|
|
;;
|
|
*)
|
|
len=${#outp[@]}
|
|
outp[$len]="$i"
|
|
;;
|
|
esac
|
|
done
|
|
echo /"${outp[*]}"
|
|
)
|
|
}
|
|
# ViashDockerAutodetectMount: auto configuring docker mounts from parameters
|
|
# $1 : The parameter value
|
|
# returns : New parameter
|
|
# $VIASH_DIRECTORY_MOUNTS : Added another parameter to be passed to docker
|
|
# $VIASH_DOCKER_AUTOMOUNT_PREFIX : The prefix to be used for the automounts
|
|
# examples:
|
|
# ViashDockerAutodetectMount /path/to/bar # returns '/viash_automount/path/to/bar'
|
|
# ViashDockerAutodetectMountArg /path/to/bar # returns '--volume="/path/to:/viash_automount/path/to"'
|
|
function ViashDockerAutodetectMount {
|
|
local abs_path=$(ViashAbsolutePath "$1")
|
|
local mount_source
|
|
local base_name
|
|
if [ -d "$abs_path" ]; then
|
|
mount_source="$abs_path"
|
|
base_name=""
|
|
else
|
|
mount_source=`dirname "$abs_path"`
|
|
base_name=`basename "$abs_path"`
|
|
fi
|
|
local mount_target="$VIASH_DOCKER_AUTOMOUNT_PREFIX$mount_source"
|
|
if [ -z "$base_name" ]; then
|
|
echo "$mount_target"
|
|
else
|
|
echo "$mount_target/$base_name"
|
|
fi
|
|
}
|
|
function ViashDockerAutodetectMountArg {
|
|
local abs_path=$(ViashAbsolutePath "$1")
|
|
local mount_source
|
|
local base_name
|
|
if [ -d "$abs_path" ]; then
|
|
mount_source="$abs_path"
|
|
base_name=""
|
|
else
|
|
mount_source=`dirname "$abs_path"`
|
|
base_name=`basename "$abs_path"`
|
|
fi
|
|
local mount_target="$VIASH_DOCKER_AUTOMOUNT_PREFIX$mount_source"
|
|
ViashDebug "ViashDockerAutodetectMountArg $1 -> $mount_source -> $mount_target"
|
|
echo "--volume=\"$mount_source:$mount_target\""
|
|
}
|
|
function ViashDockerStripAutomount {
|
|
local abs_path=$(ViashAbsolutePath "$1")
|
|
echo "${abs_path#$VIASH_DOCKER_AUTOMOUNT_PREFIX}"
|
|
}
|
|
# initialise variables
|
|
VIASH_DIRECTORY_MOUNTS=()
|
|
|
|
# configure default docker automount prefix if it is unset
|
|
if [ -z "${VIASH_DOCKER_AUTOMOUNT_PREFIX+x}" ]; then
|
|
VIASH_DOCKER_AUTOMOUNT_PREFIX="/viash_automount"
|
|
fi
|
|
|
|
# initialise docker variables
|
|
VIASH_DOCKER_RUN_ARGS=(-i --rm)
|
|
|
|
|
|
# ViashHelp: Display helpful explanation about this executable
|
|
function ViashHelp {
|
|
echo "featurecounts main"
|
|
echo ""
|
|
echo "featureCounts is a read summarization program for counting reads generated from"
|
|
echo "either RNA or genomic DNA sequencing experiments by implementing highly"
|
|
echo "efficient chromosome hashing and feature blocking techniques. It works with"
|
|
echo "either single or paired-end reads and provides a wide range of options"
|
|
echo "appropriate for different sequencing applications."
|
|
echo ""
|
|
echo "Inputs:"
|
|
echo " -a, --annotation"
|
|
echo " type: file, required parameter, file must exist"
|
|
echo " example: annotation.gtf"
|
|
echo " Name of an annotation file. GTF/GFF format by default. See '--format'"
|
|
echo " option for more format information."
|
|
echo ""
|
|
echo " -i, --input"
|
|
echo " type: file, required parameter, multiple values allowed, file must exist"
|
|
echo " example: input_file1.bam"
|
|
echo " A list of SAM or BAM format files separated by semi-colon (;). They can"
|
|
echo " be either name or location sorted. Location-sorted paired-end reads are"
|
|
echo " automatically sorted by read names."
|
|
echo ""
|
|
echo "Outputs:"
|
|
echo " -o, --counts"
|
|
echo " type: file, required parameter, output, file must exist"
|
|
echo " example: features.tsv"
|
|
echo " Name of output file including read counts in tab delimited format."
|
|
echo ""
|
|
echo " --summary"
|
|
echo " type: file, output, file must exist"
|
|
echo " example: summary.tsv"
|
|
echo " Summary statistics of counting results in tab delimited format."
|
|
echo ""
|
|
echo " --junctions"
|
|
echo " type: file, output, file must exist"
|
|
echo " example: junctions.txt"
|
|
echo " Count number of reads supporting each exon-exon junction. Junctions were"
|
|
echo " identified from those exon-spanning reads in the input (containing 'N'"
|
|
echo " in CIGAR string)."
|
|
echo ""
|
|
echo "Annotation:"
|
|
echo " -F, --format"
|
|
echo " type: string"
|
|
echo " example: GTF"
|
|
echo " choices: [ GTF, GFF, SAF ]"
|
|
echo " Specify format of the provided annotation file. Acceptable formats"
|
|
echo " include 'GTF' (or compatible GFF format) and 'SAF'. 'GTF' by default."
|
|
echo ""
|
|
echo " -t, --feature_type"
|
|
echo " type: string, multiple values allowed"
|
|
echo " example: exon"
|
|
echo " Specify feature type(s) in a GTF annotation. If multiple types are"
|
|
echo " provided, they should be separated by ';' with no space in between."
|
|
echo " 'exon' by default. Rows in the annotation with a matched feature will be"
|
|
echo " extracted and used for read mapping."
|
|
echo ""
|
|
echo " -g, --attribute_type"
|
|
echo " type: string"
|
|
echo " example: gene_id"
|
|
echo " Specify attribute type in GTF annotation. 'gene_id' by default."
|
|
echo " Meta-features used for read counting will be extracted from annotation"
|
|
echo " using the provided value."
|
|
echo ""
|
|
echo " --extra_attributes"
|
|
echo " type: string, multiple values allowed"
|
|
echo " Extract extra attribute types from the provided GTF annotation and"
|
|
echo " include them in the counting output. These attribute types will not be"
|
|
echo " used to group features. If more than one attribute type is provided they"
|
|
echo " should be separated by semicolon (;)."
|
|
echo ""
|
|
echo " -A, --chrom_alias"
|
|
echo " type: file, file must exist"
|
|
echo " example: chrom_alias.csv"
|
|
echo " Provide a chromosome name alias file to match chr names in annotation"
|
|
echo " with those in the reads. This should be a two-column comma-delimited"
|
|
echo " text file. Its first column should include chr names in the annotation"
|
|
echo " and its second column should include chr names in the reads. Chr names"
|
|
echo " are case sensitive. No column header should be included in the file."
|
|
echo ""
|
|
echo "Level of summarization:"
|
|
echo " -f, --feature_level"
|
|
echo " type: boolean_true"
|
|
echo " Perform read counting at feature level (eg. counting reads for exons"
|
|
echo " rather than genes)."
|
|
echo ""
|
|
echo "Overlap between reads and features:"
|
|
echo " -O, --overlapping"
|
|
echo " type: boolean_true"
|
|
echo " Assign reads to all their overlapping meta-features (or features if"
|
|
echo " '--feature_level' is specified)."
|
|
echo ""
|
|
echo " --min_overlap"
|
|
echo " type: integer"
|
|
echo " example: 1"
|
|
echo " Minimum number of overlapping bases in a read that is required for read"
|
|
echo " assignment. 1 by default. Number of overlapping bases is counted from"
|
|
echo " both reads if paired end. If a negative value is provided, then a gap of"
|
|
echo " up to specified size will be allowed between read and the feature that"
|
|
echo " the read is assigned to."
|
|
echo ""
|
|
echo " --frac_overlap"
|
|
echo " type: double"
|
|
echo " example: 0.0"
|
|
echo " min: 0.0"
|
|
echo " max: 1.0"
|
|
echo " Minimum fraction of overlapping bases in a read that is required for"
|
|
echo " read assignment. Value should be within range [0,1]. 0 by default."
|
|
echo " Number of overlapping bases is counted from both reads if paired end."
|
|
echo " Both this option and '--min_overlap' option need to be satisfied for"
|
|
echo " read assignment."
|
|
echo ""
|
|
echo " --frac_overlap_feature"
|
|
echo " type: double"
|
|
echo " example: 0.0"
|
|
echo " min: 0.0"
|
|
echo " max: 1.0"
|
|
echo " Minimum fraction of overlapping bases in a feature that is required for"
|
|
echo " read assignment. Value should be within range [0,1]. 0 by default."
|
|
echo ""
|
|
echo " --largest_overlap"
|
|
echo " type: boolean_true"
|
|
echo " Assign reads to a meta-feature/feature that has the largest number of"
|
|
echo " overlapping bases."
|
|
echo ""
|
|
echo " --non_overlap"
|
|
echo " type: integer"
|
|
echo " Maximum number of non-overlapping bases in a read (or a read pair) that"
|
|
echo " is allowed when being assigned to a feature. No limit is set by default."
|
|
echo ""
|
|
echo " --non_overlap_feature"
|
|
echo " type: integer"
|
|
echo " Maximum number of non-overlapping bases in a feature that is allowed in"
|
|
echo " read assignment. No limit is set by default."
|
|
echo ""
|
|
echo " --read_extension5"
|
|
echo " type: integer"
|
|
echo " Reads are extended upstream by <int> bases from their 5' end."
|
|
echo ""
|
|
echo " --read_extension3"
|
|
echo " type: integer"
|
|
echo " Reads are extended upstream by <int> bases from their 3' end."
|
|
echo ""
|
|
echo " --read2pos"
|
|
echo " type: integer"
|
|
echo " choices: [ 3, 5 ]"
|
|
echo " Reduce reads to their 5' most base or 3' most base. Read counting is"
|
|
echo " then performed based on the single base the read is reduced to."
|
|
echo ""
|
|
echo "Multi-mapping reads:"
|
|
echo " -M, --multi_mapping"
|
|
echo " type: boolean_true"
|
|
echo " Multi-mapping reads will also be counted. For a multi-mapping read, all"
|
|
echo " its reported alignments will be counted. The 'NH' tag in BAM/SAM input"
|
|
echo " is used to detect multi-mapping reads."
|
|
echo ""
|
|
echo "Fractional counting:"
|
|
echo " --fraction"
|
|
echo " type: boolean_true"
|
|
echo " Assign fractional counts to features. This option must be used together"
|
|
echo " with '--multi_mapping' or '--overlapping' or both. When"
|
|
echo " '--multi_mapping' is specified, each reported alignment from a"
|
|
echo " multi-mapping read (identified via 'NH' tag) will carry a fractional"
|
|
echo " count of 1/x, instead of 1 (one), where x is the total number of"
|
|
echo " alignments reported for the same read. When '--overlapping' is"
|
|
echo " specified, each overlapping feature will receive a fractional count of"
|
|
echo " 1/y, where y is the total number of features overlapping with the read."
|
|
echo " When both '--multi_mapping' and '--overlapping' are specified, each"
|
|
echo " alignment will carry a fractional count of 1/(x*y)."
|
|
echo ""
|
|
echo "Read filtering:"
|
|
echo " -Q, --min_map_quality"
|
|
echo " type: integer"
|
|
echo " example: 0"
|
|
echo " The minimum mapping quality score a read must satisfy in order to be"
|
|
echo " counted. For paired-end reads, at least one end should satisfy this"
|
|
echo " criteria. 0 by default."
|
|
echo ""
|
|
echo " --split_only"
|
|
echo " type: boolean_true"
|
|
echo " Count split alignments only (ie. alignments with CIGAR string containing"
|
|
echo " 'N'). An example of split alignments is exon-spanning reads in RNA-seq"
|
|
echo " data."
|
|
echo ""
|
|
echo " --non_split_only"
|
|
echo " type: boolean_true"
|
|
echo " If specified, only non-split alignments (CIGAR strings do not contain"
|
|
echo " letter 'N') will be counted. All the other alignments will be ignored."
|
|
echo ""
|
|
echo " --primary"
|
|
echo " type: boolean_true"
|
|
echo " Count primary alignments only. Primary alignments are identified using"
|
|
echo " bit 0x100 in SAM/BAM FLAG field."
|
|
echo ""
|
|
echo " --ignore_dup"
|
|
echo " type: boolean_true"
|
|
echo " Ignore duplicate reads in read counting. Duplicate reads are identified"
|
|
echo " using bit Ox400 in BAM/SAM FLAG field. The whole read pair is ignored if"
|
|
echo " one of the reads is a duplicate read for paired end data."
|
|
echo ""
|
|
echo "Strandedness:"
|
|
echo " -s, --strand"
|
|
echo " type: integer"
|
|
echo " example: 0"
|
|
echo " choices: [ 0, 1, 2 ]"
|
|
echo " Perform strand-specific read counting. A single integer value (applied"
|
|
echo " to all input files) should be provided. Possible values include: 0"
|
|
echo " (unstranded), 1 (stranded) and 2 (reversely stranded). Default value is"
|
|
echo " 0 (ie. unstranded read counting carried out for all input files)."
