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af7bcfffa4e7390025ee87b4f11f78369401908d
biobox/target/executable/bbmap/bbmap_bbsplit/bbmap_bbsplit
CI af7bcfffa4 Build branch main with version main (c733de2) 
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
2025-04-30 07:01:27 +00:00

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#!/usr/bin/env bash
# bbmap_bbsplit 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.
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 $VIASH_META_RESOURCES_DIR`
# define meta fields
VIASH_META_NAME="bbmap_bbsplit"
VIASH_META_FUNCTIONALITY_NAME="bbmap_bbsplit"
VIASH_META_EXECUTABLE="$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 ubuntu:22.04
ENTRYPOINT []
RUN apt-get update && \
apt-get install -y build-essential openjdk-17-jdk wget tar && \
wget --no-check-certificate https://sourceforge.net/projects/bbmap/files/BBMap_39.01.tar.gz && \
tar xzf BBMap_39.01.tar.gz && \
cp -r bbmap/* /usr/local/bin
RUN bbsplit.sh --version 2>&1 | awk '/BBMap version/{print "BBMAP:", $NF}' > /var/software_versions.txt
LABEL org.opencontainers.image.description="Companion container for running component bbmap bbmap_bbsplit"
LABEL org.opencontainers.image.created="2025-04-29T10:54:43Z"
LABEL org.opencontainers.image.source="https://github.com/BioInfoTools/BBMap/blob/master/sh/bbsplit.sh"
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 "bbmap_bbsplit main"
echo ""
echo "Split sequencing reads by mapping them to multiple references simultaneously."
echo ""
echo "Input:"
echo " --id"
echo " type: string"
echo " Sample ID"
echo ""
echo " --paired"
echo " type: boolean_true"
echo " Paired fastq files or not?"
echo ""
echo " --input"
echo " type: file, multiple values allowed, file must exist"
echo " example: reads.fastq"
echo " Input fastq files, either one or two (paired), separated by \";\"."
echo ""
echo " --ref"
echo " type: file, multiple values allowed, file must exist"
echo " Reference FASTA files, separated by \";\". The primary reference should be"
echo " specified first."
echo ""
echo " --only_build_index"
echo " type: boolean_true"
echo " If set, only builds the index. Otherwise, mapping is performed."
echo ""
echo " --build"
echo " type: file, file must exist"
echo " Index to be used for mapping."
echo ""
echo " --qin"
echo " type: string"
echo " Set to 33 or 64 to specify input quality value ASCII offset."
echo " Automatically detected if"
echo " not specified."
echo ""
echo " --interleaved"
echo " type: boolean_true"
echo " True forces paired/interleaved input; false forces single-ended mapping."
echo " If not specified, interleaved status will be autodetected from read"
echo " names."
echo ""
echo " --maxindel"
echo " type: integer"
echo " example: 20"
echo " Don't look for indels longer than this. Lower is faster. Set to >=100k"
echo " for RNA-seq."
echo ""
echo " --minratio"
echo " type: double"
echo " example: 0.56"
echo " Fraction of max alignment score required to keep a site. Higher is"
echo " faster."
echo ""
echo " --minhits"
echo " type: integer"
echo " example: 1"
echo " Minimum number of seed hits required for candidate sites. Higher is"
echo " faster."
echo ""
echo " --ambiguous"
echo " type: string"
echo " example: best"
echo " choices: [ best, toss, random, all ]"
echo " Set behavior on ambiguously-mapped reads (with multiple top-scoring"
echo " mapping locations)."
echo " * best Use the first best site (Default)"
echo " * toss Consider unmapped"
echo " * random Select one top-scoring site randomly"
echo " * all Retain all top-scoring sites. Does not work yet with SAM"
echo " output"
echo ""
echo " --ambiguous2"
echo " type: string"
echo " example: best"
echo " choices: [ best, toss, all, split ]"
echo " Set behavior only for reads that map ambiguously to multiple different"
echo " references."
