CI
6c588ad420
Build pipeline: viash-hub.biobox.v0.4.x-8mmrs
Source commit: 666507c86d
Source message: Merge remote-tracking branch 'origin/main' into v0.4.x
1755 lines
74 KiB
Bash
Executable File
1755 lines
74 KiB
Bash
Executable File
#!/usr/bin/env bash
|
|
|
|
# bcftools_concat v0.4.0
|
|
#
|
|
# 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:
|
|
# * Theodoro Gasperin Terra Camargo (author)
|
|
|
|
set -e
|
|
|
|
if [ -z "$VIASH_TEMP" ]; then
|
|
VIASH_TEMP=${VIASH_TEMP:-$VIASH_TMPDIR}
|
|
VIASH_TEMP=${VIASH_TEMP:-$VIASH_TEMPDIR}
|
|
VIASH_TEMP=${VIASH_TEMP:-$VIASH_TMP}
|
|
VIASH_TEMP=${VIASH_TEMP:-$TMPDIR}
|
|
VIASH_TEMP=${VIASH_TEMP:-$TMP}
|
|
VIASH_TEMP=${VIASH_TEMP:-$TEMPDIR}
|
|
VIASH_TEMP=${VIASH_TEMP:-$TEMP}
|
|
VIASH_TEMP=${VIASH_TEMP:-/tmp}
|
|
fi
|
|
|
|
# define helper functions
|
|
# ViashQuote: put quotes around non flag values
|
|
# $1 : unquoted string
|
|
# return : possibly quoted string
|
|
# examples:
|
|
# ViashQuote --foo # returns --foo
|
|
# ViashQuote bar # returns 'bar'
|
|
# Viashquote --foo=bar # returns --foo='bar'
|
|
function ViashQuote {
|
|
if [[ "$1" =~ ^-+[a-zA-Z0-9_\-]+=.+$ ]]; then
|
|
echo "$1" | sed "s#=\(.*\)#='\1'#"
|
|
elif [[ "$1" =~ ^-+[a-zA-Z0-9_\-]+$ ]]; then
|
|
echo "$1"
|
|
else
|
|
echo "'$1'"
|
|
fi
|
|
}
|
|
# ViashRemoveFlags: Remove leading flag
|
|
# $1 : string with a possible leading flag
|
|
# return : string without possible leading flag
|
|
# examples:
|
|
# ViashRemoveFlags --foo=bar # returns bar
|
|
function ViashRemoveFlags {
|
|
echo "$1" | sed 's/^--*[a-zA-Z0-9_\-]*=//'
|
|
}
|
|
# ViashSourceDir: return the path of a bash file, following symlinks
|
|
# usage : ViashSourceDir ${BASH_SOURCE[0]}
|
|
# $1 : Should always be set to ${BASH_SOURCE[0]}
|
|
# returns : The absolute path of the bash file
|
|
function ViashSourceDir {
|
|
local source="$1"
|
|
while [ -h "$source" ]; do
|
|
local dir="$( cd -P "$( dirname "$source" )" >/dev/null 2>&1 && pwd )"
|
|
source="$(readlink "$source")"
|
|
[[ $source != /* ]] && source="$dir/$source"
|
|
done
|
|
cd -P "$( dirname "$source" )" >/dev/null 2>&1 && pwd
|
|
}
|
|
# ViashFindTargetDir: return the path of the '.build.yaml' file, following symlinks
|
|
# usage : ViashFindTargetDir 'ScriptPath'
|
|
# $1 : The location from where to start the upward search
|
|
# returns : The absolute path of the '.build.yaml' file
|
|
function ViashFindTargetDir {
|
|
local source="$1"
|
|
while [[ "$source" != "" && ! -e "$source/.build.yaml" ]]; do
|
|
source=${source%/*}
|
|
done
|
|
echo $source
|
|
}
|
|
# see https://en.wikipedia.org/wiki/Syslog#Severity_level
|
|
VIASH_LOGCODE_EMERGENCY=0
|
|
VIASH_LOGCODE_ALERT=1
|
|
VIASH_LOGCODE_CRITICAL=2
|
|
VIASH_LOGCODE_ERROR=3
|
|
VIASH_LOGCODE_WARNING=4
|
|
VIASH_LOGCODE_NOTICE=5
|
|
VIASH_LOGCODE_INFO=6
|
|
VIASH_LOGCODE_DEBUG=7
|
|
VIASH_VERBOSITY=$VIASH_LOGCODE_NOTICE
|
|
|
|
# ViashLog: Log events depending on the verbosity level
|
|
# usage: ViashLog 1 alert Oh no something went wrong!
|
|
# $1: required verbosity level
|
|
# $2: display tag
|
|
# $3+: messages to display
|
|
# stdout: Your input, prepended by '[$2] '.
|
|
function ViashLog {
|
|
local required_level="$1"
|
|
local display_tag="$2"
|
|
shift 2
|
|
if [ $VIASH_VERBOSITY -ge $required_level ]; then
|
|
>&2 echo "[$display_tag]" "$@"
|
|
fi
|
|
}
|
|
|
|
# ViashEmergency: log events when the system is unstable
|
|
# usage: ViashEmergency Oh no something went wrong.
|
|
# stdout: Your input, prepended by '[emergency] '.
|
|
function ViashEmergency {
|
|
ViashLog $VIASH_LOGCODE_EMERGENCY emergency "$@"
|
|
}
|
|
|
|
# ViashAlert: log events when actions must be taken immediately (e.g. corrupted system database)
|
|
# usage: ViashAlert Oh no something went wrong.
|
|
# stdout: Your input, prepended by '[alert] '.
|
|
function ViashAlert {
|
|
ViashLog $VIASH_LOGCODE_ALERT alert "$@"
|
|
}
|
|
|
|
# ViashCritical: log events when a critical condition occurs
|
|
# usage: ViashCritical Oh no something went wrong.
|
|
# stdout: Your input, prepended by '[critical] '.
|
|
function ViashCritical {
|
|
ViashLog $VIASH_LOGCODE_CRITICAL critical "$@"
|
|
}
|
|
|
|
# ViashError: log events when an error condition occurs
|
|
# usage: ViashError Oh no something went wrong.
|
|
# stdout: Your input, prepended by '[error] '.
|
|
function ViashError {
|
|
ViashLog $VIASH_LOGCODE_ERROR error "$@"
|
|
}
|
|
|
|
# ViashWarning: log potentially abnormal events
|
|
# usage: ViashWarning Something may have gone wrong.
|
|
# stdout: Your input, prepended by '[warning] '.
|
|
function ViashWarning {
|
|
ViashLog $VIASH_LOGCODE_WARNING warning "$@"
|
|
}
|
|
|
|
# ViashNotice: log significant but normal events
|
|
# usage: ViashNotice This just happened.
|
|
# stdout: Your input, prepended by '[notice] '.
|
|
function ViashNotice {
|
|
ViashLog $VIASH_LOGCODE_NOTICE notice "$@"
|
|
}
|
|
|
|
# ViashInfo: log normal events
|
|
# usage: ViashInfo This just happened.
|
|
# stdout: Your input, prepended by '[info] '.
|
|
function ViashInfo {
|
|
ViashLog $VIASH_LOGCODE_INFO info "$@"