|
|
echo ""
|
|
echo "Exon-exon junctions:"
|
|
echo " -G, --ref_fasta"
|
|
echo " type: file, file must exist"
|
|
echo " example: reference.fasta"
|
|
echo " Provide the name of a FASTA-format file that contains the reference"
|
|
echo " sequences used in read mapping that produced the provided SAM/BAM files."
|
|
echo ""
|
|
echo "Parameters specific to paired end reads:"
|
|
echo " -p, --paired"
|
|
echo " type: boolean_true"
|
|
echo " Specify that input data contain paired-end reads. To perform fragment"
|
|
echo " counting (ie. counting read pairs), the '--countReadPairs' parameter"
|
|
echo " should also be specified in addition to this parameter."
|
|
echo ""
|
|
echo " --count_read_pairs"
|
|
echo " type: boolean_true"
|
|
echo " Count read pairs (fragments) instead of reads. This option is only"
|
|
echo " applicable for paired-end reads."
|
|
echo ""
|
|
echo " -B, --both_aligned"
|
|
echo " type: boolean_true"
|
|
echo " Count read pairs (fragments) instead of reads. This option is only"
|
|
echo " applicable for paired-end reads."
|
|
echo ""
|
|
echo " -P, --check_pe_dist"
|
|
echo " type: boolean_true"
|
|
echo " Check validity of paired-end distance when counting read pairs. Use"
|
|
echo " '--min_length' and '--max_length' to set thresholds."
|
|
echo ""
|
|
echo " -d, --min_length"
|
|
echo " type: integer"
|
|
echo " example: 50"
|
|
echo " Minimum fragment/template length, 50 by default."
|
|
echo ""
|
|
echo " -D, --max_length"
|
|
echo " type: integer"
|
|
echo " example: 600"
|
|
echo " Maximum fragment/template length, 600 by default."
|
|
echo ""
|
|
echo " -C, --same_strand"
|
|
echo " type: boolean_true"
|
|
echo " Do not count read pairs that have their two ends mapping to different"
|
|
echo " chromosomes or mapping to same chromosome but on different strands."
|
|
echo ""
|
|
echo " --donotsort"
|
|
echo " type: boolean_true"
|
|
echo " Do not sort reads in BAM/SAM input. Note that reads from the same pair"
|
|
echo " are required to be located next to each other in the input."
|
|
echo ""
|
|
echo "Read groups:"
|
|
echo " --by_read_group"
|
|
echo " type: boolean_true"
|
|
echo " Assign reads by read group. \"RG\" tag is required to be present in the"
|
|
echo " input BAM/SAM files."
|
|
echo ""
|
|
echo "Long reads:"
|
|
echo " --long_reads"
|
|
echo " type: boolean_true"
|
|
echo " Count long reads such as Nanopore and PacBio reads. Long read counting"
|
|
echo " can only run in one thread and only reads (not read-pairs) can be"
|
|
echo " counted. There is no limitation on the number of 'M' operations allowed"
|
|
echo " in a CIGAR string in long read counting."
|
|
echo ""
|
|
echo "Assignment results for each read:"
|
|
echo " --detailed_results"
|
|
echo " type: file, output, file must exist"
|
|
echo " example: detailed_results"
|
|
echo " Directory to save the detailed assignment results. Use"
|
|
echo " \`--detailed_results_format\` to determine the format of the detailed"
|
|
echo " results."
|
|
echo ""
|
|
echo " -R, --detailed_results_format"
|
|
echo " type: string"
|
|
echo " choices: [ CORE, SAM, BAM ]"
|
|
echo " Output detailed assignment results for each read or read-pair. Results"
|
|
echo " are saved to a file that is in one of the following formats: CORE, SAM"
|
|
echo " and BAM. See documentaiton for more info about these formats."
|
|
echo ""
|
|
echo "Miscellaneous:"
|
|
echo " --max_M_op"
|
|
echo " type: integer"
|
|
echo " example: 10"
|
|
echo " Maximum number of 'M' operations allowed in a CIGAR string. 10 by"
|
|
echo " default. Both 'X' and '=' are treated as 'M' and adjacent 'M' operations"
|
|
echo " are merged in the CIGAR string."
|
|
echo ""
|
|
echo " --verbose"
|
|
echo " type: boolean_true"
|
|
echo " Output verbose information for debugging, such as un-matched"
|
|
echo " chromosome/contig names."
|
|
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 "$1")"
|
|
shift 1
|
|
;;
|
|
--version)
|
|
echo "featurecounts main"
|
|
exit
|
|
;;
|
|
--annotation)
|
|
[ -n "$VIASH_PAR_ANNOTATION" ] && ViashError Bad arguments for option \'--annotation\': \'$VIASH_PAR_ANNOTATION\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_ANNOTATION="$2"
|
|
[ $# -lt 2 ] && ViashError Not enough arguments passed to --annotation. Use "--help" to get more information on the parameters. && exit 1
|
|
shift 2
|
|
;;
|
|
--annotation=*)
|
|
[ -n "$VIASH_PAR_ANNOTATION" ] && ViashError Bad arguments for option \'--annotation=*\': \'$VIASH_PAR_ANNOTATION\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_ANNOTATION=$(ViashRemoveFlags "$1")
|
|
shift 1
|
|
;;
|
|
-a)
|
|
[ -n "$VIASH_PAR_ANNOTATION" ] && ViashError Bad arguments for option \'-a\': \'$VIASH_PAR_ANNOTATION\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_ANNOTATION="$2"
|
|
[ $# -lt 2 ] && ViashError Not enough arguments passed to -a. Use "--help" to get more information on the parameters. && exit 1
|
|
shift 2
|
|
;;
|
|
--input)
|
|
if [ -z "$VIASH_PAR_INPUT" ]; then
|
|
VIASH_PAR_INPUT="$2"
|
|
else
|
|
VIASH_PAR_INPUT="$VIASH_PAR_INPUT;""$2"
|
|
fi
|
|
[ $# -lt 2 ] && ViashError Not enough arguments passed to --input. Use "--help" to get more information on the parameters. && exit 1
|
|
shift 2
|
|
;;
|
|
--input=*)
|
|
if [ -z "$VIASH_PAR_INPUT" ]; then
|
|
VIASH_PAR_INPUT=$(ViashRemoveFlags "$1")
|
|
else
|
|
VIASH_PAR_INPUT="$VIASH_PAR_INPUT;"$(ViashRemoveFlags "$1")
|
|
fi
|
|
shift 1
|
|
;;
|
|
-i)
|
|
if [ -z "$VIASH_PAR_INPUT" ]; then
|
|
VIASH_PAR_INPUT="$2"
|
|
else
|
|
VIASH_PAR_INPUT="$VIASH_PAR_INPUT;""$2"
|
|
fi
|
|
[ $# -lt 2 ] && ViashError Not enough arguments passed to -i. Use "--help" to get more information on the parameters. && exit 1
|
|
shift 2
|
|
;;
|
|
--counts)
|
|
[ -n "$VIASH_PAR_COUNTS" ] && ViashError Bad arguments for option \'--counts\': \'$VIASH_PAR_COUNTS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_COUNTS="$2"
|
|
[ $# -lt 2 ] && ViashError Not enough arguments passed to --counts. Use "--help" to get more information on the parameters. && exit 1
|
|
shift 2
|
|
;;
|
|
--counts=*)
|
|
[ -n "$VIASH_PAR_COUNTS" ] && ViashError Bad arguments for option \'--counts=*\': \'$VIASH_PAR_COUNTS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_COUNTS=$(ViashRemoveFlags "$1")
|
|
shift 1
|
|
;;
|
|
-o)
|
|
[ -n "$VIASH_PAR_COUNTS" ] && ViashError Bad arguments for option \'-o\': \'$VIASH_PAR_COUNTS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_COUNTS="$2"
|
|
[ $# -lt 2 ] && ViashError Not enough arguments passed to -o. Use "--help" to get more information on the parameters. && exit 1
|
|
shift 2
|
|
;;
|
|
--summary)
|
|
[ -n "$VIASH_PAR_SUMMARY" ] && ViashError Bad arguments for option \'--summary\': \'$VIASH_PAR_SUMMARY\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_SUMMARY="$2"
|
|
[ $# -lt 2 ] && ViashError Not enough arguments passed to --summary. Use "--help" to get more information on the parameters. && exit 1
|
|
shift 2
|
|
;;
|
|
--summary=*)
|
|
[ -n "$VIASH_PAR_SUMMARY" ] && ViashError Bad arguments for option \'--summary=*\': \'$VIASH_PAR_SUMMARY\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_SUMMARY=$(ViashRemoveFlags "$1")
|
|
shift 1
|
|
;;
|
|
--junctions)
|
|
[ -n "$VIASH_PAR_JUNCTIONS" ] && ViashError Bad arguments for option \'--junctions\': \'$VIASH_PAR_JUNCTIONS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_JUNCTIONS="$2"
|
|
[ $# -lt 2 ] && ViashError Not enough arguments passed to --junctions. Use "--help" to get more information on the parameters. && exit 1
|
|
shift 2
|
|
;;
|
|
--junctions=*)
|
|
[ -n "$VIASH_PAR_JUNCTIONS" ] && ViashError Bad arguments for option \'--junctions=*\': \'$VIASH_PAR_JUNCTIONS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_JUNCTIONS=$(ViashRemoveFlags "$1")
|
|
shift 1
|
|
;;
|
|
--format)
|
|
[ -n "$VIASH_PAR_FORMAT" ] && ViashError Bad arguments for option \'--format\': \'$VIASH_PAR_FORMAT\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_FORMAT="$2"
|
|
[ $# -lt 2 ] && ViashError Not enough arguments passed to --format. Use "--help" to get more information on the parameters. && exit 1
|
|
shift 2
|
|
;;
|
|
--format=*)
|
|
[ -n "$VIASH_PAR_FORMAT" ] && ViashError Bad arguments for option \'--format=*\': \'$VIASH_PAR_FORMAT\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_FORMAT=$(ViashRemoveFlags "$1")
|
|
shift 1
|
|
;;
|
|
-F)
|
|
[ -n "$VIASH_PAR_FORMAT" ] && ViashError Bad arguments for option \'-F\': \'$VIASH_PAR_FORMAT\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_FORMAT="$2"
|
|
[ $# -lt 2 ] && ViashError Not enough arguments passed to -F. Use "--help" to get more information on the parameters. && exit 1
|
|
shift 2
|
|
;;
|
|
--feature_type)
|
|
if [ -z "$VIASH_PAR_FEATURE_TYPE" ]; then
|
|
VIASH_PAR_FEATURE_TYPE="$2"
|
|
else
|
|
VIASH_PAR_FEATURE_TYPE="$VIASH_PAR_FEATURE_TYPE;""$2"
|
|
fi
|
|
[ $# -lt 2 ] && ViashError Not enough arguments passed to --feature_type. Use "--help" to get more information on the parameters. && exit 1
|
|
shift 2
|
|
;;
|
|
--feature_type=*)
|
|
if [ -z "$VIASH_PAR_FEATURE_TYPE" ]; then
|
|
VIASH_PAR_FEATURE_TYPE=$(ViashRemoveFlags "$1")
|
|
else
|
|
VIASH_PAR_FEATURE_TYPE="$VIASH_PAR_FEATURE_TYPE;"$(ViashRemoveFlags "$1")
|
|
fi
|
|
shift 1
|
|
;;
|
|
-t)
|
|
if [ -z "$VIASH_PAR_FEATURE_TYPE" ]; then
|
|
VIASH_PAR_FEATURE_TYPE="$2"
|
|
else
|
|
VIASH_PAR_FEATURE_TYPE="$VIASH_PAR_FEATURE_TYPE;""$2"
|
|
fi
|
|
[ $# -lt 2 ] && ViashError Not enough arguments passed to -t. Use "--help" to get more information on the parameters. && exit 1
|
|
shift 2
|
|
;;
|
|
--attribute_type)
|
|
[ -n "$VIASH_PAR_ATTRIBUTE_TYPE" ] && ViashError Bad arguments for option \'--attribute_type\': \'$VIASH_PAR_ATTRIBUTE_TYPE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_ATTRIBUTE_TYPE="$2"
|
|