echo " Normal 'ambiguous=' controls behavior on all ambiguous reads;"
echo " Ambiguous2 excludes reads that map ambiguously within a single"
echo " reference."
echo " * best Use the first best site (Default)"
echo " * toss Consider unmapped"
echo " * all Write a copy to the output for each reference to which it"
echo " maps"
echo " * split Write a copy to the AMBIGUOUS_ output for each reference to"
echo " which it maps"
echo ""
echo " --qtrim"
echo " type: string"
echo " choices: [ l, r, lr ]"
echo " Quality-trim ends to Q5 before mapping. Options are 'l' (left), 'r'"
echo " (right), and 'lr' (both)."
echo ""
echo " --untrim"
echo " type: boolean_true"
echo " Undo trimming after mapping. Untrimmed bases will be soft-clipped in"
echo " cigar strings."
echo ""
echo "Output:"
echo " --index"
echo " type: file, output, file must exist"
echo " example: BBSplit_index"
echo " Location to write the index."
echo ""
echo " --fastq_1"
echo " type: file, output, file must exist"
echo " example: read_out1.fastq"
echo " Output file for read 1."
echo ""
echo " --fastq_2"
echo " type: file, output, file must exist"
echo " example: read_out2.fastq"
echo " Output file for read 2."
echo ""
echo " --bs, --sam2bam"
echo " type: file, output, file must exist"
echo " example: script.sh"
echo " Write a shell script to 'file' that will turn the sam output into a"
echo " sorted, indexed bam file."
echo ""
echo " --scafstats"
echo " type: file, output, file must exist"
echo " example: scaffold_stats.txt"
echo " Write statistics on how many reads mapped to which scaffold to this"
echo " file."
echo ""
echo " --refstats"
echo " type: file, output, file must exist"
echo " example: reference_stats.txt"
echo " Write statistics on how many reads were assigned to which reference to"
echo " this file."
echo " Unmapped reads whose mate mapped to a reference are considered assigned"
echo " and will be counted."
echo ""
echo " --nzo"
echo " type: boolean_true"
echo " Only print lines with nonzero coverage."
echo ""
echo " --bbmap_args"
echo " type: string"
echo " Additional arguments from BBMap to pass to BBSplit."
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 "$1")"
shift 1
;;
--version)
echo "bbmap_bbsplit main"
exit
;;
--id)
[ -n "$VIASH_PAR_ID" ] && ViashError Bad arguments for option \'--id\': \'$VIASH_PAR_ID\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
VIASH_PAR_ID="$2"
[ $# -lt 2 ] && ViashError Not enough arguments passed to --id. Use "--help" to get more information on the parameters. && exit 1
shift 2
;;
--id=*)
[ -n "$VIASH_PAR_ID" ] && ViashError Bad arguments for option \'--id=*\': \'$VIASH_PAR_ID\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
VIASH_PAR_ID=$(ViashRemoveFlags "$1")
shift 1
;;
--paired)
[ -n "$VIASH_PAR_PAIRED" ] && ViashError Bad arguments for option \'--paired\': \'$VIASH_PAR_PAIRED\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
VIASH_PAR_PAIRED=true
shift 1
;;
--input)
if [ -z "$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 "$1")
fi
shift 1
;;
--ref)
if [ -z "$VIASH_PAR_REF" ]; then
VIASH_PAR_REF="$2"
else
VIASH_PAR_REF="$VIASH_PAR_REF;""$2"
fi
[ $# -lt 2 ] && ViashError Not enough arguments passed to --ref. Use "--help" to get more information on the parameters. && exit 1
shift 2
;;
--ref=*)