|
|
}
|
|
|
|
# ViashDebug: log all events, for debugging purposes
|
|
# usage: ViashDebug This just happened.
|
|
# stdout: Your input, prepended by '[debug] '.
|
|
function ViashDebug {
|
|
ViashLog $VIASH_LOGCODE_DEBUG debug "$@"
|
|
}
|
|
|
|
# find source folder of this component
|
|
VIASH_META_RESOURCES_DIR=`ViashSourceDir ${BASH_SOURCE[0]}`
|
|
|
|
# find the root of the built components & dependencies
|
|
VIASH_TARGET_DIR=`ViashFindTargetDir $VIASH_META_RESOURCES_DIR`
|
|
|
|
# define meta fields
|
|
VIASH_META_NAME="bcftools_concat"
|
|
VIASH_META_FUNCTIONALITY_NAME="bcftools_concat"
|
|
VIASH_META_EXECUTABLE="$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/bcftools:1.22--h3a4d415_1
|
|
ENTRYPOINT []
|
|
RUN bcftools --version 2>&1 | head -1 | sed 's/bcftools /bcftools: /' > /var/software_versions.txt
|
|
|
|
LABEL org.opencontainers.image.authors="Theodoro Gasperin Terra Camargo"
|
|
LABEL org.opencontainers.image.description="Companion container for running component bcftools bcftools_concat"
|
|
LABEL org.opencontainers.image.created="2025-09-17T08:35:56Z"
|
|
LABEL org.opencontainers.image.source="https://github.com/samtools/bcftools"
|
|
LABEL org.opencontainers.image.revision="666507c86de9150bfbdffdb2dbabc1dbde3c3262"
|
|
LABEL org.opencontainers.image.version="v0.4.0"
|
|
|
|
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 "bcftools_concat v0.4.0"
|
|
echo ""
|
|
echo "Concatenate or combine VCF/BCF files. All source files must have the same sample"
|
|
echo "columns appearing in the same order. The program can be used, for example, to"
|
|
echo "concatenate chromosome VCFs into one VCF, or combine a SNP VCF and an indel"
|
|
echo "VCF into one. The input files must be sorted by chr and position. The files"
|
|
echo "must be given in the correct order to produce sorted VCF on output unless"
|
|
echo "the -a, --allow-overlaps option is specified. With the --naive option, the files"
|
|
echo "are concatenated without being recompressed, which is very fast."
|
|
echo ""
|
|
echo "Inputs:"
|
|
echo " -i, --input"
|
|
echo " type: file, multiple values allowed, file must exist"
|
|
echo " example: input1.vcf.gz input2.vcf.gz"
|
|
echo " Input VCF/BCF files to concatenate."
|
|
echo " All source files must have the same sample columns appearing in"
|
|
echo " the same order. Files must be sorted by chr and position."
|
|
echo ""
|
|
echo " -f, --file_list"
|
|
echo " type: file, file must exist"
|
|
echo " example: files_list.txt"
|
|
echo " Read the list of VCF/BCF files from a file, one file name per line."
|
|
echo " Alternative to providing multiple --input files."
|
|
echo ""
|
|
echo "Outputs:"
|
|
echo " -o, --output"
|
|
echo " type: file, required parameter, output, file must exist"
|
|
echo " example: concatenated.vcf.gz"
|
|
echo " Write output to a file."
|
|
echo " If not specified, output goes to standard output."
|
|
echo ""
|
|
echo "Options:"
|
|
echo " -a, --allow_overlaps"
|
|
echo " type: boolean_true"
|
|
echo " First coordinate of the next file can precede last record of the current"
|
|
echo " file."
|
|
echo " Allows overlapping records between files during concatenation."
|
|
echo ""
|
|
echo " -c, --compact_ps"
|
|
echo " type: boolean_true"
|
|
echo " Do not output PS tag at each site, only at the start of a new phase set"
|
|
echo " block."
|
|
echo " Reduces output size for phased data."
|
|
echo ""
|
|
echo " -d, --rm_dups"
|
|
echo " type: string"
|
|
echo " example: exact"
|
|
echo " choices: [ snps, indels, both, all, exact ]"
|
|
echo " Output duplicate records present in multiple files only once."
|
|
echo " **Options:**"
|
|
echo " - \`snps\`: Remove duplicate SNPs"
|
|
echo " - \`indels\`: Remove duplicate indels"
|
|
echo " - \`both\`: Remove duplicate SNPs and indels"
|
|
echo " - \`all\`: Remove all duplicates"
|
|
echo " - \`exact\`: Remove exact duplicates only"
|
|
echo ""
|
|
echo " -D, --remove_duplicates"
|
|
echo " type: boolean_true"
|
|
echo " Alias for --rm_dups exact."
|
|
echo " Remove exact duplicate records present in multiple files."
|
|
echo ""
|
|
echo " -G, --drop_genotypes"
|
|
echo " type: boolean_true"
|
|
echo " Drop individual genotype information."
|
|
echo " Removes all sample-specific data from output."
|
|
echo ""
|
|
echo " -l, --ligate"
|
|
echo " type: boolean_true"
|
|
echo " Ligate phased VCFs by matching phase at overlapping haplotypes."
|
|
echo " Connects phase information across files."
|
|
echo ""
|
|
echo " --ligate_force"
|
|
echo " type: boolean_true"
|
|
echo " Ligate even non-overlapping chunks, keep all sites."
|
|
echo " Forces ligation without requiring overlap validation."
|
|
echo ""
|
|
echo " --ligate_warn"
|
|
echo " type: boolean_true"
|
|
echo " Drop sites in imperfect overlaps."
|
|
echo " Conservative ligation that removes problematic sites."
|
|
echo ""
|
|
echo " --no_version"
|
|
echo " type: boolean_true"
|
|
echo " Do not append version and command line to the header."
|
|
echo " Produces cleaner output headers."
|
|
echo ""
|
|
echo " -n, --naive"
|
|
echo " type: boolean_true"
|
|
echo " Concatenate files without recompression."
|
|
echo " Very fast operation with header compatibility check."
|
|
echo ""
|
|
echo " --naive_force"
|
|
echo " type: boolean_true"
|
|
echo " Same as --naive, but header compatibility is not checked."
|
|
echo " **Warning:** Dangerous option, use with caution."
|
|
echo ""
|
|
echo " -O, --output_type"
|
|
echo " type: string"
|
|
echo " example: z"
|
|
echo " choices: [ u, z, b, v ]"
|
|
echo " Output type and compression level."
|
|
echo " **Options:**"
|
|
echo " - \`u\`: uncompressed BCF"
|
|
echo " - \`b\`: compressed BCF"
|
|
echo " - \`v\`: uncompressed VCF"
|
|
echo " - \`z\`: compressed VCF (with optional compression level 0-9)"
|
|
echo ""
|
|
echo " -q, --min_pq"
|
|
echo " type: integer"
|
|
echo " example: 30"
|
|
echo " Break phase set if phasing quality is lower than specified value."
|
|
echo " Only relevant when working with phased data."
|
|
echo ""
|
|
echo " -r, --regions"
|
|
echo " type: string"
|
|
echo " example: chr20:1000000-2000000"
|
|
echo " Restrict to comma-separated list of regions."
|
|
echo " **Formats supported:** chr|chr:pos|chr:beg-end|chr:beg-[,…]"
|
|
echo ""
|
|
echo " -R, --regions_file"
|
|
echo " type: file, file must exist"
|
|
echo " example: regions.bed"
|
|
echo " Restrict to regions listed in a file."
|
|
echo " Regions can be specified in VCF, BED, or tab-delimited format."
|
|
echo ""
|
|
echo " --regions_overlap"
|
|
echo " type: string"
|
|
echo " example: 1"
|
|
echo " choices: [ 0, 1, 2 ]"
|
|
echo " Include if POS in the region (0), record overlaps (1), variant overlaps"
|
|
echo " (2)."