[ $# -lt 2 ] && ViashError Not enough arguments passed to --attribute_type. Use "--help" to get more information on the parameters. && exit 1
|
|
shift 2
|
|
;;
|
|
--attribute_type=*)
|
|
[ -n "$VIASH_PAR_ATTRIBUTE_TYPE" ] && ViashError Bad arguments for option \'--attribute_type=*\': \'$VIASH_PAR_ATTRIBUTE_TYPE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_ATTRIBUTE_TYPE=$(ViashRemoveFlags "$1")
|
|
shift 1
|
|
;;
|
|
-g)
|
|
[ -n "$VIASH_PAR_ATTRIBUTE_TYPE" ] && ViashError Bad arguments for option \'-g\': \'$VIASH_PAR_ATTRIBUTE_TYPE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_ATTRIBUTE_TYPE="$2"
|
|
[ $# -lt 2 ] && ViashError Not enough arguments passed to -g. Use "--help" to get more information on the parameters. && exit 1
|
|
shift 2
|
|
;;
|
|
--extra_attributes)
|
|
if [ -z "$VIASH_PAR_EXTRA_ATTRIBUTES" ]; then
|
|
VIASH_PAR_EXTRA_ATTRIBUTES="$2"
|
|
else
|
|
VIASH_PAR_EXTRA_ATTRIBUTES="$VIASH_PAR_EXTRA_ATTRIBUTES;""$2"
|
|
fi
|
|
[ $# -lt 2 ] && ViashError Not enough arguments passed to --extra_attributes. Use "--help" to get more information on the parameters. && exit 1
|
|
shift 2
|
|
;;
|
|
--extra_attributes=*)
|
|
if [ -z "$VIASH_PAR_EXTRA_ATTRIBUTES" ]; then
|
|
VIASH_PAR_EXTRA_ATTRIBUTES=$(ViashRemoveFlags "$1")
|
|
else
|
|
VIASH_PAR_EXTRA_ATTRIBUTES="$VIASH_PAR_EXTRA_ATTRIBUTES;"$(ViashRemoveFlags "$1")
|
|
fi
|
|
shift 1
|
|
;;
|
|
--chrom_alias)
|
|
[ -n "$VIASH_PAR_CHROM_ALIAS" ] && ViashError Bad arguments for option \'--chrom_alias\': \'$VIASH_PAR_CHROM_ALIAS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_CHROM_ALIAS="$2"
|
|
[ $# -lt 2 ] && ViashError Not enough arguments passed to --chrom_alias. Use "--help" to get more information on the parameters. && exit 1
|
|
shift 2
|
|
;;
|
|
--chrom_alias=*)
|
|
[ -n "$VIASH_PAR_CHROM_ALIAS" ] && ViashError Bad arguments for option \'--chrom_alias=*\': \'$VIASH_PAR_CHROM_ALIAS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_CHROM_ALIAS=$(ViashRemoveFlags "$1")
|
|
shift 1
|
|
;;
|
|
-A)
|
|
[ -n "$VIASH_PAR_CHROM_ALIAS" ] && ViashError Bad arguments for option \'-A\': \'$VIASH_PAR_CHROM_ALIAS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_CHROM_ALIAS="$2"
|
|
[ $# -lt 2 ] && ViashError Not enough arguments passed to -A. Use "--help" to get more information on the parameters. && exit 1
|
|
shift 2
|
|
;;
|
|
--feature_level)
|
|
[ -n "$VIASH_PAR_FEATURE_LEVEL" ] && ViashError Bad arguments for option \'--feature_level\': \'$VIASH_PAR_FEATURE_LEVEL\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_FEATURE_LEVEL=true
|
|
shift 1
|
|
;;
|
|
-f)
|
|
[ -n "$VIASH_PAR_FEATURE_LEVEL" ] && ViashError Bad arguments for option \'-f\': \'$VIASH_PAR_FEATURE_LEVEL\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_FEATURE_LEVEL=true
|
|
shift 1
|
|
;;
|
|
--overlapping)
|
|
[ -n "$VIASH_PAR_OVERLAPPING" ] && ViashError Bad arguments for option \'--overlapping\': \'$VIASH_PAR_OVERLAPPING\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_OVERLAPPING=true
|
|
shift 1
|
|
;;
|
|
-O)
|
|
[ -n "$VIASH_PAR_OVERLAPPING" ] && ViashError Bad arguments for option \'-O\': \'$VIASH_PAR_OVERLAPPING\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_OVERLAPPING=true
|
|
shift 1
|
|
;;
|
|
--min_overlap)
|
|
[ -n "$VIASH_PAR_MIN_OVERLAP" ] && ViashError Bad arguments for option \'--min_overlap\': \'$VIASH_PAR_MIN_OVERLAP\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_MIN_OVERLAP="$2"
|
|
[ $# -lt 2 ] && ViashError Not enough arguments passed to --min_overlap. Use "--help" to get more information on the parameters. && exit 1
|
|
shift 2
|
|
;;
|
|
--min_overlap=*)
|
|
[ -n "$VIASH_PAR_MIN_OVERLAP" ] && ViashError Bad arguments for option \'--min_overlap=*\': \'$VIASH_PAR_MIN_OVERLAP\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_MIN_OVERLAP=$(ViashRemoveFlags "$1")
|
|
shift 1
|
|
;;
|
|
--frac_overlap)
|
|
[ -n "$VIASH_PAR_FRAC_OVERLAP" ] && ViashError Bad arguments for option \'--frac_overlap\': \'$VIASH_PAR_FRAC_OVERLAP\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_FRAC_OVERLAP="$2"
|
|
[ $# -lt 2 ] && ViashError Not enough arguments passed to --frac_overlap. Use "--help" to get more information on the parameters. && exit 1
|
|
shift 2
|
|
;;
|
|
--frac_overlap=*)
|
|
[ -n "$VIASH_PAR_FRAC_OVERLAP" ] && ViashError Bad arguments for option \'--frac_overlap=*\': \'$VIASH_PAR_FRAC_OVERLAP\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_FRAC_OVERLAP=$(ViashRemoveFlags "$1")
|
|
shift 1
|
|
;;
|
|
--frac_overlap_feature)
|
|
[ -n "$VIASH_PAR_FRAC_OVERLAP_FEATURE" ] && ViashError Bad arguments for option \'--frac_overlap_feature\': \'$VIASH_PAR_FRAC_OVERLAP_FEATURE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_FRAC_OVERLAP_FEATURE="$2"
|
|
[ $# -lt 2 ] && ViashError Not enough arguments passed to --frac_overlap_feature. Use "--help" to get more information on the parameters. && exit 1
|
|
shift 2
|
|
;;
|
|
--frac_overlap_feature=*)
|
|
[ -n "$VIASH_PAR_FRAC_OVERLAP_FEATURE" ] && ViashError Bad arguments for option \'--frac_overlap_feature=*\': \'$VIASH_PAR_FRAC_OVERLAP_FEATURE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_FRAC_OVERLAP_FEATURE=$(ViashRemoveFlags "$1")
|
|
shift 1
|
|
;;
|
|
--largest_overlap)
|
|
[ -n "$VIASH_PAR_LARGEST_OVERLAP" ] && ViashError Bad arguments for option \'--largest_overlap\': \'$VIASH_PAR_LARGEST_OVERLAP\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_LARGEST_OVERLAP=true
|
|
shift 1
|
|
;;
|
|
--non_overlap)
|
|
[ -n "$VIASH_PAR_NON_OVERLAP" ] && ViashError Bad arguments for option \'--non_overlap\': \'$VIASH_PAR_NON_OVERLAP\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_NON_OVERLAP="$2"
|
|
[ $# -lt 2 ] && ViashError Not enough arguments passed to --non_overlap. Use "--help" to get more information on the parameters. && exit 1
|
|
shift 2
|
|
;;
|
|
--non_overlap=*)
|
|
[ -n "$VIASH_PAR_NON_OVERLAP" ] && ViashError Bad arguments for option \'--non_overlap=*\': \'$VIASH_PAR_NON_OVERLAP\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_NON_OVERLAP=$(ViashRemoveFlags "$1")
|
|
shift 1
|
|
;;
|
|
--non_overlap_feature)
|
|
[ -n "$VIASH_PAR_NON_OVERLAP_FEATURE" ] && ViashError Bad arguments for option \'--non_overlap_feature\': \'$VIASH_PAR_NON_OVERLAP_FEATURE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_NON_OVERLAP_FEATURE="$2"
|
|
[ $# -lt 2 ] && ViashError Not enough arguments passed to --non_overlap_feature. Use "--help" to get more information on the parameters. && exit 1
|
|
shift 2
|
|
;;
|
|
--non_overlap_feature=*)
|
|
[ -n "$VIASH_PAR_NON_OVERLAP_FEATURE" ] && ViashError Bad arguments for option \'--non_overlap_feature=*\': \'$VIASH_PAR_NON_OVERLAP_FEATURE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_NON_OVERLAP_FEATURE=$(ViashRemoveFlags "$1")
|
|
shift 1
|
|
;;
|
|
--read_extension5)
|
|
[ -n "$VIASH_PAR_READ_EXTENSION5" ] && ViashError Bad arguments for option \'--read_extension5\': \'$VIASH_PAR_READ_EXTENSION5\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_READ_EXTENSION5="$2"
|
|
[ $# -lt 2 ] && ViashError Not enough arguments passed to --read_extension5. Use "--help" to get more information on the parameters. && exit 1
|
|
shift 2
|
|
;;
|
|
--read_extension5=*)
|
|
[ -n "$VIASH_PAR_READ_EXTENSION5" ] && ViashError Bad arguments for option \'--read_extension5=*\': \'$VIASH_PAR_READ_EXTENSION5\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_READ_EXTENSION5=$(ViashRemoveFlags "$1")
|
|
shift 1
|
|
;;
|
|
--read_extension3)
|
|
[ -n "$VIASH_PAR_READ_EXTENSION3" ] && ViashError Bad arguments for option \'--read_extension3\': \'$VIASH_PAR_READ_EXTENSION3\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_READ_EXTENSION3="$2"
|
|
[ $# -lt 2 ] && ViashError Not enough arguments passed to --read_extension3. Use "--help" to get more information on the parameters. && exit 1
|
|
shift 2
|
|
;;
|
|
--read_extension3=*)
|
|
[ -n "$VIASH_PAR_READ_EXTENSION3" ] && ViashError Bad arguments for option \'--read_extension3=*\': \'$VIASH_PAR_READ_EXTENSION3\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_READ_EXTENSION3=$(ViashRemoveFlags "$1")
|
|
shift 1
|
|
;;
|
|
--read2pos)
|
|
[ -n "$VIASH_PAR_READ2POS" ] && ViashError Bad arguments for option \'--read2pos\': \'$VIASH_PAR_READ2POS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_READ2POS="$2"
|
|
[ $# -lt 2 ] && ViashError Not enough arguments passed to --read2pos. Use "--help" to get more information on the parameters. && exit 1
|
|
shift 2
|
|
;;
|
|
--read2pos=*)
|
|
[ -n "$VIASH_PAR_READ2POS" ] && ViashError Bad arguments for option \'--read2pos=*\': \'$VIASH_PAR_READ2POS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_READ2POS=$(ViashRemoveFlags "$1")
|
|
shift 1
|
|
;;
|
|
--multi_mapping)
|
|
[ -n "$VIASH_PAR_MULTI_MAPPING" ] && ViashError Bad arguments for option \'--multi_mapping\': \'$VIASH_PAR_MULTI_MAPPING\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_MULTI_MAPPING=true
|
|
shift 1
|
|
;;
|
|
-M)
|
|
[ -n "$VIASH_PAR_MULTI_MAPPING" ] && ViashError Bad arguments for option \'-M\': \'$VIASH_PAR_MULTI_MAPPING\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_MULTI_MAPPING=true
|
|
shift 1
|
|
;;
|
|
--fraction)
|
|
[ -n "$VIASH_PAR_FRACTION" ] && ViashError Bad arguments for option \'--fraction\': \'$VIASH_PAR_FRACTION\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_FRACTION=true
|
|
shift 1
|
|
;;
|
|
--min_map_quality)
|
|
[ -n "$VIASH_PAR_MIN_MAP_QUALITY" ] && ViashError Bad arguments for option \'--min_map_quality\': \'$VIASH_PAR_MIN_MAP_QUALITY\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_MIN_MAP_QUALITY="$2"
|
|
[ $# -lt 2 ] && ViashError Not enough arguments passed to --min_map_quality. Use "--help" to get more information on the parameters. && exit 1
|
|
shift 2
|
|
;;
|
|
--min_map_quality=*)
|
|