if [ -z "$VIASH_PAR_REF" ]; then
VIASH_PAR_REF=$(ViashRemoveFlags "$1")
else
VIASH_PAR_REF="$VIASH_PAR_REF;"$(ViashRemoveFlags "$1")
fi
shift 1
;;
--only_build_index)
[ -n "$VIASH_PAR_ONLY_BUILD_INDEX" ] && ViashError Bad arguments for option \'--only_build_index\': \'$VIASH_PAR_ONLY_BUILD_INDEX\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
VIASH_PAR_ONLY_BUILD_INDEX=true
shift 1
;;
--build)
[ -n "$VIASH_PAR_BUILD" ] && ViashError Bad arguments for option \'--build\': \'$VIASH_PAR_BUILD\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
VIASH_PAR_BUILD="$2"
[ $# -lt 2 ] && ViashError Not enough arguments passed to --build. Use "--help" to get more information on the parameters. && exit 1
shift 2
;;
--build=*)
[ -n "$VIASH_PAR_BUILD" ] && ViashError Bad arguments for option \'--build=*\': \'$VIASH_PAR_BUILD\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
VIASH_PAR_BUILD=$(ViashRemoveFlags "$1")
shift 1
;;
--qin)
[ -n "$VIASH_PAR_QIN" ] && ViashError Bad arguments for option \'--qin\': \'$VIASH_PAR_QIN\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
VIASH_PAR_QIN="$2"
[ $# -lt 2 ] && ViashError Not enough arguments passed to --qin. Use "--help" to get more information on the parameters. && exit 1
shift 2
;;
--qin=*)
[ -n "$VIASH_PAR_QIN" ] && ViashError Bad arguments for option \'--qin=*\': \'$VIASH_PAR_QIN\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
VIASH_PAR_QIN=$(ViashRemoveFlags "$1")
shift 1
;;
--interleaved)
[ -n "$VIASH_PAR_INTERLEAVED" ] && ViashError Bad arguments for option \'--interleaved\': \'$VIASH_PAR_INTERLEAVED\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
VIASH_PAR_INTERLEAVED=true
shift 1
;;
--maxindel)
[ -n "$VIASH_PAR_MAXINDEL" ] && ViashError Bad arguments for option \'--maxindel\': \'$VIASH_PAR_MAXINDEL\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
VIASH_PAR_MAXINDEL="$2"
[ $# -lt 2 ] && ViashError Not enough arguments passed to --maxindel. Use "--help" to get more information on the parameters. && exit 1
shift 2
;;
--maxindel=*)
[ -n "$VIASH_PAR_MAXINDEL" ] && ViashError Bad arguments for option \'--maxindel=*\': \'$VIASH_PAR_MAXINDEL\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
VIASH_PAR_MAXINDEL=$(ViashRemoveFlags "$1")
shift 1
;;
--minratio)
[ -n "$VIASH_PAR_MINRATIO" ] && ViashError Bad arguments for option \'--minratio\': \'$VIASH_PAR_MINRATIO\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
VIASH_PAR_MINRATIO="$2"
[ $# -lt 2 ] && ViashError Not enough arguments passed to --minratio. Use "--help" to get more information on the parameters. && exit 1
shift 2
;;
--minratio=*)
[ -n "$VIASH_PAR_MINRATIO" ] && ViashError Bad arguments for option \'--minratio=*\': \'$VIASH_PAR_MINRATIO\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
VIASH_PAR_MINRATIO=$(ViashRemoveFlags "$1")
shift 1
;;
--minhits)
[ -n "$VIASH_PAR_MINHITS" ] && ViashError Bad arguments for option \'--minhits\': \'$VIASH_PAR_MINHITS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
VIASH_PAR_MINHITS="$2"
[ $# -lt 2 ] && ViashError Not enough arguments passed to --minhits. Use "--help" to get more information on the parameters. && exit 1
shift 2
;;
--minhits=*)
[ -n "$VIASH_PAR_MINHITS" ] && ViashError Bad arguments for option \'--minhits=*\': \'$VIASH_PAR_MINHITS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