|
|
echo " **Options:**"
|
|
echo " - \`0\`: POS inside region (default for -t/-T)"
|
|
echo " - \`1\`: overlapping records included (default for -r/-R)"
|
|
echo " - \`2\`: true overlapping variation only"
|
|
echo ""
|
|
echo " -v, --verbosity"
|
|
echo " type: integer"
|
|
echo " example: 1"
|
|
echo " Set verbosity level."
|
|
echo " Controls amount of diagnostic output."
|
|
echo ""
|
|
echo " -W, --write_index"
|
|
echo " type: string"
|
|
echo " example: tbi"
|
|
echo " Automatically index the output files."
|
|
echo " **Format:** Specify index format or use default."
|
|
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 "$1")"
|
|
shift 1
|
|
;;
|
|
--version)
|
|
echo "bcftools_concat v0.4.0"
|
|
exit
|
|
;;
|
|
--input)
|
|
if [ -z "$VIASH_PAR_INPUT" ]; then
|
|
VIASH_PAR_INPUT="$2"
|
|
else
|
|
VIASH_PAR_INPUT="$VIASH_PAR_INPUT;""$2"
|
|
fi
|
|
[ $# -lt 2 ] && ViashError Not enough arguments passed to --input. Use "--help" to get more information on the parameters. && exit 1
|
|
shift 2
|
|
;;
|
|
--input=*)
|
|
if [ -z "$VIASH_PAR_INPUT" ]; then
|
|
VIASH_PAR_INPUT=$(ViashRemoveFlags "$1")
|
|
else
|
|
VIASH_PAR_INPUT="$VIASH_PAR_INPUT;"$(ViashRemoveFlags "$1")
|
|
fi
|
|
shift 1
|
|
;;
|
|
-i)
|
|
if [ -z "$VIASH_PAR_INPUT" ]; then
|
|
VIASH_PAR_INPUT="$2"
|
|
else
|
|
VIASH_PAR_INPUT="$VIASH_PAR_INPUT;""$2"
|
|
fi
|
|
[ $# -lt 2 ] && ViashError Not enough arguments passed to -i. Use "--help" to get more information on the parameters. && exit 1
|
|
shift 2
|
|
;;
|
|
--file_list)
|
|
[ -n "$VIASH_PAR_FILE_LIST" ] && ViashError Bad arguments for option \'--file_list\': \'$VIASH_PAR_FILE_LIST\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_FILE_LIST="$2"
|
|
[ $# -lt 2 ] && ViashError Not enough arguments passed to --file_list. Use "--help" to get more information on the parameters. && exit 1
|
|
shift 2
|
|
;;
|
|
--file_list=*)
|
|
[ -n "$VIASH_PAR_FILE_LIST" ] && ViashError Bad arguments for option \'--file_list=*\': \'$VIASH_PAR_FILE_LIST\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_FILE_LIST=$(ViashRemoveFlags "$1")
|
|
shift 1
|
|
;;
|
|
-f)
|
|
[ -n "$VIASH_PAR_FILE_LIST" ] && ViashError Bad arguments for option \'-f\': \'$VIASH_PAR_FILE_LIST\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_FILE_LIST="$2"
|
|
[ $# -lt 2 ] && ViashError Not enough arguments passed to -f. Use "--help" to get more information on the parameters. && exit 1
|
|
shift 2
|
|
;;
|
|
--output)
|
|
[ -n "$VIASH_PAR_OUTPUT" ] && ViashError Bad arguments for option \'--output\': \'$VIASH_PAR_OUTPUT\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_OUTPUT="$2"
|
|
[ $# -lt 2 ] && ViashError Not enough arguments passed to --output. Use "--help" to get more information on the parameters. && exit 1
|
|
shift 2
|
|
;;
|
|
--output=*)
|
|
[ -n "$VIASH_PAR_OUTPUT" ] && ViashError Bad arguments for option \'--output=*\': \'$VIASH_PAR_OUTPUT\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_OUTPUT=$(ViashRemoveFlags "$1")
|
|
shift 1
|
|
;;
|
|
-o)
|
|
[ -n "$VIASH_PAR_OUTPUT" ] && ViashError Bad arguments for option \'-o\': \'$VIASH_PAR_OUTPUT\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_OUTPUT="$2"
|
|
[ $# -lt 2 ] && ViashError Not enough arguments passed to -o. Use "--help" to get more information on the parameters. && exit 1
|
|
shift 2
|
|
;;
|
|
--allow_overlaps)
|
|
[ -n "$VIASH_PAR_ALLOW_OVERLAPS" ] && ViashError Bad arguments for option \'--allow_overlaps\': \'$VIASH_PAR_ALLOW_OVERLAPS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_ALLOW_OVERLAPS=true
|
|
shift 1
|
|
;;
|
|
-a)
|
|
[ -n "$VIASH_PAR_ALLOW_OVERLAPS" ] && ViashError Bad arguments for option \'-a\': \'$VIASH_PAR_ALLOW_OVERLAPS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_ALLOW_OVERLAPS=true
|
|
shift 1
|
|
;;
|
|
--compact_ps)
|
|
[ -n "$VIASH_PAR_COMPACT_PS" ] && ViashError Bad arguments for option \'--compact_ps\': \'$VIASH_PAR_COMPACT_PS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_COMPACT_PS=true
|
|
shift 1
|
|
;;
|
|
-c)
|
|
[ -n "$VIASH_PAR_COMPACT_PS" ] && ViashError Bad arguments for option \'-c\': \'$VIASH_PAR_COMPACT_PS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_COMPACT_PS=true
|
|
shift 1
|
|
;;
|
|
--rm_dups)
|
|
[ -n "$VIASH_PAR_RM_DUPS" ] && ViashError Bad arguments for option \'--rm_dups\': \'$VIASH_PAR_RM_DUPS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_RM_DUPS="$2"
|
|
[ $# -lt 2 ] && ViashError Not enough arguments passed to --rm_dups. Use "--help" to get more information on the parameters. && exit 1
|
|
shift 2
|
|
;;
|
|
--rm_dups=*)
|
|
[ -n "$VIASH_PAR_RM_DUPS" ] && ViashError Bad arguments for option \'--rm_dups=*\': \'$VIASH_PAR_RM_DUPS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_RM_DUPS=$(ViashRemoveFlags "$1")
|
|
shift 1
|
|
;;
|
|
-d)
|
|
[ -n "$VIASH_PAR_RM_DUPS" ] && ViashError Bad arguments for option \'-d\': \'$VIASH_PAR_RM_DUPS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_RM_DUPS="$2"
|
|
[ $# -lt 2 ] && ViashError Not enough arguments passed to -d. Use "--help" to get more information on the parameters. && exit 1
|
|
shift 2
|
|
;;
|
|
--remove_duplicates)
|
|
[ -n "$VIASH_PAR_REMOVE_DUPLICATES" ] && ViashError Bad arguments for option \'--remove_duplicates\': \'$VIASH_PAR_REMOVE_DUPLICATES\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_REMOVE_DUPLICATES=true
|
|
shift 1
|
|
;;
|
|
-D)
|
|
[ -n "$VIASH_PAR_REMOVE_DUPLICATES" ] && ViashError Bad arguments for option \'-D\': \'$VIASH_PAR_REMOVE_DUPLICATES\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_REMOVE_DUPLICATES=true
|
|
shift 1
|
|
;;
|
|
--drop_genotypes)
|
|
[ -n "$VIASH_PAR_DROP_GENOTYPES" ] && ViashError Bad arguments for option \'--drop_genotypes\': \'$VIASH_PAR_DROP_GENOTYPES\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_DROP_GENOTYPES=true