[ -n "$VIASH_PAR_MIN_MAP_QUALITY" ] && ViashError Bad arguments for option \'--min_map_quality=*\': \'$VIASH_PAR_MIN_MAP_QUALITY\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_MIN_MAP_QUALITY=$(ViashRemoveFlags "$1")
|
|
shift 1
|
|
;;
|
|
-Q)
|
|
[ -n "$VIASH_PAR_MIN_MAP_QUALITY" ] && ViashError Bad arguments for option \'-Q\': \'$VIASH_PAR_MIN_MAP_QUALITY\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_MIN_MAP_QUALITY="$2"
|
|
[ $# -lt 2 ] && ViashError Not enough arguments passed to -Q. Use "--help" to get more information on the parameters. && exit 1
|
|
shift 2
|
|
;;
|
|
--split_only)
|
|
[ -n "$VIASH_PAR_SPLIT_ONLY" ] && ViashError Bad arguments for option \'--split_only\': \'$VIASH_PAR_SPLIT_ONLY\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_SPLIT_ONLY=true
|
|
shift 1
|
|
;;
|
|
--non_split_only)
|
|
[ -n "$VIASH_PAR_NON_SPLIT_ONLY" ] && ViashError Bad arguments for option \'--non_split_only\': \'$VIASH_PAR_NON_SPLIT_ONLY\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_NON_SPLIT_ONLY=true
|
|
shift 1
|
|
;;
|
|
--primary)
|
|
[ -n "$VIASH_PAR_PRIMARY" ] && ViashError Bad arguments for option \'--primary\': \'$VIASH_PAR_PRIMARY\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_PRIMARY=true
|
|
shift 1
|
|
;;
|
|
--ignore_dup)
|
|
[ -n "$VIASH_PAR_IGNORE_DUP" ] && ViashError Bad arguments for option \'--ignore_dup\': \'$VIASH_PAR_IGNORE_DUP\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_IGNORE_DUP=true
|
|
shift 1
|
|
;;
|
|
--strand)
|
|
[ -n "$VIASH_PAR_STRAND" ] && ViashError Bad arguments for option \'--strand\': \'$VIASH_PAR_STRAND\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_STRAND="$2"
|
|
[ $# -lt 2 ] && ViashError Not enough arguments passed to --strand. Use "--help" to get more information on the parameters. && exit 1
|
|
shift 2
|
|
;;
|
|
--strand=*)
|
|
[ -n "$VIASH_PAR_STRAND" ] && ViashError Bad arguments for option \'--strand=*\': \'$VIASH_PAR_STRAND\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_STRAND=$(ViashRemoveFlags "$1")
|
|
shift 1
|
|
;;
|
|
-s)
|
|
[ -n "$VIASH_PAR_STRAND" ] && ViashError Bad arguments for option \'-s\': \'$VIASH_PAR_STRAND\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_STRAND="$2"
|
|
[ $# -lt 2 ] && ViashError Not enough arguments passed to -s. Use "--help" to get more information on the parameters. && exit 1
|
|
shift 2
|
|
;;
|
|
--ref_fasta)
|
|
[ -n "$VIASH_PAR_REF_FASTA" ] && ViashError Bad arguments for option \'--ref_fasta\': \'$VIASH_PAR_REF_FASTA\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_REF_FASTA="$2"
|
|
[ $# -lt 2 ] && ViashError Not enough arguments passed to --ref_fasta. Use "--help" to get more information on the parameters. && exit 1
|
|
shift 2
|
|
;;
|
|
--ref_fasta=*)
|
|
[ -n "$VIASH_PAR_REF_FASTA" ] && ViashError Bad arguments for option \'--ref_fasta=*\': \'$VIASH_PAR_REF_FASTA\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_REF_FASTA=$(ViashRemoveFlags "$1")
|
|
shift 1
|
|
;;
|
|
-G)
|
|
[ -n "$VIASH_PAR_REF_FASTA" ] && ViashError Bad arguments for option \'-G\': \'$VIASH_PAR_REF_FASTA\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_REF_FASTA="$2"
|
|
[ $# -lt 2 ] && ViashError Not enough arguments passed to -G. Use "--help" to get more information on the parameters. && exit 1
|
|
shift 2
|
|
;;
|
|
--paired)
|
|
[ -n "$VIASH_PAR_PAIRED" ] && ViashError Bad arguments for option \'--paired\': \'$VIASH_PAR_PAIRED\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_PAIRED=true
|
|
shift 1
|
|
;;
|
|
-p)
|
|
[ -n "$VIASH_PAR_PAIRED" ] && ViashError Bad arguments for option \'-p\': \'$VIASH_PAR_PAIRED\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_PAIRED=true
|
|
shift 1
|
|
;;
|
|
--count_read_pairs)
|
|
[ -n "$VIASH_PAR_COUNT_READ_PAIRS" ] && ViashError Bad arguments for option \'--count_read_pairs\': \'$VIASH_PAR_COUNT_READ_PAIRS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_COUNT_READ_PAIRS=true
|
|
shift 1
|
|
;;
|
|
--both_aligned)
|
|
[ -n "$VIASH_PAR_BOTH_ALIGNED" ] && ViashError Bad arguments for option \'--both_aligned\': \'$VIASH_PAR_BOTH_ALIGNED\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_BOTH_ALIGNED=true
|
|
shift 1
|
|
;;
|
|
-B)
|
|
[ -n "$VIASH_PAR_BOTH_ALIGNED" ] && ViashError Bad arguments for option \'-B\': \'$VIASH_PAR_BOTH_ALIGNED\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_BOTH_ALIGNED=true
|
|
shift 1
|
|
;;
|
|
--check_pe_dist)
|
|
[ -n "$VIASH_PAR_CHECK_PE_DIST" ] && ViashError Bad arguments for option \'--check_pe_dist\': \'$VIASH_PAR_CHECK_PE_DIST\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_CHECK_PE_DIST=true
|
|
shift 1
|
|
;;
|
|
-P)
|
|
[ -n "$VIASH_PAR_CHECK_PE_DIST" ] && ViashError Bad arguments for option \'-P\': \'$VIASH_PAR_CHECK_PE_DIST\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_CHECK_PE_DIST=true
|
|
shift 1
|
|
;;
|
|
--min_length)
|
|
[ -n "$VIASH_PAR_MIN_LENGTH" ] && ViashError Bad arguments for option \'--min_length\': \'$VIASH_PAR_MIN_LENGTH\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_MIN_LENGTH="$2"
|
|
[ $# -lt 2 ] && ViashError Not enough arguments passed to --min_length. Use "--help" to get more information on the parameters. && exit 1
|
|
shift 2
|
|
;;
|
|
--min_length=*)
|
|
[ -n "$VIASH_PAR_MIN_LENGTH" ] && ViashError Bad arguments for option \'--min_length=*\': \'$VIASH_PAR_MIN_LENGTH\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_MIN_LENGTH=$(ViashRemoveFlags "$1")
|
|
shift 1
|
|
;;
|
|
-d)
|
|
[ -n "$VIASH_PAR_MIN_LENGTH" ] && ViashError Bad arguments for option \'-d\': \'$VIASH_PAR_MIN_LENGTH\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_MIN_LENGTH="$2"
|
|
[ $# -lt 2 ] && ViashError Not enough arguments passed to -d. Use "--help" to get more information on the parameters. && exit 1
|
|
shift 2
|
|
;;
|
|
--max_length)
|
|
[ -n "$VIASH_PAR_MAX_LENGTH" ] && ViashError Bad arguments for option \'--max_length\': \'$VIASH_PAR_MAX_LENGTH\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_MAX_LENGTH="$2"
|
|
[ $# -lt 2 ] && ViashError Not enough arguments passed to --max_length. Use "--help" to get more information on the parameters. && exit 1
|
|
shift 2
|
|
;;
|
|
--max_length=*)
|
|
[ -n "$VIASH_PAR_MAX_LENGTH" ] && ViashError Bad arguments for option \'--max_length=*\': \'$VIASH_PAR_MAX_LENGTH\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_MAX_LENGTH=$(ViashRemoveFlags "$1")
|
|
shift 1
|
|
;;
|
|
-D)
|
|
[ -n "$VIASH_PAR_MAX_LENGTH" ] && ViashError Bad arguments for option \'-D\': \'$VIASH_PAR_MAX_LENGTH\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_MAX_LENGTH="$2"
|
|
[ $# -lt 2 ] && ViashError Not enough arguments passed to -D. Use "--help" to get more information on the parameters. && exit 1
|
|
shift 2
|
|
;;
|
|
--same_strand)
|
|
[ -n "$VIASH_PAR_SAME_STRAND" ] && ViashError Bad arguments for option \'--same_strand\': \'$VIASH_PAR_SAME_STRAND\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_SAME_STRAND=true
|
|
shift 1
|
|
;;
|
|
-C)
|
|
[ -n "$VIASH_PAR_SAME_STRAND" ] && ViashError Bad arguments for option \'-C\': \'$VIASH_PAR_SAME_STRAND\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_SAME_STRAND=true
|
|
shift 1
|
|
;;
|
|
--donotsort)
|
|
[ -n "$VIASH_PAR_DONOTSORT" ] && ViashError Bad arguments for option \'--donotsort\': \'$VIASH_PAR_DONOTSORT\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_DONOTSORT=true
|
|
shift 1
|
|
;;
|
|
--by_read_group)
|
|
[ -n "$VIASH_PAR_BY_READ_GROUP" ] && ViashError Bad arguments for option \'--by_read_group\': \'$VIASH_PAR_BY_READ_GROUP\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_BY_READ_GROUP=true
|
|
shift 1
|
|
;;
|
|
--long_reads)
|
|
[ -n "$VIASH_PAR_LONG_READS" ] && ViashError Bad arguments for option \'--long_reads\': \'$VIASH_PAR_LONG_READS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_LONG_READS=true
|
|
shift 1
|
|
;;
|
|
--detailed_results)
|
|
[ -n "$VIASH_PAR_DETAILED_RESULTS" ] && ViashError Bad arguments for option \'--detailed_results\': \'$VIASH_PAR_DETAILED_RESULTS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_DETAILED_RESULTS="$2"
|
|
[ $# -lt 2 ] && ViashError Not enough arguments passed to --detailed_results. Use "--help" to get more information on the parameters. && exit 1
|
|
shift 2
|
|
;;
|
|
--detailed_results=*)
|
|
[ -n "$VIASH_PAR_DETAILED_RESULTS" ] && ViashError Bad arguments for option \'--detailed_results=*\': \'$VIASH_PAR_DETAILED_RESULTS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_DETAILED_RESULTS=$(ViashRemoveFlags "$1")
|
|
shift 1
|
|
;;
|
|
--detailed_results_format)
|
|
[ -n "$VIASH_PAR_DETAILED_RESULTS_FORMAT" ] && ViashError Bad arguments for option \'--detailed_results_format\': \'$VIASH_PAR_DETAILED_RESULTS_FORMAT\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_DETAILED_RESULTS_FORMAT="$2"
|
|
[ $# -lt 2 ] && ViashError Not enough arguments passed to --detailed_results_format. Use "--help" to get more information on the parameters. && exit 1
|
|
shift 2
|
|
;;
|
|
--detailed_results_format=*)
|
|
[ -n "$VIASH_PAR_DETAILED_RESULTS_FORMAT" ] && ViashError Bad arguments for option \'--detailed_results_format=*\': \'$VIASH_PAR_DETAILED_RESULTS_FORMAT\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_DETAILED_RESULTS_FORMAT=$(ViashRemoveFlags "$1")
|
|
shift 1
|
|
;;
|
|
-R)
|
|
[ -n "$VIASH_PAR_DETAILED_RESULTS_FORMAT" ] && ViashError Bad arguments for option \'-R\': \'$VIASH_PAR_DETAILED_RESULTS_FORMAT\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_DETAILED_RESULTS_FORMAT="$2"
|
|
[ $# -lt 2 ] && ViashError Not enough arguments passed to -R. Use "--help" to get more information on the parameters. && exit 1
|
|
shift 2
|
|
;;
|
|
--max_M_op)
|
|
[ -n "$VIASH_PAR_MAX_M_OP" ] && ViashError Bad arguments for option \'--max_M_op\': \'$VIASH_PAR_MAX_M_OP\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_MAX_M_OP="$2"