VIASH_PAR_MINHITS=$(ViashRemoveFlags "$1")
shift 1
;;
--ambiguous)
[ -n "$VIASH_PAR_AMBIGUOUS" ] && ViashError Bad arguments for option \'--ambiguous\': \'$VIASH_PAR_AMBIGUOUS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
VIASH_PAR_AMBIGUOUS="$2"
[ $# -lt 2 ] && ViashError Not enough arguments passed to --ambiguous. Use "--help" to get more information on the parameters. && exit 1
shift 2
;;
--ambiguous=*)
[ -n "$VIASH_PAR_AMBIGUOUS" ] && ViashError Bad arguments for option \'--ambiguous=*\': \'$VIASH_PAR_AMBIGUOUS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
VIASH_PAR_AMBIGUOUS=$(ViashRemoveFlags "$1")
shift 1
;;
--ambiguous2)
[ -n "$VIASH_PAR_AMBIGUOUS2" ] && ViashError Bad arguments for option \'--ambiguous2\': \'$VIASH_PAR_AMBIGUOUS2\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
VIASH_PAR_AMBIGUOUS2="$2"
[ $# -lt 2 ] && ViashError Not enough arguments passed to --ambiguous2. Use "--help" to get more information on the parameters. && exit 1
shift 2
;;
--ambiguous2=*)
[ -n "$VIASH_PAR_AMBIGUOUS2" ] && ViashError Bad arguments for option \'--ambiguous2=*\': \'$VIASH_PAR_AMBIGUOUS2\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
VIASH_PAR_AMBIGUOUS2=$(ViashRemoveFlags "$1")
shift 1
;;
--qtrim)
[ -n "$VIASH_PAR_QTRIM" ] && ViashError Bad arguments for option \'--qtrim\': \'$VIASH_PAR_QTRIM\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
VIASH_PAR_QTRIM="$2"
[ $# -lt 2 ] && ViashError Not enough arguments passed to --qtrim. Use "--help" to get more information on the parameters. && exit 1
shift 2
;;
--qtrim=*)
[ -n "$VIASH_PAR_QTRIM" ] && ViashError Bad arguments for option \'--qtrim=*\': \'$VIASH_PAR_QTRIM\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
VIASH_PAR_QTRIM=$(ViashRemoveFlags "$1")
shift 1
;;
--untrim)
[ -n "$VIASH_PAR_UNTRIM" ] && ViashError Bad arguments for option \'--untrim\': \'$VIASH_PAR_UNTRIM\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
VIASH_PAR_UNTRIM=true
shift 1
;;
--index)
[ -n "$VIASH_PAR_INDEX" ] && ViashError Bad arguments for option \'--index\': \'$VIASH_PAR_INDEX\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
VIASH_PAR_INDEX="$2"
[ $# -lt 2 ] && ViashError Not enough arguments passed to --index. Use "--help" to get more information on the parameters. && exit 1
shift 2
;;
--index=*)
[ -n "$VIASH_PAR_INDEX" ] && ViashError Bad arguments for option \'--index=*\': \'$VIASH_PAR_INDEX\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
VIASH_PAR_INDEX=$(ViashRemoveFlags "$1")
shift 1
;;
--fastq_1)
[ -n "$VIASH_PAR_FASTQ_1" ] && ViashError Bad arguments for option \'--fastq_1\': \'$VIASH_PAR_FASTQ_1\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
VIASH_PAR_FASTQ_1="$2"
[ $# -lt 2 ] && ViashError Not enough arguments passed to --fastq_1. Use "--help" to get more information on the parameters. && exit 1
shift 2
;;
--fastq_1=*)
[ -n "$VIASH_PAR_FASTQ_1" ] && ViashError Bad arguments for option \'--fastq_1=*\': \'$VIASH_PAR_FASTQ_1\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
VIASH_PAR_FASTQ_1=$(ViashRemoveFlags "$1")
shift 1
;;
--fastq_2)
[ -n "$VIASH_PAR_FASTQ_2" ] && ViashError Bad arguments for option \'--fastq_2\': \'$VIASH_PAR_FASTQ_2\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