|
|
shift 1
|
|
;;
|
|
-G)
|
|
[ -n "$VIASH_PAR_DROP_GENOTYPES" ] && ViashError Bad arguments for option \'-G\': \'$VIASH_PAR_DROP_GENOTYPES\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_DROP_GENOTYPES=true
|
|
shift 1
|
|
;;
|
|
--ligate)
|
|
[ -n "$VIASH_PAR_LIGATE" ] && ViashError Bad arguments for option \'--ligate\': \'$VIASH_PAR_LIGATE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_LIGATE=true
|
|
shift 1
|
|
;;
|
|
-l)
|
|
[ -n "$VIASH_PAR_LIGATE" ] && ViashError Bad arguments for option \'-l\': \'$VIASH_PAR_LIGATE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_LIGATE=true
|
|
shift 1
|
|
;;
|
|
--ligate_force)
|
|
[ -n "$VIASH_PAR_LIGATE_FORCE" ] && ViashError Bad arguments for option \'--ligate_force\': \'$VIASH_PAR_LIGATE_FORCE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_LIGATE_FORCE=true
|
|
shift 1
|
|
;;
|
|
--ligate_warn)
|
|
[ -n "$VIASH_PAR_LIGATE_WARN" ] && ViashError Bad arguments for option \'--ligate_warn\': \'$VIASH_PAR_LIGATE_WARN\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_LIGATE_WARN=true
|
|
shift 1
|
|
;;
|
|
--no_version)
|
|
[ -n "$VIASH_PAR_NO_VERSION" ] && ViashError Bad arguments for option \'--no_version\': \'$VIASH_PAR_NO_VERSION\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_NO_VERSION=true
|
|
shift 1
|
|
;;
|
|
--naive)
|
|
[ -n "$VIASH_PAR_NAIVE" ] && ViashError Bad arguments for option \'--naive\': \'$VIASH_PAR_NAIVE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_NAIVE=true
|
|
shift 1
|
|
;;
|
|
-n)
|
|
[ -n "$VIASH_PAR_NAIVE" ] && ViashError Bad arguments for option \'-n\': \'$VIASH_PAR_NAIVE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_NAIVE=true
|
|
shift 1
|
|
;;
|
|
--naive_force)
|
|
[ -n "$VIASH_PAR_NAIVE_FORCE" ] && ViashError Bad arguments for option \'--naive_force\': \'$VIASH_PAR_NAIVE_FORCE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_NAIVE_FORCE=true
|
|
shift 1
|
|
;;
|
|
--output_type)
|
|
[ -n "$VIASH_PAR_OUTPUT_TYPE" ] && ViashError Bad arguments for option \'--output_type\': \'$VIASH_PAR_OUTPUT_TYPE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_OUTPUT_TYPE="$2"
|
|
[ $# -lt 2 ] && ViashError Not enough arguments passed to --output_type. Use "--help" to get more information on the parameters. && exit 1
|
|
shift 2
|
|
;;
|
|
--output_type=*)
|
|
[ -n "$VIASH_PAR_OUTPUT_TYPE" ] && ViashError Bad arguments for option \'--output_type=*\': \'$VIASH_PAR_OUTPUT_TYPE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_OUTPUT_TYPE=$(ViashRemoveFlags "$1")
|
|
shift 1
|
|
;;
|
|
-O)
|
|
[ -n "$VIASH_PAR_OUTPUT_TYPE" ] && ViashError Bad arguments for option \'-O\': \'$VIASH_PAR_OUTPUT_TYPE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_OUTPUT_TYPE="$2"
|
|
[ $# -lt 2 ] && ViashError Not enough arguments passed to -O. Use "--help" to get more information on the parameters. && exit 1
|
|
shift 2
|
|
;;
|
|
--min_pq)
|
|
[ -n "$VIASH_PAR_MIN_PQ" ] && ViashError Bad arguments for option \'--min_pq\': \'$VIASH_PAR_MIN_PQ\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_MIN_PQ="$2"
|
|
[ $# -lt 2 ] && ViashError Not enough arguments passed to --min_pq. Use "--help" to get more information on the parameters. && exit 1
|
|
shift 2
|
|
;;
|
|
--min_pq=*)
|
|
[ -n "$VIASH_PAR_MIN_PQ" ] && ViashError Bad arguments for option \'--min_pq=*\': \'$VIASH_PAR_MIN_PQ\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_MIN_PQ=$(ViashRemoveFlags "$1")
|
|
shift 1
|
|
;;
|
|
-q)
|
|
[ -n "$VIASH_PAR_MIN_PQ" ] && ViashError Bad arguments for option \'-q\': \'$VIASH_PAR_MIN_PQ\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_MIN_PQ="$2"
|
|
[ $# -lt 2 ] && ViashError Not enough arguments passed to -q. Use "--help" to get more information on the parameters. && exit 1
|
|
shift 2
|
|
;;
|
|
--regions)
|
|
[ -n "$VIASH_PAR_REGIONS" ] && ViashError Bad arguments for option \'--regions\': \'$VIASH_PAR_REGIONS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_REGIONS="$2"
|
|
[ $# -lt 2 ] && ViashError Not enough arguments passed to --regions. Use "--help" to get more information on the parameters. && exit 1
|
|
shift 2
|
|
;;
|
|
--regions=*)
|
|
[ -n "$VIASH_PAR_REGIONS" ] && ViashError Bad arguments for option \'--regions=*\': \'$VIASH_PAR_REGIONS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_REGIONS=$(ViashRemoveFlags "$1")
|
|
shift 1
|
|
;;
|
|
-r)
|
|
[ -n "$VIASH_PAR_REGIONS" ] && ViashError Bad arguments for option \'-r\': \'$VIASH_PAR_REGIONS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_REGIONS="$2"
|
|
[ $# -lt 2 ] && ViashError Not enough arguments passed to -r. Use "--help" to get more information on the parameters. && exit 1
|
|
shift 2
|
|
;;
|
|
--regions_file)
|
|
[ -n "$VIASH_PAR_REGIONS_FILE" ] && ViashError Bad arguments for option \'--regions_file\': \'$VIASH_PAR_REGIONS_FILE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_REGIONS_FILE="$2"
|
|
[ $# -lt 2 ] && ViashError Not enough arguments passed to --regions_file. Use "--help" to get more information on the parameters. && exit 1
|
|
shift 2
|
|
;;
|
|
--regions_file=*)
|
|
[ -n "$VIASH_PAR_REGIONS_FILE" ] && ViashError Bad arguments for option \'--regions_file=*\': \'$VIASH_PAR_REGIONS_FILE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_REGIONS_FILE=$(ViashRemoveFlags "$1")
|
|
shift 1
|
|
;;
|
|
-R)
|
|
[ -n "$VIASH_PAR_REGIONS_FILE" ] && ViashError Bad arguments for option \'-R\': \'$VIASH_PAR_REGIONS_FILE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_REGIONS_FILE="$2"
|
|
[ $# -lt 2 ] && ViashError Not enough arguments passed to -R. Use "--help" to get more information on the parameters. && exit 1
|
|
shift 2
|
|
;;
|
|
--regions_overlap)
|
|