|
|
[ $# -lt 2 ] && ViashError Not enough arguments passed to --max_M_op. Use "--help" to get more information on the parameters. && exit 1
|
|
shift 2
|
|
;;
|
|
--max_M_op=*)
|
|
[ -n "$VIASH_PAR_MAX_M_OP" ] && ViashError Bad arguments for option \'--max_M_op=*\': \'$VIASH_PAR_MAX_M_OP\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_MAX_M_OP=$(ViashRemoveFlags "$1")
|
|
shift 1
|
|
;;
|
|
--verbose)
|
|
[ -n "$VIASH_PAR_VERBOSE" ] && ViashError Bad arguments for option \'--verbose\': \'$VIASH_PAR_VERBOSE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_VERBOSE=true
|
|
shift 1
|
|
;;
|
|
---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/featurecounts:main'
|
|
fi
|
|
|
|
# print dockerfile
|
|
if [ "$VIASH_MODE" == "dockerfile" ]; then
|
|
ViashDockerfile "$VIASH_ENGINE_ID"
|
|
exit 0
|
|
|
|
elif [ "$VIASH_MODE" == "docker_image_id" ]; then
|
|
echo "$VIASH_DOCKER_IMAGE_ID"
|
|
exit 0
|
|
|
|
# enter docker container
|
|
elif [[ "$VIASH_MODE" == "debug" ]]; then
|
|
VIASH_CMD="docker run --entrypoint=bash ${VIASH_DOCKER_RUN_ARGS[@]} -v '$(pwd)':/pwd --workdir /pwd -t $VIASH_DOCKER_IMAGE_ID"
|
|
ViashNotice "+ $VIASH_CMD"
|
|
eval $VIASH_CMD
|
|
exit
|
|
|
|
# build docker image
|
|
elif [ "$VIASH_MODE" == "setup" ]; then
|
|
ViashDockerSetup "$VIASH_DOCKER_IMAGE_ID" "$VIASH_SETUP_STRATEGY"
|
|
ViashDockerCheckCommands "$VIASH_DOCKER_IMAGE_ID" 'ps' 'bash'
|
|
exit 0
|
|
fi
|
|
|
|
# check if docker image exists
|
|
ViashDockerSetup "$VIASH_DOCKER_IMAGE_ID" ifneedbepullelsecachedbuild
|
|
ViashDockerCheckCommands "$VIASH_DOCKER_IMAGE_ID" 'ps' 'bash'
|
|
fi
|
|
|
|
# setting computational defaults
|
|
|
|
# helper function for parsing memory strings
|
|
function ViashMemoryAsBytes {
|
|
local memory=`echo "$1" | tr '[:upper:]' '[:lower:]' | tr -d '[:space:]'`
|
|
local memory_regex='^([0-9]+)([kmgtp]i?b?|b)$'
|
|
if [[ $memory =~ $memory_regex ]]; then
|
|
local number=${memory/[^0-9]*/}
|
|
local symbol=${memory/*[0-9]/}
|
|
|
|
case $symbol in
|
|
b) memory_b=$number ;;
|
|
kb|k) memory_b=$(( $number * 1000 )) ;;
|
|
mb|m) memory_b=$(( $number * 1000 * 1000 )) ;;
|
|
gb|g) memory_b=$(( $number * 1000 * 1000 * 1000 )) ;;
|
|
tb|t) memory_b=$(( $number * 1000 * 1000 * 1000 * 1000 )) ;;
|
|
pb|p) memory_b=$(( $number * 1000 * 1000 * 1000 * 1000 * 1000 )) ;;
|
|
kib|ki) memory_b=$(( $number * 1024 )) ;;
|
|
mib|mi) memory_b=$(( $number * 1024 * 1024 )) ;;
|
|
gib|gi) memory_b=$(( $number * 1024 * 1024 * 1024 )) ;;
|
|
tib|ti) memory_b=$(( $number * 1024 * 1024 * 1024 * 1024 )) ;;
|
|
pib|pi) memory_b=$(( $number * 1024 * 1024 * 1024 * 1024 * 1024 )) ;;
|
|
esac
|
|
echo "$memory_b"
|
|
fi
|
|
}
|
|
# compute memory in different units
|
|
if [ ! -z ${VIASH_META_MEMORY+x} ]; then
|
|
VIASH_META_MEMORY_B=`ViashMemoryAsBytes $VIASH_META_MEMORY`
|
|
# do not define other variables if memory_b is an empty string
|
|
if [ ! -z "$VIASH_META_MEMORY_B" ]; then
|
|
VIASH_META_MEMORY_KB=$(( ($VIASH_META_MEMORY_B+999) / 1000 ))
|
|
VIASH_META_MEMORY_MB=$(( ($VIASH_META_MEMORY_KB+999) / 1000 ))
|
|
VIASH_META_MEMORY_GB=$(( ($VIASH_META_MEMORY_MB+999) / 1000 ))
|
|
VIASH_META_MEMORY_TB=$(( ($VIASH_META_MEMORY_GB+999) / 1000 ))
|
|
VIASH_META_MEMORY_PB=$(( ($VIASH_META_MEMORY_TB+999) / 1000 ))
|
|
VIASH_META_MEMORY_KIB=$(( ($VIASH_META_MEMORY_B+1023) / 1024 ))
|
|
VIASH_META_MEMORY_MIB=$(( ($VIASH_META_MEMORY_KIB+1023) / 1024 ))
|
|
VIASH_META_MEMORY_GIB=$(( ($VIASH_META_MEMORY_MIB+1023) / 1024 ))
|
|
VIASH_META_MEMORY_TIB=$(( ($VIASH_META_MEMORY_GIB+1023) / 1024 ))
|
|
VIASH_META_MEMORY_PIB=$(( ($VIASH_META_MEMORY_TIB+1023) / 1024 ))
|
|
else
|
|
# unset memory if string is empty
|
|
unset $VIASH_META_MEMORY_B
|
|
fi
|
|
fi
|
|
# unset nproc if string is empty
|
|
if [ -z "$VIASH_META_CPUS" ]; then
|
|
unset $VIASH_META_CPUS
|
|
fi
|
|
|
|
|
|
# check whether required parameters exist
|
|
if [ -z ${VIASH_PAR_ANNOTATION+x} ]; then
|
|
ViashError '--annotation' is a required argument. Use "--help" to get more information on the parameters.
|
|
exit 1
|
|
fi
|
|
if [ -z ${VIASH_PAR_INPUT+x} ]; then
|
|
ViashError '--input' is a required argument. Use "--help" to get more information on the parameters.
|
|
exit 1
|
|
fi
|
|
if [ -z ${VIASH_PAR_COUNTS+x} ]; then
|
|
ViashError '--counts' 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_FEATURE_LEVEL+x} ]; then
|
|
VIASH_PAR_FEATURE_LEVEL="false"
|
|
fi
|
|
if [ -z ${VIASH_PAR_OVERLAPPING+x} ]; then
|
|
VIASH_PAR_OVERLAPPING="false"
|
|
fi
|
|
if [ -z ${VIASH_PAR_LARGEST_OVERLAP+x} ]; then
|
|
VIASH_PAR_LARGEST_OVERLAP="false"
|
|
fi
|
|
if [ -z ${VIASH_PAR_MULTI_MAPPING+x} ]; then
|
|
VIASH_PAR_MULTI_MAPPING="false"
|
|
fi
|
|
if [ -z ${VIASH_PAR_FRACTION+x} ]; then
|
|
VIASH_PAR_FRACTION="false"
|
|
fi
|
|
if [ -z ${VIASH_PAR_SPLIT_ONLY+x} ]; then
|
|
VIASH_PAR_SPLIT_ONLY="false"
|
|
fi
|
|
if [ -z ${VIASH_PAR_NON_SPLIT_ONLY+x} ]; then
|
|
VIASH_PAR_NON_SPLIT_ONLY="false"
|
|
fi
|
|
if [ -z ${VIASH_PAR_PRIMARY+x} ]; then
|
|
VIASH_PAR_PRIMARY="false"
|
|
fi
|
|
if [ -z ${VIASH_PAR_IGNORE_DUP+x} ]; then
|
|
VIASH_PAR_IGNORE_DUP="false"
|
|
fi
|
|
if [ -z ${VIASH_PAR_PAIRED+x} ]; then
|
|
VIASH_PAR_PAIRED="false"
|
|
fi
|
|
if [ -z ${VIASH_PAR_COUNT_READ_PAIRS+x} ]; then
|
|
VIASH_PAR_COUNT_READ_PAIRS="false"
|
|
fi
|
|
if [ -z ${VIASH_PAR_BOTH_ALIGNED+x} ]; then
|
|
VIASH_PAR_BOTH_ALIGNED="false"
|
|
fi
|
|
if [ -z ${VIASH_PAR_CHECK_PE_DIST+x} ]; then
|
|
VIASH_PAR_CHECK_PE_DIST="false"
|
|
fi
|
|
if [ -z ${VIASH_PAR_SAME_STRAND+x} ]; then
|
|
VIASH_PAR_SAME_STRAND="false"
|
|
fi
|
|
if [ -z ${VIASH_PAR_DONOTSORT+x} ]; then
|
|
VIASH_PAR_DONOTSORT="false"
|
|
fi
|
|
if [ -z ${VIASH_PAR_BY_READ_GROUP+x} ]; then
|
|
VIASH_PAR_BY_READ_GROUP="false"
|
|
fi
|
|
if [ -z ${VIASH_PAR_LONG_READS+x} ]; then
|
|
VIASH_PAR_LONG_READS="false"
|
|
fi
|
|
if [ -z ${VIASH_PAR_VERBOSE+x} ]; then
|
|
VIASH_PAR_VERBOSE="false"
|
|
fi
|
|
|
|
# check whether required files exist
|
|
if [ ! -z "$VIASH_PAR_ANNOTATION" ] && [ ! -e "$VIASH_PAR_ANNOTATION" ]; then
|
|
ViashError "Input file '$VIASH_PAR_ANNOTATION' does not exist."
|
|
exit 1
|
|
fi
|
|
if [ ! -z "$VIASH_PAR_INPUT" ]; then
|
|
IFS=';'
|
|
set -f
|
|
for file in $VIASH_PAR_INPUT; do
|
|
unset IFS
|
|
if [ ! -e "$file" ]; then
|
|
ViashError "Input file '$file' does not exist."
|
|
exit 1
|
|
fi
|
|
done
|
|
set +f
|
|
fi
|
|
if [ ! -z "$VIASH_PAR_CHROM_ALIAS" ] && [ ! -e "$VIASH_PAR_CHROM_ALIAS" ]; then
|
|
ViashError "Input file '$VIASH_PAR_CHROM_ALIAS' does not exist."
|
|
exit 1
|
|
fi
|
|
if [ ! -z "$VIASH_PAR_REF_FASTA" ] && [ ! -e "$VIASH_PAR_REF_FASTA" ]; then
|
|
ViashError "Input file '$VIASH_PAR_REF_FASTA' does not exist."
|
|
exit 1
|
|
fi
|
|
|
|
# check whether parameters values are of the right type
|
|
if [[ -n "$VIASH_PAR_FEATURE_LEVEL" ]]; then
|
|
if ! [[ "$VIASH_PAR_FEATURE_LEVEL" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then
|
|
ViashError '--feature_level' has to be a boolean_true. Use "--help" to get more information on the parameters.
|
|
exit 1
|
|
fi
|
|
fi
|
|
if [[ -n "$VIASH_PAR_OVERLAPPING" ]]; then
|
|
if ! [[ "$VIASH_PAR_OVERLAPPING" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then
|
|
ViashError '--overlapping' has to be a boolean_true. Use "--help" to get more information on the parameters.
|
|
exit 1
|
|
fi
|
|
fi
|
|
if [[ -n "$VIASH_PAR_MIN_OVERLAP" ]]; then
|
|
if ! [[ "$VIASH_PAR_MIN_OVERLAP" =~ ^[-+]?[0-9]+$ ]]; then
|
|
ViashError '--min_overlap' has to be an integer. Use "--help" to get more information on the parameters.
|
|
exit 1
|
|
fi
|
|
fi
|
|
if [[ -n "$VIASH_PAR_FRAC_OVERLAP" ]]; then
|
|
if ! [[ "$VIASH_PAR_FRAC_OVERLAP" =~ ^[-+]?(\.[0-9]+|[0-9]+(\.[0-9]*)?)([eE][-+]?[0-9]+)?$ ]]; then
|
|
ViashError '--frac_overlap' has to be a double. Use "--help" to get more information on the parameters.
|
|
exit 1
|
|
fi
|
|
if command -v bc &> /dev/null; then
|
|
if ! [[ `echo $VIASH_PAR_FRAC_OVERLAP '>=' 0.0 | bc` -eq 1 ]]; then
|
|
ViashError '--frac_overlap' has be more than or equal to 0.0. Use "--help" to get more information on the parameters.
|
|
exit 1
|
|
fi
|
|
elif command -v awk &> /dev/null; then
|
|
if ! [[ `awk -v n1=$VIASH_PAR_FRAC_OVERLAP -v n2=0.0 'BEGIN { print (n1 >= n2) ? "1" : "0" }'` -eq 1 ]]; then
|
|
ViashError '--frac_overlap' has be more than or equal to 0.0. Use "--help" to get more information on the parameters.
|
|
exit 1
|
|
fi
|
|
else
|
|
ViashWarning '--frac_overlap' specifies a minimum value but the value was not verified as neither \'bc\' or \`awk\` are present on the system.
|
|
fi
|
|
if command -v bc &> /dev/null; then
|
|
if ! [[ `echo $VIASH_PAR_FRAC_OVERLAP '<=' 1.0 | bc` -eq 1 ]]; then
|
|
ViashError '--frac_overlap' has to be less than or equal to 1.0. Use "--help" to get more information on the parameters.
|
|
exit 1
|
|
fi
|
|
elif command -v awk &> /dev/null; then
|
|
if ! [[ `awk -v n1=$VIASH_PAR_FRAC_OVERLAP -v n2=1.0 'BEGIN { print (n1 <= n2) ? "1" : "0" }'` -eq 1 ]]; then
|
|
ViashError '--frac_overlap' has be less than or equal to 1.0. Use "--help" to get more information on the parameters.
|
|
exit 1
|
|
fi
|
|
else
|
|
ViashWarning '--frac_overlap' specifies a maximum value but the value was not verified as neither \'bc\' or \'awk\' are present on the system.
|
|
fi
|
|
fi
|
|
if [[ -n "$VIASH_PAR_FRAC_OVERLAP_FEATURE" ]]; then
|
|
if ! [[ "$VIASH_PAR_FRAC_OVERLAP_FEATURE" =~ ^[-+]?(\.[0-9]+|[0-9]+(\.[0-9]*)?)([eE][-+]?[0-9]+)?$ ]]; then
|
|
ViashError '--frac_overlap_feature' has to be a double. Use "--help" to get more information on the parameters.
|
|
exit 1
|
|
fi
|
|
if command -v bc &> /dev/null; then
|
|
if ! [[ `echo $VIASH_PAR_FRAC_OVERLAP_FEATURE '>=' 0.0 | bc` -eq 1 ]]; then
|
|
ViashError '--frac_overlap_feature' has be more than or equal to 0.0. Use "--help" to get more information on the parameters.