VIASH_PAR_FASTQ_2="$2"
[ $# -lt 2 ] && ViashError Not enough arguments passed to --fastq_2. Use "--help" to get more information on the parameters. && exit 1
shift 2
;;
--fastq_2=*)
[ -n "$VIASH_PAR_FASTQ_2" ] && ViashError Bad arguments for option \'--fastq_2=*\': \'$VIASH_PAR_FASTQ_2\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
VIASH_PAR_FASTQ_2=$(ViashRemoveFlags "$1")
shift 1
;;
--sam2bam)
[ -n "$VIASH_PAR_SAM2BAM" ] && ViashError Bad arguments for option \'--sam2bam\': \'$VIASH_PAR_SAM2BAM\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
VIASH_PAR_SAM2BAM="$2"
[ $# -lt 2 ] && ViashError Not enough arguments passed to --sam2bam. Use "--help" to get more information on the parameters. && exit 1
shift 2
;;
--sam2bam=*)
[ -n "$VIASH_PAR_SAM2BAM" ] && ViashError Bad arguments for option \'--sam2bam=*\': \'$VIASH_PAR_SAM2BAM\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
VIASH_PAR_SAM2BAM=$(ViashRemoveFlags "$1")
shift 1
;;
--bs)
[ -n "$VIASH_PAR_SAM2BAM" ] && ViashError Bad arguments for option \'--bs\': \'$VIASH_PAR_SAM2BAM\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
VIASH_PAR_SAM2BAM="$2"
[ $# -lt 2 ] && ViashError Not enough arguments passed to --bs. Use "--help" to get more information on the parameters. && exit 1
shift 2
;;
--scafstats)
[ -n "$VIASH_PAR_SCAFSTATS" ] && ViashError Bad arguments for option \'--scafstats\': \'$VIASH_PAR_SCAFSTATS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
VIASH_PAR_SCAFSTATS="$2"
[ $# -lt 2 ] && ViashError Not enough arguments passed to --scafstats. Use "--help" to get more information on the parameters. && exit 1
shift 2
;;
--scafstats=*)
[ -n "$VIASH_PAR_SCAFSTATS" ] && ViashError Bad arguments for option \'--scafstats=*\': \'$VIASH_PAR_SCAFSTATS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
VIASH_PAR_SCAFSTATS=$(ViashRemoveFlags "$1")
shift 1
;;
--refstats)
[ -n "$VIASH_PAR_REFSTATS" ] && ViashError Bad arguments for option \'--refstats\': \'$VIASH_PAR_REFSTATS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
VIASH_PAR_REFSTATS="$2"
[ $# -lt 2 ] && ViashError Not enough arguments passed to --refstats. Use "--help" to get more information on the parameters. && exit 1
shift 2
;;
--refstats=*)
[ -n "$VIASH_PAR_REFSTATS" ] && ViashError Bad arguments for option \'--refstats=*\': \'$VIASH_PAR_REFSTATS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
VIASH_PAR_REFSTATS=$(ViashRemoveFlags "$1")
shift 1
;;
--nzo)
[ -n "$VIASH_PAR_NZO" ] && ViashError Bad arguments for option \'--nzo\': \'$VIASH_PAR_NZO\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
VIASH_PAR_NZO=true
shift 1
;;
--bbmap_args)
[ -n "$VIASH_PAR_BBMAP_ARGS" ] && ViashError Bad arguments for option \'--bbmap_args\': \'$VIASH_PAR_BBMAP_ARGS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
VIASH_PAR_BBMAP_ARGS="$2"
[ $# -lt 2 ] && ViashError Not enough arguments passed to --bbmap_args. Use "--help" to get more information on the parameters. && exit 1
shift 2
;;
--bbmap_args=*)
[ -n "$VIASH_PAR_BBMAP_ARGS" ] && ViashError Bad arguments for option \'--bbmap_args=*\': \'$VIASH_PAR_BBMAP_ARGS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
VIASH_PAR_BBMAP_ARGS=$(ViashRemoveFlags "$1")
shift 1
;;
---engine)
VIASH_ENGINE_ID="$2"
shift 2
;;
---engine=*)
VIASH_ENGINE_ID="$(ViashRemoveFlags "$1")"