[ -n "$VIASH_PAR_REGIONS_OVERLAP" ] && ViashError Bad arguments for option \'--regions_overlap\': \'$VIASH_PAR_REGIONS_OVERLAP\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_REGIONS_OVERLAP="$2"
|
|
[ $# -lt 2 ] && ViashError Not enough arguments passed to --regions_overlap. Use "--help" to get more information on the parameters. && exit 1
|
|
shift 2
|
|
;;
|
|
--regions_overlap=*)
|
|
[ -n "$VIASH_PAR_REGIONS_OVERLAP" ] && ViashError Bad arguments for option \'--regions_overlap=*\': \'$VIASH_PAR_REGIONS_OVERLAP\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_REGIONS_OVERLAP=$(ViashRemoveFlags "$1")
|
|
shift 1
|
|
;;
|
|
--verbosity)
|
|
[ -n "$VIASH_PAR_VERBOSITY" ] && ViashError Bad arguments for option \'--verbosity\': \'$VIASH_PAR_VERBOSITY\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_VERBOSITY="$2"
|
|
[ $# -lt 2 ] && ViashError Not enough arguments passed to --verbosity. Use "--help" to get more information on the parameters. && exit 1
|
|
shift 2
|
|
;;
|
|
--verbosity=*)
|
|
[ -n "$VIASH_PAR_VERBOSITY" ] && ViashError Bad arguments for option \'--verbosity=*\': \'$VIASH_PAR_VERBOSITY\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_VERBOSITY=$(ViashRemoveFlags "$1")
|
|
shift 1
|
|
;;
|
|
-v)
|
|
[ -n "$VIASH_PAR_VERBOSITY" ] && ViashError Bad arguments for option \'-v\': \'$VIASH_PAR_VERBOSITY\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_VERBOSITY="$2"
|
|
[ $# -lt 2 ] && ViashError Not enough arguments passed to -v. Use "--help" to get more information on the parameters. && exit 1
|
|
shift 2
|
|
;;
|
|
--write_index)
|
|
[ -n "$VIASH_PAR_WRITE_INDEX" ] && ViashError Bad arguments for option \'--write_index\': \'$VIASH_PAR_WRITE_INDEX\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_WRITE_INDEX="$2"
|
|
[ $# -lt 2 ] && ViashError Not enough arguments passed to --write_index. Use "--help" to get more information on the parameters. && exit 1
|
|
shift 2
|
|
;;
|
|
--write_index=*)
|
|
[ -n "$VIASH_PAR_WRITE_INDEX" ] && ViashError Bad arguments for option \'--write_index=*\': \'$VIASH_PAR_WRITE_INDEX\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_WRITE_INDEX=$(ViashRemoveFlags "$1")
|
|
shift 1
|
|
;;
|
|
-W)
|
|
[ -n "$VIASH_PAR_WRITE_INDEX" ] && ViashError Bad arguments for option \'-W\': \'$VIASH_PAR_WRITE_INDEX\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_WRITE_INDEX="$2"
|
|
[ $# -lt 2 ] && ViashError Not enough arguments passed to -W. Use "--help" to get more information on the parameters. && exit 1
|
|
shift 2
|
|
;;
|
|
---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/bcftools/bcftools_concat:v0.4.0'
|
|
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 "$VIASH_DOCKER_IMAGE_ID" 'bcftools' 'ps' 'bash'
|
|
exit 0
|
|
fi
|
|
|
|
# check if docker image exists
|
|
ViashDockerSetup "$VIASH_DOCKER_IMAGE_ID" ifneedbepullelsecachedbuild
|
|
ViashDockerCheckCommands "$VIASH_DOCKER_IMAGE_ID" 'bcftools' '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_OUTPUT+x} ]; then
|
|
ViashError '--output' 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_ALLOW_OVERLAPS+x} ]; then
|
|
VIASH_PAR_ALLOW_OVERLAPS="false"
|
|
fi
|
|
if [ -z ${VIASH_PAR_COMPACT_PS+x} ]; then
|
|
VIASH_PAR_COMPACT_PS="false"
|
|
fi
|
|
if [ -z ${VIASH_PAR_REMOVE_DUPLICATES+x} ]; then
|
|
VIASH_PAR_REMOVE_DUPLICATES="false"
|
|
fi
|
|
if [ -z ${VIASH_PAR_DROP_GENOTYPES+x} ]; then
|
|
VIASH_PAR_DROP_GENOTYPES="false"
|
|
fi
|
|
if [ -z ${VIASH_PAR_LIGATE+x} ]; then
|
|
VIASH_PAR_LIGATE="false"
|
|
fi
|
|
if [ -z ${VIASH_PAR_LIGATE_FORCE+x} ]; then
|
|
VIASH_PAR_LIGATE_FORCE="false"
|
|
fi
|
|
if [ -z ${VIASH_PAR_LIGATE_WARN+x} ]; then
|
|
VIASH_PAR_LIGATE_WARN="false"
|
|
fi
|
|
if [ -z ${VIASH_PAR_NO_VERSION+x} ]; then
|
|
VIASH_PAR_NO_VERSION="false"
|
|
fi
|
|
if [ -z ${VIASH_PAR_NAIVE+x} ]; then
|
|
VIASH_PAR_NAIVE="false"
|
|
fi
|
|
if [ -z ${VIASH_PAR_NAIVE_FORCE+x} ]; then
|
|
VIASH_PAR_NAIVE_FORCE="false"
|
|
fi
|
|
|
|
# check whether required files exist
|
|
if [ ! -z "$VIASH_PAR_INPUT" ]; then
|
|
IFS=';'
|
|
set -f
|
|
for file in $VIASH_PAR_INPUT; do
|
|
unset IFS
|
|
if [ ! -e "$file" ]; then
|
|
ViashError "Input file '$file' does not exist."
|
|
exit 1
|
|
fi
|
|
done
|
|
set +f
|
|
fi
|
|
if [ ! -z "$VIASH_PAR_FILE_LIST" ] && [ ! -e "$VIASH_PAR_FILE_LIST" ]; then
|
|
ViashError "Input file '$VIASH_PAR_FILE_LIST' does not exist."
|
|
exit 1
|
|
fi
|
|
if [ ! -z "$VIASH_PAR_REGIONS_FILE" ] && [ ! -e "$VIASH_PAR_REGIONS_FILE" ]; then
|
|
ViashError "Input file '$VIASH_PAR_REGIONS_FILE' does not exist."
|
|
exit 1
|
|
fi
|
|
|
|
# check whether parameters values are of the right type
|
|
if [[ -n "$VIASH_PAR_ALLOW_OVERLAPS" ]]; then
|
|
if ! [[ "$VIASH_PAR_ALLOW_OVERLAPS" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then
|
|
ViashError '--allow_overlaps' has to be a boolean_true. Use "--help" to get more information on the parameters.
|
|
exit 1
|
|
fi
|
|
fi
|
|
if [[ -n "$VIASH_PAR_COMPACT_PS" ]]; then
|
|
if ! [[ "$VIASH_PAR_COMPACT_PS" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then
|
|
ViashError '--compact_ps' has to be a boolean_true. Use "--help" to get more information on the parameters.
|
|
exit 1
|
|
fi
|
|
fi
|
|
if [[ -n "$VIASH_PAR_REMOVE_DUPLICATES" ]]; then
|
|
if ! [[ "$VIASH_PAR_REMOVE_DUPLICATES" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then
|
|
ViashError '--remove_duplicates' has to be a boolean_true. Use "--help" to get more information on the parameters.
|
|
exit 1
|
|
fi
|
|
fi
|
|
if [[ -n "$VIASH_PAR_DROP_GENOTYPES" ]]; then
|
|
if ! [[ "$VIASH_PAR_DROP_GENOTYPES" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then
|
|
ViashError '--drop_genotypes' has to be a boolean_true. Use "--help" to get more information on the parameters.