|
|
exit 1
|
|
fi
|
|
elif command -v awk &> /dev/null; then
|
|
if ! [[ `awk -v n1=$VIASH_PAR_FRAC_OVERLAP_FEATURE -v n2=0.0 'BEGIN { print (n1 >= n2) ? "1" : "0" }'` -eq 1 ]]; then
|
|
ViashError '--frac_overlap_feature' has be more than or equal to 0.0. Use "--help" to get more information on the parameters.
|
|
exit 1
|
|
fi
|
|
else
|
|
ViashWarning '--frac_overlap_feature' specifies a minimum value but the value was not verified as neither \'bc\' or \`awk\` are present on the system.
|
|
fi
|
|
if command -v bc &> /dev/null; then
|
|
if ! [[ `echo $VIASH_PAR_FRAC_OVERLAP_FEATURE '<=' 1.0 | bc` -eq 1 ]]; then
|
|
ViashError '--frac_overlap_feature' has to be less than or equal to 1.0. Use "--help" to get more information on the parameters.
|
|
exit 1
|
|
fi
|
|
elif command -v awk &> /dev/null; then
|
|
if ! [[ `awk -v n1=$VIASH_PAR_FRAC_OVERLAP_FEATURE -v n2=1.0 'BEGIN { print (n1 <= n2) ? "1" : "0" }'` -eq 1 ]]; then
|
|
ViashError '--frac_overlap_feature' has be less than or equal to 1.0. Use "--help" to get more information on the parameters.
|
|
exit 1
|
|
fi
|
|
else
|
|
ViashWarning '--frac_overlap_feature' specifies a maximum value but the value was not verified as neither \'bc\' or \'awk\' are present on the system.
|
|
fi
|
|
fi
|
|
if [[ -n "$VIASH_PAR_LARGEST_OVERLAP" ]]; then
|
|
if ! [[ "$VIASH_PAR_LARGEST_OVERLAP" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then
|
|
ViashError '--largest_overlap' has to be a boolean_true. Use "--help" to get more information on the parameters.
|
|
exit 1
|
|
fi
|
|
fi
|
|
if [[ -n "$VIASH_PAR_NON_OVERLAP" ]]; then
|
|
if ! [[ "$VIASH_PAR_NON_OVERLAP" =~ ^[-+]?[0-9]+$ ]]; then
|
|
ViashError '--non_overlap' has to be an integer. Use "--help" to get more information on the parameters.
|
|
exit 1
|
|
fi
|
|
fi
|
|
if [[ -n "$VIASH_PAR_NON_OVERLAP_FEATURE" ]]; then
|
|
if ! [[ "$VIASH_PAR_NON_OVERLAP_FEATURE" =~ ^[-+]?[0-9]+$ ]]; then
|
|
ViashError '--non_overlap_feature' has to be an integer. Use "--help" to get more information on the parameters.
|
|
exit 1
|
|
fi
|
|
fi
|
|
if [[ -n "$VIASH_PAR_READ_EXTENSION5" ]]; then
|
|
if ! [[ "$VIASH_PAR_READ_EXTENSION5" =~ ^[-+]?[0-9]+$ ]]; then
|
|
ViashError '--read_extension5' has to be an integer. Use "--help" to get more information on the parameters.
|
|
exit 1
|
|
fi
|
|
fi
|
|
if [[ -n "$VIASH_PAR_READ_EXTENSION3" ]]; then
|
|
if ! [[ "$VIASH_PAR_READ_EXTENSION3" =~ ^[-+]?[0-9]+$ ]]; then
|
|
ViashError '--read_extension3' has to be an integer. Use "--help" to get more information on the parameters.
|
|
exit 1
|
|
fi
|
|
fi
|
|
if [[ -n "$VIASH_PAR_READ2POS" ]]; then
|
|
if ! [[ "$VIASH_PAR_READ2POS" =~ ^[-+]?[0-9]+$ ]]; then
|
|
ViashError '--read2pos' has to be an integer. Use "--help" to get more information on the parameters.
|
|
exit 1
|
|
fi
|
|
fi
|
|
if [[ -n "$VIASH_PAR_MULTI_MAPPING" ]]; then
|
|
if ! [[ "$VIASH_PAR_MULTI_MAPPING" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then
|
|
ViashError '--multi_mapping' has to be a boolean_true. Use "--help" to get more information on the parameters.
|
|
exit 1
|
|
fi
|
|
fi
|
|
if [[ -n "$VIASH_PAR_FRACTION" ]]; then
|
|
if ! [[ "$VIASH_PAR_FRACTION" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then
|
|
ViashError '--fraction' has to be a boolean_true. Use "--help" to get more information on the parameters.
|
|
exit 1
|
|
fi
|
|
fi
|
|
if [[ -n "$VIASH_PAR_MIN_MAP_QUALITY" ]]; then
|
|
if ! [[ "$VIASH_PAR_MIN_MAP_QUALITY" =~ ^[-+]?[0-9]+$ ]]; then
|
|
ViashError '--min_map_quality' has to be an integer. Use "--help" to get more information on the parameters.
|
|
exit 1
|
|
fi
|
|
fi
|
|
if [[ -n "$VIASH_PAR_SPLIT_ONLY" ]]; then
|
|
if ! [[ "$VIASH_PAR_SPLIT_ONLY" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then
|
|
ViashError '--split_only' has to be a boolean_true. Use "--help" to get more information on the parameters.
|
|
exit 1
|
|
fi
|
|
fi
|
|
if [[ -n "$VIASH_PAR_NON_SPLIT_ONLY" ]]; then
|
|
if ! [[ "$VIASH_PAR_NON_SPLIT_ONLY" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then
|
|
ViashError '--non_split_only' has to be a boolean_true. Use "--help" to get more information on the parameters.
|
|
exit 1
|
|
fi
|
|
fi
|
|
if [[ -n "$VIASH_PAR_PRIMARY" ]]; then
|
|
if ! [[ "$VIASH_PAR_PRIMARY" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then
|
|
ViashError '--primary' has to be a boolean_true. Use "--help" to get more information on the parameters.
|
|
exit 1
|
|
fi
|
|
fi
|
|
if [[ -n "$VIASH_PAR_IGNORE_DUP" ]]; then
|
|
if ! [[ "$VIASH_PAR_IGNORE_DUP" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then
|
|
ViashError '--ignore_dup' has to be a boolean_true. Use "--help" to get more information on the parameters.
|
|
exit 1
|
|
fi
|
|
fi
|
|
if [[ -n "$VIASH_PAR_STRAND" ]]; then
|
|
if ! [[ "$VIASH_PAR_STRAND" =~ ^[-+]?[0-9]+$ ]]; then
|
|
ViashError '--strand' has to be an integer. Use "--help" to get more information on the parameters.
|
|
exit 1
|
|
fi
|
|
fi
|
|
if [[ -n "$VIASH_PAR_PAIRED" ]]; then
|
|
if ! [[ "$VIASH_PAR_PAIRED" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then
|
|
ViashError '--paired' has to be a boolean_true. Use "--help" to get more information on the parameters.
|
|
exit 1
|
|
fi
|
|
fi
|
|
if [[ -n "$VIASH_PAR_COUNT_READ_PAIRS" ]]; then
|
|
if ! [[ "$VIASH_PAR_COUNT_READ_PAIRS" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then
|
|
ViashError '--count_read_pairs' has to be a boolean_true. Use "--help" to get more information on the parameters.
|
|
exit 1
|
|
fi
|
|
fi
|
|
if [[ -n "$VIASH_PAR_BOTH_ALIGNED" ]]; then
|
|
if ! [[ "$VIASH_PAR_BOTH_ALIGNED" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then
|
|
ViashError '--both_aligned' has to be a boolean_true. Use "--help" to get more information on the parameters.
|
|
exit 1
|
|
fi
|
|
fi
|
|
if [[ -n "$VIASH_PAR_CHECK_PE_DIST" ]]; then
|
|
if ! [[ "$VIASH_PAR_CHECK_PE_DIST" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then
|
|
ViashError '--check_pe_dist' has to be a boolean_true. Use "--help" to get more information on the parameters.
|
|
exit 1
|
|
fi
|
|
fi
|
|
if [[ -n "$VIASH_PAR_MIN_LENGTH" ]]; then
|
|
if ! [[ "$VIASH_PAR_MIN_LENGTH" =~ ^[-+]?[0-9]+$ ]]; then
|
|
ViashError '--min_length' has to be an integer. Use "--help" to get more information on the parameters.
|
|
exit 1
|
|
fi
|
|
fi
|
|
if [[ -n "$VIASH_PAR_MAX_LENGTH" ]]; then
|
|
if ! [[ "$VIASH_PAR_MAX_LENGTH" =~ ^[-+]?[0-9]+$ ]]; then
|
|
ViashError '--max_length' has to be an integer. Use "--help" to get more information on the parameters.
|
|
exit 1
|
|
fi
|
|
fi
|
|
if [[ -n "$VIASH_PAR_SAME_STRAND" ]]; then
|
|
if ! [[ "$VIASH_PAR_SAME_STRAND" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then
|
|
ViashError '--same_strand' has to be a boolean_true. Use "--help" to get more information on the parameters.
|
|
exit 1
|
|
fi
|
|
fi
|
|
if [[ -n "$VIASH_PAR_DONOTSORT" ]]; then
|
|
if ! [[ "$VIASH_PAR_DONOTSORT" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then
|
|
ViashError '--donotsort' has to be a boolean_true. Use "--help" to get more information on the parameters.
|
|
exit 1
|
|
fi
|
|
fi
|
|
if [[ -n "$VIASH_PAR_BY_READ_GROUP" ]]; then
|
|
if ! [[ "$VIASH_PAR_BY_READ_GROUP" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then
|
|
ViashError '--by_read_group' has to be a boolean_true. Use "--help" to get more information on the parameters.
|
|
exit 1
|
|
fi
|
|
fi
|
|
if [[ -n "$VIASH_PAR_LONG_READS" ]]; then
|
|
if ! [[ "$VIASH_PAR_LONG_READS" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then
|
|
ViashError '--long_reads' has to be a boolean_true. Use "--help" to get more information on the parameters.
|
|
exit 1
|
|
fi
|
|
fi
|
|
if [[ -n "$VIASH_PAR_MAX_M_OP" ]]; then
|
|
if ! [[ "$VIASH_PAR_MAX_M_OP" =~ ^[-+]?[0-9]+$ ]]; then
|
|
ViashError '--max_M_op' has to be an integer. Use "--help" to get more information on the parameters.
|
|
exit 1
|
|
fi
|
|
fi
|
|
if [[ -n "$VIASH_PAR_VERBOSE" ]]; then
|
|
if ! [[ "$VIASH_PAR_VERBOSE" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then
|
|
ViashError '--verbose' has to be a boolean_true. Use "--help" to get more information on the parameters.
|
|
exit 1
|
|
fi
|
|
fi
|
|
if [[ -n "$VIASH_META_CPUS" ]]; then
|
|
if ! [[ "$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 "$VIASH_PAR_FORMAT" ]; then
|
|
VIASH_PAR_FORMAT_CHOICES=("GTF;GFF;SAF")
|
|
IFS=';'
|
|
set -f
|
|
if ! [[ ";${VIASH_PAR_FORMAT_CHOICES[*]};" =~ ";$VIASH_PAR_FORMAT;" ]]; then
|
|
ViashError '--format' specified value of \'$VIASH_PAR_FORMAT\' is not in the list of allowed values. Use "--help" to get more information on the parameters.
|
|
exit 1
|
|
fi
|
|
set +f
|
|
unset IFS
|
|
fi
|
|
|
|
if [ ! -z "$VIASH_PAR_READ2POS" ]; then
|
|
VIASH_PAR_READ2POS_CHOICES=("3;5")
|
|
IFS=';'
|
|
set -f
|
|
if ! [[ ";${VIASH_PAR_READ2POS_CHOICES[*]};" =~ ";$VIASH_PAR_READ2POS;" ]]; then
|
|
ViashError '--read2pos' specified value of \'$VIASH_PAR_READ2POS\' 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 "$VIASH_PAR_STRAND" ]; then
|
|
VIASH_PAR_STRAND_CHOICES=("0;1;2")
|
|
IFS=';'
|
|
set -f
|
|
if ! [[ ";${VIASH_PAR_STRAND_CHOICES[*]};" =~ ";$VIASH_PAR_STRAND;" ]]; then
|
|
ViashError '--strand' specified value of \'$VIASH_PAR_STRAND\' 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 "$VIASH_PAR_DETAILED_RESULTS_FORMAT" ]; then
|
|
VIASH_PAR_DETAILED_RESULTS_FORMAT_CHOICES=("CORE;SAM;BAM")
|
|
IFS=';'
|
|
set -f
|
|
if ! [[ ";${VIASH_PAR_DETAILED_RESULTS_FORMAT_CHOICES[*]};" =~ ";$VIASH_PAR_DETAILED_RESULTS_FORMAT;" ]]; then
|
|
ViashError '--detailed_results_format' specified value of \'$VIASH_PAR_DETAILED_RESULTS_FORMAT\' is not in the list of allowed values. Use "--help" to get more information on the parameters.