shift 1
;;
---setup)
VIASH_MODE='setup'
VIASH_SETUP_STRATEGY="$2"
shift 2
;;
---setup=*)
VIASH_MODE='setup'
VIASH_SETUP_STRATEGY="$(ViashRemoveFlags "$1")"
shift 1
;;
---dockerfile)
VIASH_MODE='dockerfile'
shift 1
;;
---docker_run_args)
VIASH_DOCKER_RUN_ARGS+=("$2")
shift 2
;;
---docker_run_args=*)
VIASH_DOCKER_RUN_ARGS+=("$(ViashRemoveFlags "$1")")
shift 1
;;
---docker_image_id)
VIASH_MODE='docker_image_id'
shift 1
;;
---debug)
VIASH_MODE='debug'
shift 1
;;
---cpus)
[ -n "$VIASH_META_CPUS" ] && ViashError Bad arguments for option \'---cpus\': \'$VIASH_META_CPUS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
VIASH_META_CPUS="$2"
[ $# -lt 2 ] && ViashError Not enough arguments passed to ---cpus. Use "--help" to get more information on the parameters. && exit 1
shift 2
;;
---cpus=*)
[ -n "$VIASH_META_CPUS" ] && ViashError Bad arguments for option \'---cpus=*\': \'$VIASH_META_CPUS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
VIASH_META_CPUS=$(ViashRemoveFlags "$1")
shift 1
;;
---memory)
[ -n "$VIASH_META_MEMORY" ] && ViashError Bad arguments for option \'---memory\': \'$VIASH_META_MEMORY\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
VIASH_META_MEMORY="$2"
[ $# -lt 2 ] && ViashError Not enough arguments passed to ---memory. Use "--help" to get more information on the parameters. && exit 1
shift 2
;;
---memory=*)
[ -n "$VIASH_META_MEMORY" ] && ViashError Bad arguments for option \'---memory=*\': \'$VIASH_META_MEMORY\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
VIASH_META_MEMORY=$(ViashRemoveFlags "$1")
shift 1
;;
*) # positional arg or unknown option
# since the positional args will be eval'd, can we always quote, instead of using ViashQuote
VIASH_POSITIONAL_ARGS="$VIASH_POSITIONAL_ARGS '$1'"
[[ $1 == -* ]] && ViashWarning $1 looks like a parameter but is not a defined parameter and will instead be treated as a positional argument. Use "--help" to get more information on the parameters.
shift # past argument
;;
esac
done
# parse positional parameters
eval set -- $VIASH_POSITIONAL_ARGS
if [ "$VIASH_ENGINE_ID" == "native" ] ; then
VIASH_ENGINE_TYPE='native'
elif [ "$VIASH_ENGINE_ID" == "docker" ] ; then
VIASH_ENGINE_TYPE='docker'
else
ViashError "Engine '$VIASH_ENGINE_ID' is not recognized. Options are: docker, native."
exit 1
fi
if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then
# check if docker is installed properly
ViashDockerInstallationCheck
# determine docker image id
if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then
VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/biobox/bbmap/bbmap_bbsplit: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_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_PAIRED+x} ]; then
VIASH_PAR_PAIRED="false"
fi
if [ -z ${VIASH_PAR_ONLY_BUILD_INDEX+x} ]; then
VIASH_PAR_ONLY_BUILD_INDEX="false"
fi
if [ -z ${VIASH_PAR_INTERLEAVED+x} ]; then
VIASH_PAR_INTERLEAVED="false"
fi
if [ -z ${VIASH_PAR_UNTRIM+x} ]; then
VIASH_PAR_UNTRIM="false"
fi
if [ -z ${VIASH_PAR_NZO+x} ]; then
VIASH_PAR_NZO="false"
fi
# check whether required files exist
if [ ! -z "$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_REF" ]; then
IFS=';'
set -f
for file in $VIASH_PAR_REF; do
unset IFS
if [ ! -e "$file" ]; then
ViashError "Input file '$file' does not exist."