|
|
exit 1
|
|
fi
|
|
fi
|
|
if [[ -n "$VIASH_PAR_LIGATE" ]]; then
|
|
if ! [[ "$VIASH_PAR_LIGATE" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then
|
|
ViashError '--ligate' has to be a boolean_true. Use "--help" to get more information on the parameters.
|
|
exit 1
|
|
fi
|
|
fi
|
|
if [[ -n "$VIASH_PAR_LIGATE_FORCE" ]]; then
|
|
if ! [[ "$VIASH_PAR_LIGATE_FORCE" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then
|
|
ViashError '--ligate_force' has to be a boolean_true. Use "--help" to get more information on the parameters.
|
|
exit 1
|
|
fi
|
|
fi
|
|
if [[ -n "$VIASH_PAR_LIGATE_WARN" ]]; then
|
|
if ! [[ "$VIASH_PAR_LIGATE_WARN" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then
|
|
ViashError '--ligate_warn' has to be a boolean_true. Use "--help" to get more information on the parameters.
|
|
exit 1
|
|
fi
|
|
fi
|
|
if [[ -n "$VIASH_PAR_NO_VERSION" ]]; then
|
|
if ! [[ "$VIASH_PAR_NO_VERSION" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then
|
|
ViashError '--no_version' has to be a boolean_true. Use "--help" to get more information on the parameters.
|
|
exit 1
|
|
fi
|
|
fi
|
|
if [[ -n "$VIASH_PAR_NAIVE" ]]; then
|
|
if ! [[ "$VIASH_PAR_NAIVE" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then
|
|
ViashError '--naive' has to be a boolean_true. Use "--help" to get more information on the parameters.
|
|
exit 1
|
|
fi
|
|
fi
|
|
if [[ -n "$VIASH_PAR_NAIVE_FORCE" ]]; then
|
|
if ! [[ "$VIASH_PAR_NAIVE_FORCE" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then
|
|
ViashError '--naive_force' has to be a boolean_true. Use "--help" to get more information on the parameters.
|
|
exit 1
|
|
fi
|
|
fi
|
|
if [[ -n "$VIASH_PAR_MIN_PQ" ]]; then
|
|
if ! [[ "$VIASH_PAR_MIN_PQ" =~ ^[-+]?[0-9]+$ ]]; then
|
|
ViashError '--min_pq' has to be an integer. Use "--help" to get more information on the parameters.
|
|
exit 1
|
|
fi
|
|
fi
|
|
if [[ -n "$VIASH_PAR_VERBOSITY" ]]; then
|
|
if ! [[ "$VIASH_PAR_VERBOSITY" =~ ^[-+]?[0-9]+$ ]]; then
|
|
ViashError '--verbosity' has to be an integer. 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 "$VIASH_PAR_RM_DUPS" ]; then
|
|
VIASH_PAR_RM_DUPS_CHOICES=("snps;indels;both;all;exact")
|
|
IFS=';'
|
|
set -f
|
|
if ! [[ ";${VIASH_PAR_RM_DUPS_CHOICES[*]};" =~ ";$VIASH_PAR_RM_DUPS;" ]]; then
|
|
ViashError '--rm_dups' specified value of \'$VIASH_PAR_RM_DUPS\' 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 "$VIASH_PAR_OUTPUT_TYPE" ]; then
|
|
VIASH_PAR_OUTPUT_TYPE_CHOICES=("u;z;b;v")
|
|
IFS=';'
|
|
set -f
|
|
if ! [[ ";${VIASH_PAR_OUTPUT_TYPE_CHOICES[*]};" =~ ";$VIASH_PAR_OUTPUT_TYPE;" ]]; then
|
|
ViashError '--output_type' specified value of \'$VIASH_PAR_OUTPUT_TYPE\' 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 "$VIASH_PAR_REGIONS_OVERLAP" ]; then
|
|
VIASH_PAR_REGIONS_OVERLAP_CHOICES=("0;1;2")
|
|
IFS=';'
|
|
set -f
|
|
if ! [[ ";${VIASH_PAR_REGIONS_OVERLAP_CHOICES[*]};" =~ ";$VIASH_PAR_REGIONS_OVERLAP;" ]]; then
|
|
ViashError '--regions_overlap' specified value of \'$VIASH_PAR_REGIONS_OVERLAP\' is not in the list of allowed values. Use "--help" to get more information on the parameters.
|
|
exit 1
|
|
fi
|
|
set +f
|
|
unset IFS
|
|
fi
|
|
|
|
# create parent directories of output files, if so desired
|
|
if [ ! -z "$VIASH_PAR_OUTPUT" ] && [ ! -d "$(dirname "$VIASH_PAR_OUTPUT")" ]; then
|
|
mkdir -p "$(dirname "$VIASH_PAR_OUTPUT")"
|
|
fi
|
|
|
|
if [ "$VIASH_ENGINE_ID" == "native" ] ; then
|
|
if [ "$VIASH_MODE" == "run" ]; then
|
|
VIASH_CMD="bash"
|
|
else
|
|
ViashError "Engine '$VIASH_ENGINE_ID' does not support mode '$VIASH_MODE'."
|
|
exit 1
|
|
fi
|
|
fi
|
|
|
|
if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then
|
|
# detect volumes from file arguments
|
|
VIASH_CHOWN_VARS=()
|
|
if [ ! -z "$VIASH_PAR_INPUT" ]; then
|
|
VIASH_TEST_INPUT=()
|
|
IFS=';'
|
|
for var in $VIASH_PAR_INPUT; do
|
|
unset IFS
|
|
VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$var")" )
|
|
var=$(ViashDockerAutodetectMount "$var")
|
|
VIASH_TEST_INPUT+=( "$var" )
|
|
done
|
|
VIASH_PAR_INPUT=$(IFS=';' ; echo "${VIASH_TEST_INPUT[*]}")
|
|
fi
|
|
if [ ! -z "$VIASH_PAR_FILE_LIST" ]; then
|
|
VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$VIASH_PAR_FILE_LIST")" )
|
|
VIASH_PAR_FILE_LIST=$(ViashDockerAutodetectMount "$VIASH_PAR_FILE_LIST")
|
|
fi
|
|
if [ ! -z "$VIASH_PAR_OUTPUT" ]; then
|
|
VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$VIASH_PAR_OUTPUT")" )
|
|
VIASH_PAR_OUTPUT=$(ViashDockerAutodetectMount "$VIASH_PAR_OUTPUT")
|
|
VIASH_CHOWN_VARS+=( "$VIASH_PAR_OUTPUT" )
|
|
fi
|
|
if [ ! -z "$VIASH_PAR_REGIONS_FILE" ]; then
|
|
VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$VIASH_PAR_REGIONS_FILE")" )
|
|
VIASH_PAR_REGIONS_FILE=$(ViashDockerAutodetectMount "$VIASH_PAR_REGIONS_FILE")
|
|
fi
|
|
if [ ! -z "$VIASH_META_RESOURCES_DIR" ]; then
|
|
VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$VIASH_META_RESOURCES_DIR")" )
|
|
VIASH_META_RESOURCES_DIR=$(ViashDockerAutodetectMount "$VIASH_META_RESOURCES_DIR")
|
|
fi
|
|
if [ ! -z "$VIASH_META_EXECUTABLE" ]; then
|
|
VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$VIASH_META_EXECUTABLE")" )
|
|
VIASH_META_EXECUTABLE=$(ViashDockerAutodetectMount "$VIASH_META_EXECUTABLE")
|
|
fi
|
|
if [ ! -z "$VIASH_META_CONFIG" ]; then
|
|
VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$VIASH_META_CONFIG")" )
|
|
VIASH_META_CONFIG=$(ViashDockerAutodetectMount "$VIASH_META_CONFIG")
|
|
fi
|
|
if [ ! -z "$VIASH_META_TEMP_DIR" ]; then
|
|
VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$VIASH_META_TEMP_DIR")" )
|
|
VIASH_META_TEMP_DIR=$(ViashDockerAutodetectMount "$VIASH_META_TEMP_DIR")
|
|
fi
|
|
|
|
# get unique mounts
|
|
VIASH_UNIQUE_MOUNTS=($(for val in "${VIASH_DIRECTORY_MOUNTS[@]}"; do echo "$val"; done | sort -u))
|
|
fi
|
|
|
|
if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then
|
|
# change file ownership
|
|
function ViashPerformChown {
|
|
if (( ${#VIASH_CHOWN_VARS[@]} )); then
|
|
set +e
|
|
VIASH_CMD="docker run --entrypoint=bash --rm ${VIASH_UNIQUE_MOUNTS[@]} $VIASH_DOCKER_IMAGE_ID -c 'chown $(id -u):$(id -g) --silent --recursive ${VIASH_CHOWN_VARS[@]}'"
|
|
ViashDebug "+ $VIASH_CMD"
|
|
eval $VIASH_CMD
|
|
set -e
|
|
fi
|
|
}
|
|
trap ViashPerformChown EXIT
|
|
fi
|
|
|
|
if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then
|
|
# helper function for filling in extra docker args
|
|
if [ ! -z "$VIASH_META_MEMORY_B" ]; then
|
|
VIASH_DOCKER_RUN_ARGS+=("--memory=${VIASH_META_MEMORY_B}")
|
|
fi
|
|
if [ ! -z "$VIASH_META_CPUS" ]; then
|
|
VIASH_DOCKER_RUN_ARGS+=("--cpus=${VIASH_META_CPUS}")
|
|
fi
|
|
fi
|
|
|
|
if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then
|
|
VIASH_CMD="docker run --entrypoint=bash ${VIASH_DOCKER_RUN_ARGS[@]} ${VIASH_UNIQUE_MOUNTS[@]} $VIASH_DOCKER_IMAGE_ID"
|
|
fi
|
|
|
|
|
|
# set dependency paths
|
|
|
|
|
|
ViashDebug "Running command: $(echo $VIASH_CMD)"
|
|
cat << VIASHEOF | eval $VIASH_CMD
|
|
set -e
|
|
tempscript=\$(mktemp "$VIASH_META_TEMP_DIR/viash-run-bcftools_concat-XXXXXX").sh
|
|
function clean_up {
|
|
rm "\$tempscript"
|
|
}
|
|
function interrupt {
|
|
echo -e "\nCTRL-C Pressed..."
|
|
exit 1
|
|
}
|
|
trap clean_up EXIT
|
|
trap interrupt INT SIGINT
|
|
cat > "\$tempscript" << 'VIASHMAIN'
|
|
#!/bin/bash
|
|
|
|
## VIASH START
|
|
# The following code has been auto-generated by Viash.
|
|
$( if [ ! -z ${VIASH_PAR_INPUT+x} ]; then echo "${VIASH_PAR_INPUT}" | sed "s#'#'\"'\"'#g;s#.*#par_input='&'#" ; else echo "# par_input="; fi )
|
|
$( if [ ! -z ${VIASH_PAR_FILE_LIST+x} ]; then echo "${VIASH_PAR_FILE_LIST}" | sed "s#'#'\"'\"'#g;s#.*#par_file_list='&'#" ; else echo "# par_file_list="; fi )
|
|
$( if [ ! -z ${VIASH_PAR_OUTPUT+x} ]; then echo "${VIASH_PAR_OUTPUT}" | sed "s#'#'\"'\"'#g;s#.*#par_output='&'#" ; else echo "# par_output="; fi )
|
|
$( if [ ! -z ${VIASH_PAR_ALLOW_OVERLAPS+x} ]; then echo "${VIASH_PAR_ALLOW_OVERLAPS}" | sed "s#'#'\"'\"'#g;s#.*#par_allow_overlaps='&'#" ; else echo "# par_allow_overlaps="; fi )
|
|
$( if [ ! -z ${VIASH_PAR_COMPACT_PS+x} ]; then echo "${VIASH_PAR_COMPACT_PS}" | sed "s#'#'\"'\"'#g;s#.*#par_compact_ps='&'#" ; else echo "# par_compact_ps="; fi )
|
|
$( if [ ! -z ${VIASH_PAR_RM_DUPS+x} ]; then echo "${VIASH_PAR_RM_DUPS}" | sed "s#'#'\"'\"'#g;s#.*#par_rm_dups='&'#" ; else echo "# par_rm_dups="; fi )
|
|
$( if [ ! -z ${VIASH_PAR_REMOVE_DUPLICATES+x} ]; then echo "${VIASH_PAR_REMOVE_DUPLICATES}" | sed "s#'#'\"'\"'#g;s#.*#par_remove_duplicates='&'#" ; else echo "# par_remove_duplicates="; fi )
|
|
$( if [ ! -z ${VIASH_PAR_DROP_GENOTYPES+x} ]; then echo "${VIASH_PAR_DROP_GENOTYPES}" | sed "s#'#'\"'\"'#g;s#.*#par_drop_genotypes='&'#" ; else echo "# par_drop_genotypes="; fi )
|
|
$( if [ ! -z ${VIASH_PAR_LIGATE+x} ]; then echo "${VIASH_PAR_LIGATE}" | sed "s#'#'\"'\"'#g;s#.*#par_ligate='&'#" ; else echo "# par_ligate="; fi )
|
|
$( if [ ! -z ${VIASH_PAR_LIGATE_FORCE+x} ]; then echo "${VIASH_PAR_LIGATE_FORCE}" | sed "s#'#'\"'\"'#g;s#.*#par_ligate_force='&'#" ; else echo "# par_ligate_force="; fi )
|
|
$( if [ ! -z ${VIASH_PAR_LIGATE_WARN+x} ]; then echo "${VIASH_PAR_LIGATE_WARN}" | sed "s#'#'\"'\"'#g;s#.*#par_ligate_warn='&'#" ; else echo "# par_ligate_warn="; fi )
|
|
$( if [ ! -z ${VIASH_PAR_NO_VERSION+x} ]; then echo "${VIASH_PAR_NO_VERSION}" | sed "s#'#'\"'\"'#g;s#.*#par_no_version='&'#" ; else echo "# par_no_version="; fi )
|
|
$( if [ ! -z ${VIASH_PAR_NAIVE+x} ]; then echo "${VIASH_PAR_NAIVE}" | sed "s#'#'\"'\"'#g;s#.*#par_naive='&'#" ; else echo "# par_naive="; fi )
|
|
$( if [ ! -z ${VIASH_PAR_NAIVE_FORCE+x} ]; then echo "${VIASH_PAR_NAIVE_FORCE}" | sed "s#'#'\"'\"'#g;s#.*#par_naive_force='&'#" ; else echo "# par_naive_force="; fi )
|
|