|
|
exit 1
|
|
fi
|
|
set +f
|
|
unset IFS
|
|
fi
|
|
|
|
# create parent directories of output files, if so desired
|
|
if [ ! -z "$VIASH_PAR_COUNTS" ] && [ ! -d "$(dirname "$VIASH_PAR_COUNTS")" ]; then
|
|
mkdir -p "$(dirname "$VIASH_PAR_COUNTS")"
|
|
fi
|
|
if [ ! -z "$VIASH_PAR_SUMMARY" ] && [ ! -d "$(dirname "$VIASH_PAR_SUMMARY")" ]; then
|
|
mkdir -p "$(dirname "$VIASH_PAR_SUMMARY")"
|
|
fi
|
|
if [ ! -z "$VIASH_PAR_JUNCTIONS" ] && [ ! -d "$(dirname "$VIASH_PAR_JUNCTIONS")" ]; then
|
|
mkdir -p "$(dirname "$VIASH_PAR_JUNCTIONS")"
|
|
fi
|
|
if [ ! -z "$VIASH_PAR_DETAILED_RESULTS" ] && [ ! -d "$(dirname "$VIASH_PAR_DETAILED_RESULTS")" ]; then
|
|
mkdir -p "$(dirname "$VIASH_PAR_DETAILED_RESULTS")"
|
|
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_ANNOTATION" ]; then
|
|
VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$VIASH_PAR_ANNOTATION")" )
|
|
VIASH_PAR_ANNOTATION=$(ViashDockerAutodetectMount "$VIASH_PAR_ANNOTATION")
|
|
fi
|
|
if [ ! -z "$VIASH_PAR_INPUT" ]; then
|
|
VIASH_TEST_INPUT=()
|
|
IFS=';'
|
|
for var in $VIASH_PAR_INPUT; do
|
|
unset IFS
|
|
VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$var")" )
|
|
var=$(ViashDockerAutodetectMount "$var")
|
|
VIASH_TEST_INPUT+=( "$var" )
|
|
done
|
|
VIASH_PAR_INPUT=$(IFS=';' ; echo "${VIASH_TEST_INPUT[*]}")
|
|
fi
|
|
if [ ! -z "$VIASH_PAR_COUNTS" ]; then
|
|
VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$VIASH_PAR_COUNTS")" )
|
|
VIASH_PAR_COUNTS=$(ViashDockerAutodetectMount "$VIASH_PAR_COUNTS")
|
|
VIASH_CHOWN_VARS+=( "$VIASH_PAR_COUNTS" )
|
|
fi
|
|
if [ ! -z "$VIASH_PAR_SUMMARY" ]; then
|
|
VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$VIASH_PAR_SUMMARY")" )
|
|
VIASH_PAR_SUMMARY=$(ViashDockerAutodetectMount "$VIASH_PAR_SUMMARY")
|
|
VIASH_CHOWN_VARS+=( "$VIASH_PAR_SUMMARY" )
|
|
fi
|
|
if [ ! -z "$VIASH_PAR_JUNCTIONS" ]; then
|
|
VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$VIASH_PAR_JUNCTIONS")" )
|
|
VIASH_PAR_JUNCTIONS=$(ViashDockerAutodetectMount "$VIASH_PAR_JUNCTIONS")
|
|
VIASH_CHOWN_VARS+=( "$VIASH_PAR_JUNCTIONS" )
|
|
fi
|
|
if [ ! -z "$VIASH_PAR_CHROM_ALIAS" ]; then
|
|
VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$VIASH_PAR_CHROM_ALIAS")" )
|
|
VIASH_PAR_CHROM_ALIAS=$(ViashDockerAutodetectMount "$VIASH_PAR_CHROM_ALIAS")
|
|
fi
|
|
if [ ! -z "$VIASH_PAR_REF_FASTA" ]; then
|
|
VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$VIASH_PAR_REF_FASTA")" )
|
|
VIASH_PAR_REF_FASTA=$(ViashDockerAutodetectMount "$VIASH_PAR_REF_FASTA")
|
|
fi
|
|
if [ ! -z "$VIASH_PAR_DETAILED_RESULTS" ]; then
|
|
VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$VIASH_PAR_DETAILED_RESULTS")" )
|
|
VIASH_PAR_DETAILED_RESULTS=$(ViashDockerAutodetectMount "$VIASH_PAR_DETAILED_RESULTS")
|
|
VIASH_CHOWN_VARS+=( "$VIASH_PAR_DETAILED_RESULTS" )
|
|
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-featurecounts-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
|
|
|
|
set -e
|
|
|
|
## VIASH START
|
|
# The following code has been auto-generated by Viash.
|
|
$( if [ ! -z ${VIASH_PAR_ANNOTATION+x} ]; then echo "${VIASH_PAR_ANNOTATION}" | sed "s#'#'\"'\"'#g;s#.*#par_annotation='&'#" ; else echo "# par_annotation="; fi )
|
|
$( if [ ! -z ${VIASH_PAR_INPUT+x} ]; then echo "${VIASH_PAR_INPUT}" | sed "s#'#'\"'\"'#g;s#.*#par_input='&'#" ; else echo "# par_input="; fi )
|
|
$( if [ ! -z ${VIASH_PAR_COUNTS+x} ]; then echo "${VIASH_PAR_COUNTS}" | sed "s#'#'\"'\"'#g;s#.*#par_counts='&'#" ; else echo "# par_counts="; fi )
|
|
$( if [ ! -z ${VIASH_PAR_SUMMARY+x} ]; then echo "${VIASH_PAR_SUMMARY}" | sed "s#'#'\"'\"'#g;s#.*#par_summary='&'#" ; else echo "# par_summary="; fi )
|
|
$( if [ ! -z ${VIASH_PAR_JUNCTIONS+x} ]; then echo "${VIASH_PAR_JUNCTIONS}" | sed "s#'#'\"'\"'#g;s#.*#par_junctions='&'#" ; else echo "# par_junctions="; fi )
|
|
$( if [ ! -z ${VIASH_PAR_FORMAT+x} ]; then echo "${VIASH_PAR_FORMAT}" | sed "s#'#'\"'\"'#g;s#.*#par_format='&'#" ; else echo "# par_format="; fi )
|
|
$( if [ ! -z ${VIASH_PAR_FEATURE_TYPE+x} ]; then echo "${VIASH_PAR_FEATURE_TYPE}" | sed "s#'#'\"'\"'#g;s#.*#par_feature_type='&'#" ; else echo "# par_feature_type="; fi )
|
|
$( if [ ! -z ${VIASH_PAR_ATTRIBUTE_TYPE+x} ]; then echo "${VIASH_PAR_ATTRIBUTE_TYPE}" | sed "s#'#'\"'\"'#g;s#.*#par_attribute_type='&'#" ; else echo "# par_attribute_type="; fi )
|
|
$( if [ ! -z ${VIASH_PAR_EXTRA_ATTRIBUTES+x} ]; then echo "${VIASH_PAR_EXTRA_ATTRIBUTES}" | sed "s#'#'\"'\"'#g;s#.*#par_extra_attributes='&'#" ; else echo "# par_extra_attributes="; fi )
|
|
$( if [ ! -z ${VIASH_PAR_CHROM_ALIAS+x} ]; then echo "${VIASH_PAR_CHROM_ALIAS}" | sed "s#'#'\"'\"'#g;s#.*#par_chrom_alias='&'#" ; else echo "# par_chrom_alias="; fi )
|
|
$( if [ ! -z ${VIASH_PAR_FEATURE_LEVEL+x} ]; then echo "${VIASH_PAR_FEATURE_LEVEL}" | sed "s#'#'\"'\"'#g;s#.*#par_feature_level='&'#" ; else echo "# par_feature_level="; fi )
|
|
$( if [ ! -z ${VIASH_PAR_OVERLAPPING+x} ]; then echo "${VIASH_PAR_OVERLAPPING}" | sed "s#'#'\"'\"'#g;s#.*#par_overlapping='&'#" ; else echo "# par_overlapping="; fi )
|
|
$( if [ ! -z ${VIASH_PAR_MIN_OVERLAP+x} ]; then echo "${VIASH_PAR_MIN_OVERLAP}" | sed "s#'#'\"'\"'#g;s#.*#par_min_overlap='&'#" ; else echo "# par_min_overlap="; fi )
|
|
$( if [ ! -z ${VIASH_PAR_FRAC_OVERLAP+x} ]; then echo "${VIASH_PAR_FRAC_OVERLAP}" | sed "s#'#'\"'\"'#g;s#.*#par_frac_overlap='&'#" ; else echo "# par_frac_overlap="; fi )
|
|
$( if [ ! -z ${VIASH_PAR_FRAC_OVERLAP_FEATURE+x} ]; then echo "${VIASH_PAR_FRAC_OVERLAP_FEATURE}" | sed "s#'#'\"'\"'#g;s#.*#par_frac_overlap_feature='&'#" ; else echo "# par_frac_overlap_feature="; fi )
|
|
$( if [ ! -z ${VIASH_PAR_LARGEST_OVERLAP+x} ]; then echo "${VIASH_PAR_LARGEST_OVERLAP}" | sed "s#'#'\"'\"'#g;s#.*#par_largest_overlap='&'#" ; else echo "# par_largest_overlap="; fi )
|
|
$( if [ ! -z ${VIASH_PAR_NON_OVERLAP+x} ]; then echo "${VIASH_PAR_NON_OVERLAP}" | sed "s#'#'\"'\"'#g;s#.*#par_non_overlap='&'#" ; else echo "# par_non_overlap="; fi )
|
|
$( if [ ! -z ${VIASH_PAR_NON_OVERLAP_FEATURE+x} ]; then echo "${VIASH_PAR_NON_OVERLAP_FEATURE}" | sed "s#'#'\"'\"'#g;s#.*#par_non_overlap_feature='&'#" ; else echo "# par_non_overlap_feature="; fi )
|
|
$( if [ ! -z ${VIASH_PAR_READ_EXTENSION5+x} ]; then echo "${VIASH_PAR_READ_EXTENSION5}" | sed "s#'#'\"'\"'#g;s#.*#par_read_extension5='&'#" ; else echo "# par_read_extension5="; fi )
|
|
$( if [ ! -z ${VIASH_PAR_READ_EXTENSION3+x} ]; then echo "${VIASH_PAR_READ_EXTENSION3}" | sed "s#'#'\"'\"'#g;s#.*#par_read_extension3='&'#" ; else echo "# par_read_extension3="; fi )
|
|
$( if [ ! -z ${VIASH_PAR_READ2POS+x} ]; then echo "${VIASH_PAR_READ2POS}" | sed "s#'#'\"'\"'#g;s#.*#par_read2pos='&'#" ; else echo "# par_read2pos="; fi )
|
|
$( if [ ! -z ${VIASH_PAR_MULTI_MAPPING+x} ]; then echo "${VIASH_PAR_MULTI_MAPPING}" | sed "s#'#'\"'\"'#g;s#.*#par_multi_mapping='&'#" ; else echo "# par_multi_mapping="; fi )
|
|
$( if [ ! -z ${VIASH_PAR_FRACTION+x} ]; then echo "${VIASH_PAR_FRACTION}" | sed "s#'#'\"'\"'#g;s#.*#par_fraction='&'#" ; else echo "# par_fraction="; fi )
|
|
$( if [ ! -z ${VIASH_PAR_MIN_MAP_QUALITY+x} ]; then echo "${VIASH_PAR_MIN_MAP_QUALITY}" | sed "s#'#'\"'\"'#g;s#.*#par_min_map_quality='&'#" ; else echo "# par_min_map_quality="; fi )
|
|
$( if [ ! -z ${VIASH_PAR_SPLIT_ONLY+x} ]; then echo "${VIASH_PAR_SPLIT_ONLY}" | sed "s#'#'\"'\"'#g;s#.*#par_split_only='&'#" ; else echo "# par_split_only="; fi )
|
|
$( if [ ! -z ${VIASH_PAR_NON_SPLIT_ONLY+x} ]; then echo "${VIASH_PAR_NON_SPLIT_ONLY}" | sed "s#'#'\"'\"'#g;s#.*#par_non_split_only='&'#" ; else echo "# par_non_split_only="; fi )
|
|
$( if [ ! -z ${VIASH_PAR_PRIMARY+x} ]; then echo "${VIASH_PAR_PRIMARY}" | sed "s#'#'\"'\"'#g;s#.*#par_primary='&'#" ; else echo "# par_primary="; fi )
|
|
$( if [ ! -z ${VIASH_PAR_IGNORE_DUP+x} ]; then echo "${VIASH_PAR_IGNORE_DUP}" | sed "s#'#'\"'\"'#g;s#.*#par_ignore_dup='&'#" ; else echo "# par_ignore_dup="; fi )
|
|
$( if [ ! -z ${VIASH_PAR_STRAND+x} ]; then echo "${VIASH_PAR_STRAND}" | sed "s#'#'\"'\"'#g;s#.*#par_strand='&'#" ; else echo "# par_strand="; fi )
|
|
$( if [ ! -z ${VIASH_PAR_REF_FASTA+x} ]; then echo "${VIASH_PAR_REF_FASTA}" | sed "s#'#'\"'\"'#g;s#.*#par_ref_fasta='&'#" ; else echo "# par_ref_fasta="; fi )
|
|
$( if [ ! -z ${VIASH_PAR_PAIRED+x} ]; then echo "${VIASH_PAR_PAIRED}" | sed "s#'#'\"'\"'#g;s#.*#par_paired='&'#" ; else echo "# par_paired="; fi )