$( if [ ! -z ${VIASH_PAR_OUTPUT_TYPE+x} ]; then echo "${VIASH_PAR_OUTPUT_TYPE}" | sed "s#'#'\"'\"'#g;s#.*#par_output_type='&'#" ; else echo "# par_output_type="; fi )
|
|
$( if [ ! -z ${VIASH_PAR_MIN_PQ+x} ]; then echo "${VIASH_PAR_MIN_PQ}" | sed "s#'#'\"'\"'#g;s#.*#par_min_pq='&'#" ; else echo "# par_min_pq="; fi )
|
|
$( if [ ! -z ${VIASH_PAR_REGIONS+x} ]; then echo "${VIASH_PAR_REGIONS}" | sed "s#'#'\"'\"'#g;s#.*#par_regions='&'#" ; else echo "# par_regions="; fi )
|
|
$( if [ ! -z ${VIASH_PAR_REGIONS_FILE+x} ]; then echo "${VIASH_PAR_REGIONS_FILE}" | sed "s#'#'\"'\"'#g;s#.*#par_regions_file='&'#" ; else echo "# par_regions_file="; fi )
|
|
$( if [ ! -z ${VIASH_PAR_REGIONS_OVERLAP+x} ]; then echo "${VIASH_PAR_REGIONS_OVERLAP}" | sed "s#'#'\"'\"'#g;s#.*#par_regions_overlap='&'#" ; else echo "# par_regions_overlap="; fi )
|
|
$( if [ ! -z ${VIASH_PAR_VERBOSITY+x} ]; then echo "${VIASH_PAR_VERBOSITY}" | sed "s#'#'\"'\"'#g;s#.*#par_verbosity='&'#" ; else echo "# par_verbosity="; fi )
|
|
$( if [ ! -z ${VIASH_PAR_WRITE_INDEX+x} ]; then echo "${VIASH_PAR_WRITE_INDEX}" | sed "s#'#'\"'\"'#g;s#.*#par_write_index='&'#" ; else echo "# par_write_index="; 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
|
|
|
|
set -eo pipefail
|
|
|
|
# Unset false boolean parameters
|
|
unset_if_false=(
|
|
par_allow_overlaps
|
|
par_compact_ps
|
|
par_remove_duplicates
|
|
par_drop_genotypes
|
|
par_ligate
|
|
par_ligate_force
|
|
par_ligate_warn
|
|
par_no_version
|
|
par_naive
|
|
par_naive_force
|
|
)
|
|
|
|
for par in \${unset_if_false[@]}; do
|
|
test_val="\${!par}"
|
|
[[ "\$test_val" == "false" ]] && unset \$par
|
|
done
|
|
|
|
# Check that either input files or file_list is provided
|
|
if [[ -z "\${par_input}" && -z "\${par_file_list}" ]]; then
|
|
echo "Error: One of the parameters '--input' or '--file_list' must be used."
|
|
exit 1
|
|
fi
|
|
|
|
# Handle multiple input files (semicolon-separated from Viash)
|
|
if [[ -n "\$par_input" ]]; then
|
|
IFS=';' read -ra input_files <<< "\$par_input"
|
|
fi
|
|
|
|
# Build command array
|
|
cmd_args=(
|
|
bcftools concat
|
|
\${par_allow_overlaps:+--allow-overlaps}
|
|
\${par_compact_ps:+--compact-PS}
|
|
\${par_rm_dups:+--rm-dups "\$par_rm_dups"}
|
|
\${par_remove_duplicates:+--remove-duplicates}
|
|
\${par_drop_genotypes:+--drop-genotypes}
|
|
\${par_ligate:+--ligate}
|
|
\${par_ligate_force:+--ligate-force}
|
|
\${par_ligate_warn:+--ligate-warn}
|
|
\${par_no_version:+--no-version}
|
|
\${par_naive:+--naive}
|
|
\${par_naive_force:+--naive-force}
|
|
\${par_output_type:+--output-type "\$par_output_type"}
|
|
\${par_min_pq:+--min-PQ "\$par_min_pq"}
|
|
\${par_regions:+--regions "\$par_regions"}
|
|
\${par_regions_file:+--regions-file "\$par_regions_file"}
|
|
\${par_regions_overlap:+--regions-overlap "\$par_regions_overlap"}
|
|
\${meta_cpus:+--threads "\$meta_cpus"}
|
|
\${par_verbosity:+--verbosity "\$par_verbosity"}
|
|
\${par_write_index:+--write-index="\$par_write_index"}
|
|
\${par_output:+--output "\$par_output"}
|
|
\${par_file_list:+--file-list "\$par_file_list"}
|
|
)
|
|
|
|
# Add input files to command array
|
|
if [[ -n "\$par_input" ]]; then
|
|
cmd_args+=("\${input_files[@]}")
|
|
fi
|
|
|
|
# Execute command
|
|
"\${cmd_args[@]}"
|
|
VIASHMAIN
|
|
bash "\$tempscript" &
|
|
wait "\$!"
|
|
|
|
VIASHEOF
|
|
|
|
|
|
if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then
|
|
# strip viash automount from file paths
|
|
|
|
if [ ! -z "$VIASH_PAR_INPUT" ]; then
|
|
unset VIASH_TEST_INPUT
|
|
IFS=';'
|
|
for var in $VIASH_PAR_INPUT; do
|
|
unset IFS
|
|
if [ -z "$VIASH_TEST_INPUT" ]; then
|
|
VIASH_TEST_INPUT="$(ViashDockerStripAutomount "$var")"
|
|
else
|
|
VIASH_TEST_INPUT="$VIASH_TEST_INPUT;""$(ViashDockerStripAutomount "$var")"
|
|
fi
|
|
done
|
|
VIASH_PAR_INPUT="$VIASH_TEST_INPUT"
|
|
fi
|
|
if [ ! -z "$VIASH_PAR_FILE_LIST" ]; then
|
|
VIASH_PAR_FILE_LIST=$(ViashDockerStripAutomount "$VIASH_PAR_FILE_LIST")
|
|
fi
|
|
if [ ! -z "$VIASH_PAR_OUTPUT" ]; then
|
|
VIASH_PAR_OUTPUT=$(ViashDockerStripAutomount "$VIASH_PAR_OUTPUT")
|
|
fi
|
|
if [ ! -z "$VIASH_PAR_REGIONS_FILE" ]; then
|
|
VIASH_PAR_REGIONS_FILE=$(ViashDockerStripAutomount "$VIASH_PAR_REGIONS_FILE")
|
|
fi
|
|
if [ ! -z "$VIASH_META_RESOURCES_DIR" ]; then
|
|
VIASH_META_RESOURCES_DIR=$(ViashDockerStripAutomount "$VIASH_META_RESOURCES_DIR")
|
|
fi
|
|
if [ ! -z "$VIASH_META_EXECUTABLE" ]; then
|
|
VIASH_META_EXECUTABLE=$(ViashDockerStripAutomount "$VIASH_META_EXECUTABLE")
|
|
fi
|
|
if [ ! -z "$VIASH_META_CONFIG" ]; then
|
|
VIASH_META_CONFIG=$(ViashDockerStripAutomount "$VIASH_META_CONFIG")
|
|
fi
|
|
if [ ! -z "$VIASH_META_TEMP_DIR" ]; then
|
|
VIASH_META_TEMP_DIR=$(ViashDockerStripAutomount "$VIASH_META_TEMP_DIR")
|
|
fi
|
|
fi
|
|
|
|
|
|
# check whether required files exist
|
|
if [ ! -z "$VIASH_PAR_OUTPUT" ] && [ ! -e "$VIASH_PAR_OUTPUT" ]; then
|
|
ViashError "Output file '$VIASH_PAR_OUTPUT' does not exist."
|
|
exit 1
|
|
fi
|
|
|
|
|
|
exit 0
|