|
|
$( if [ ! -z ${VIASH_PAR_COUNT_READ_PAIRS+x} ]; then echo "${VIASH_PAR_COUNT_READ_PAIRS}" | sed "s#'#'\"'\"'#g;s#.*#par_count_read_pairs='&'#" ; else echo "# par_count_read_pairs="; fi )
|
|
$( if [ ! -z ${VIASH_PAR_BOTH_ALIGNED+x} ]; then echo "${VIASH_PAR_BOTH_ALIGNED}" | sed "s#'#'\"'\"'#g;s#.*#par_both_aligned='&'#" ; else echo "# par_both_aligned="; fi )
|
|
$( if [ ! -z ${VIASH_PAR_CHECK_PE_DIST+x} ]; then echo "${VIASH_PAR_CHECK_PE_DIST}" | sed "s#'#'\"'\"'#g;s#.*#par_check_pe_dist='&'#" ; else echo "# par_check_pe_dist="; fi )
|
|
$( if [ ! -z ${VIASH_PAR_MIN_LENGTH+x} ]; then echo "${VIASH_PAR_MIN_LENGTH}" | sed "s#'#'\"'\"'#g;s#.*#par_min_length='&'#" ; else echo "# par_min_length="; fi )
|
|
$( if [ ! -z ${VIASH_PAR_MAX_LENGTH+x} ]; then echo "${VIASH_PAR_MAX_LENGTH}" | sed "s#'#'\"'\"'#g;s#.*#par_max_length='&'#" ; else echo "# par_max_length="; fi )
|
|
$( if [ ! -z ${VIASH_PAR_SAME_STRAND+x} ]; then echo "${VIASH_PAR_SAME_STRAND}" | sed "s#'#'\"'\"'#g;s#.*#par_same_strand='&'#" ; else echo "# par_same_strand="; fi )
|
|
$( if [ ! -z ${VIASH_PAR_DONOTSORT+x} ]; then echo "${VIASH_PAR_DONOTSORT}" | sed "s#'#'\"'\"'#g;s#.*#par_donotsort='&'#" ; else echo "# par_donotsort="; fi )
|
|
$( if [ ! -z ${VIASH_PAR_BY_READ_GROUP+x} ]; then echo "${VIASH_PAR_BY_READ_GROUP}" | sed "s#'#'\"'\"'#g;s#.*#par_by_read_group='&'#" ; else echo "# par_by_read_group="; fi )
|
|
$( if [ ! -z ${VIASH_PAR_LONG_READS+x} ]; then echo "${VIASH_PAR_LONG_READS}" | sed "s#'#'\"'\"'#g;s#.*#par_long_reads='&'#" ; else echo "# par_long_reads="; fi )
|
|
$( if [ ! -z ${VIASH_PAR_DETAILED_RESULTS+x} ]; then echo "${VIASH_PAR_DETAILED_RESULTS}" | sed "s#'#'\"'\"'#g;s#.*#par_detailed_results='&'#" ; else echo "# par_detailed_results="; fi )
|
|
$( if [ ! -z ${VIASH_PAR_DETAILED_RESULTS_FORMAT+x} ]; then echo "${VIASH_PAR_DETAILED_RESULTS_FORMAT}" | sed "s#'#'\"'\"'#g;s#.*#par_detailed_results_format='&'#" ; else echo "# par_detailed_results_format="; fi )
|
|
$( if [ ! -z ${VIASH_PAR_MAX_M_OP+x} ]; then echo "${VIASH_PAR_MAX_M_OP}" | sed "s#'#'\"'\"'#g;s#.*#par_max_M_op='&'#" ; else echo "# par_max_M_op="; fi )
|
|
$( if [ ! -z ${VIASH_PAR_VERBOSE+x} ]; then echo "${VIASH_PAR_VERBOSE}" | sed "s#'#'\"'\"'#g;s#.*#par_verbose='&'#" ; else echo "# par_verbose="; fi )
|
|
$( if [ ! -z ${VIASH_META_NAME+x} ]; then echo "${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
|
|
|
|
# create temporary directory
|
|
tmp_dir=\$(mktemp -d -p "\$meta_temp_dir" "\${meta_name}_XXXXXX")
|
|
mkdir -p "\$tmp_dir/temp"
|
|
|
|
# create detailed_results directory if variable is set and directory does not exist
|
|
if [[ ! -z "\$par_detailed_results" ]] && [[ ! -d "\$par_detailed_results" ]]; then
|
|
mkdir -p "\$par_detailed_results"
|
|
fi
|
|
|
|
# replace comma with semicolon
|
|
par_feature_type=\$(echo \$par_feature_type | tr ',' ';')
|
|
par_extra_attributes=\$(echo \$par_extra_attributes | tr ',' ';')
|
|
|
|
# unset flag variables
|
|
unset_if_false=(
|
|
par_feature_level
|
|
par_overlapping
|
|
par_largest_overlap
|
|
par_multi_mapping
|
|
par_fraction
|
|
par_split_only
|
|
par_non_split_only
|
|
par_primary
|
|
par_ignore_dup
|
|
par_paired
|
|
par_count_read_pairs
|
|
par_both_aligned
|
|
par_check_pe_dist
|
|
par_same_strand
|
|
par_donotsort
|
|
par_by_read_group
|
|
par_long_reads
|
|
par_verbose
|
|
)
|
|
|
|
for par in \${unset_if_false[@]}; do
|
|
test_val="\${!par}"
|
|
[[ "\$test_val" == "false" ]] && unset \$par
|
|
done
|
|
|
|
IFS=";" read -ra input <<< \$par_input
|
|
|
|
featureCounts \\
|
|
\${par_format:+-F "\${par_format}"} \\
|
|
\${par_feature_type:+-t "\${par_feature_type}"} \\
|
|
\${par_attribute_type:+-g "\${par_attribute_type}"} \\
|
|
\${par_extra_attributes:+--extraAttributes "\${extra_attributes}"} \\
|
|
\${par_chrom_alias:+-A "\${par_chrom_alias}"} \\
|
|
\${par_feature_level:+-f} \\
|
|
\${par_overlapping:+-O} \\
|
|
\${par_min_overlap:+--minOverlap "\${par_min_overlap}"} \\
|
|
\${par_frac_overlap:+--fracOverlap "\${par_frac_overlap}"} \\
|
|
\${par_frac_overlap_feature:+--fracOverlapFeature "\${par_frac_overlap_feature}"} \\
|
|
\${par_largest_overlap:+--largestOverlap} \\
|
|
\${par_non_overlap:+--nonOverlap "\${par_non_overlap}"} \\
|
|
\${par_non_overlap_feature:+--nonOverlapFeature "\${par_non_overlap_feature}"} \\
|
|
\${par_read_extension5:+--readExtension5 "\${par_read_extension5}"} \\
|
|
\${par_read_extension3:+--readExtension3 "\${par_read_extension3}"} \\
|
|
\${par_read2pos:+--read2pos "\${par_read2pos}"} \\
|
|
\${par_multi_mapping:+-M} \\
|
|
\${par_fraction:+--fraction} \\
|
|
\${par_min_map_quality:+-Q "\${par_min_map_quality}"} \\
|
|
\${par_split_only:+--splitOnly} \\
|
|
\${par_non_split_only:+--nonSplitOnly} \\
|
|
\${par_primary:+--primary} \\
|
|
\${par_ignore_dup:+--ignoreDup} \\
|
|
\${par_strand:+-s "\${par_strand}"} \\
|
|
\${par_junctions:+-J} \\
|
|
\${par_ref_fasta:+-G "\${par_ref_fasta}"} \\
|
|
\${par_paired:+-p} \\
|
|
\${par_count_read_pairs:+--countReadPairs} \\
|
|
\${par_both_aligned:+-B} \\
|
|
\${par_check_pe_dist:+-P} \\
|
|
\${par_min_length:+-d "\${par_min_length}"} \\
|
|
\${par_max_length:+-D "\${par_max_length}"} \\
|
|
\${par_same_strand:+-C} \\
|
|
\${par_donotsort:+--donotsort} \\
|
|
\${par_by_read_group:+--byReadGroup} \\
|
|
\${par_long_reads:+-L} \\
|
|
\${par_detailed_results:+--Rpath "\${par_detailed_results}"} \\
|
|
\${par_detailed_results_format:+-R "\${par_detailed_results_format}"} \\
|
|
\${par_max_M_op:+--maxMOp "\${par_max_M_op}"} \\
|
|
\${par_verbose:+--verbose} \\
|
|
\${meta_cpus:+-T "\${meta_cpus}"} \\
|
|
--tmpDir "\$tmp_dir/temp" \\
|
|
-a "\$par_annotation" \\
|
|
-o "\$tmp_dir/output.txt" \\
|
|
"\${input[*]}"
|
|
|
|
[[ ! -z "\$par_counts" ]] && mv "\$tmp_dir/output.txt" "\$par_counts"
|
|
[[ ! -z "\$par_summary" ]] && mv "\$tmp_dir/output.txt.summary" "\$par_summary"
|
|
if [[ ! -z "\$par_junctions" ]] && [[ -e "\$tmp_dir/output.txt.jcounts" ]]; then
|
|
mv "\$tmp_dir/output.txt.jcounts" "\$par_junctions"
|
|
fi
|
|
VIASHMAIN
|
|
bash "\$tempscript" &
|
|
wait "\$!"
|
|
|
|
VIASHEOF
|
|
|
|
|
|
if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then
|
|
# strip viash automount from file paths
|
|
|
|
if [ ! -z "$VIASH_PAR_ANNOTATION" ]; then
|
|
VIASH_PAR_ANNOTATION=$(ViashDockerStripAutomount "$VIASH_PAR_ANNOTATION")
|
|
fi
|
|
if [ ! -z "$VIASH_PAR_INPUT" ]; then
|
|
unset VIASH_TEST_INPUT
|
|
IFS=';'
|
|
for var in $VIASH_PAR_INPUT; do
|
|
unset IFS
|
|
if [ -z "$VIASH_TEST_INPUT" ]; then
|
|
VIASH_TEST_INPUT="$(ViashDockerStripAutomount "$var")"
|
|
else
|
|
VIASH_TEST_INPUT="$VIASH_TEST_INPUT;""$(ViashDockerStripAutomount "$var")"
|
|
fi
|
|
done
|
|
VIASH_PAR_INPUT="$VIASH_TEST_INPUT"
|
|
fi
|
|
if [ ! -z "$VIASH_PAR_COUNTS" ]; then
|
|
VIASH_PAR_COUNTS=$(ViashDockerStripAutomount "$VIASH_PAR_COUNTS")
|
|
fi
|
|
if [ ! -z "$VIASH_PAR_SUMMARY" ]; then
|
|
VIASH_PAR_SUMMARY=$(ViashDockerStripAutomount "$VIASH_PAR_SUMMARY")
|
|
fi
|
|
if [ ! -z "$VIASH_PAR_JUNCTIONS" ]; then
|
|
VIASH_PAR_JUNCTIONS=$(ViashDockerStripAutomount "$VIASH_PAR_JUNCTIONS")
|
|
fi
|
|
if [ ! -z "$VIASH_PAR_CHROM_ALIAS" ]; then
|
|
VIASH_PAR_CHROM_ALIAS=$(ViashDockerStripAutomount "$VIASH_PAR_CHROM_ALIAS")
|
|
fi
|
|
if [ ! -z "$VIASH_PAR_REF_FASTA" ]; then
|
|
VIASH_PAR_REF_FASTA=$(ViashDockerStripAutomount "$VIASH_PAR_REF_FASTA")
|
|
fi
|
|
if [ ! -z "$VIASH_PAR_DETAILED_RESULTS" ]; then
|
|
VIASH_PAR_DETAILED_RESULTS=$(ViashDockerStripAutomount "$VIASH_PAR_DETAILED_RESULTS")
|
|
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 "$VIASH_PAR_COUNTS" ] && [ ! -e "$VIASH_PAR_COUNTS" ]; then
|
|
ViashError "Output file '$VIASH_PAR_COUNTS' does not exist."
|
|
exit 1
|
|
fi
|
|
if [ ! -z "$VIASH_PAR_SUMMARY" ] && [ ! -e "$VIASH_PAR_SUMMARY" ]; then
|
|
ViashError "Output file '$VIASH_PAR_SUMMARY' does not exist."
|
|
exit 1
|
|
fi
|
|
if [ ! -z "$VIASH_PAR_JUNCTIONS" ] && [ ! -e "$VIASH_PAR_JUNCTIONS" ]; then
|
|
ViashError "Output file '$VIASH_PAR_JUNCTIONS' does not exist."
|
|
exit 1
|
|
fi
|
|
if [ ! -z "$VIASH_PAR_DETAILED_RESULTS" ] && [ ! -e "$VIASH_PAR_DETAILED_RESULTS" ]; then
|
|
ViashError "Output file '$VIASH_PAR_DETAILED_RESULTS' does not exist."
|
|
exit 1
|
|
fi
|
|
|
|
|
|
exit 0
|