exit 1
fi
done
set +f
fi
if [ ! -z "$VIASH_PAR_BUILD" ] && [ ! -e "$VIASH_PAR_BUILD" ]; then
ViashError "Input file '$VIASH_PAR_BUILD' does not exist."
exit 1
fi
# check whether parameters values are of the right type
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 "$VIASH_PAR_ONLY_BUILD_INDEX" ]]; then
if ! [[ "$VIASH_PAR_ONLY_BUILD_INDEX" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then
ViashError '--only_build_index' has to be a boolean_true. Use "--help" to get more information on the parameters.
exit 1
fi
fi
if [[ -n "$VIASH_PAR_INTERLEAVED" ]]; then
if ! [[ "$VIASH_PAR_INTERLEAVED" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then
ViashError '--interleaved' has to be a boolean_true. Use "--help" to get more information on the parameters.
exit 1
fi
fi
if [[ -n "$VIASH_PAR_MAXINDEL" ]]; then
if ! [[ "$VIASH_PAR_MAXINDEL" =~ ^[-+]?[0-9]+$ ]]; then
ViashError '--maxindel' has to be an integer. Use "--help" to get more information on the parameters.
exit 1
fi
fi
if [[ -n "$VIASH_PAR_MINRATIO" ]]; then
if ! [[ "$VIASH_PAR_MINRATIO" =~ ^[-+]?(\.[0-9]+|[0-9]+(\.[0-9]*)?)([eE][-+]?[0-9]+)?$ ]]; then
ViashError '--minratio' has to be a double. Use "--help" to get more information on the parameters.
exit 1
fi
fi
if [[ -n "$VIASH_PAR_MINHITS" ]]; then
if ! [[ "$VIASH_PAR_MINHITS" =~ ^[-+]?[0-9]+$ ]]; then
ViashError '--minhits' has to be an integer. Use "--help" to get more information on the parameters.
exit 1
fi
fi
if [[ -n "$VIASH_PAR_UNTRIM" ]]; then
if ! [[ "$VIASH_PAR_UNTRIM" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then
ViashError '--untrim' has to be a boolean_true. Use "--help" to get more information on the parameters.
exit 1
fi
fi
if [[ -n "$VIASH_PAR_NZO" ]]; then
if ! [[ "$VIASH_PAR_NZO" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then
ViashError '--nzo' 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 "$VIASH_PAR_AMBIGUOUS" ]; then
VIASH_PAR_AMBIGUOUS_CHOICES=("best;toss;random;all")
IFS=';'
set -f
if ! [[ ";${VIASH_PAR_AMBIGUOUS_CHOICES[*]};" =~ ";$VIASH_PAR_AMBIGUOUS;" ]]; then
ViashError '--ambiguous' specified value of \'$VIASH_PAR_AMBIGUOUS\' 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 "$VIASH_PAR_AMBIGUOUS2" ]; then
VIASH_PAR_AMBIGUOUS2_CHOICES=("best;toss;all;split")
IFS=';'
set -f
if ! [[ ";${VIASH_PAR_AMBIGUOUS2_CHOICES[*]};" =~ ";$VIASH_PAR_AMBIGUOUS2;" ]]; then
ViashError '--ambiguous2' specified value of \'$VIASH_PAR_AMBIGUOUS2\' 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 "$VIASH_PAR_QTRIM" ]; then
VIASH_PAR_QTRIM_CHOICES=("l;r;lr")
IFS=';'
set -f
if ! [[ ";${VIASH_PAR_QTRIM_CHOICES[*]};" =~ ";$VIASH_PAR_QTRIM;" ]]; then
ViashError '--qtrim' specified value of \'$VIASH_PAR_QTRIM\' 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 "$VIASH_PAR_INDEX" ] && [ ! -d "$(dirname "$VIASH_PAR_INDEX")" ]; then
mkdir -p "$(dirname "$VIASH_PAR_INDEX")"
fi
if [ ! -z "$VIASH_PAR_FASTQ_1" ] && [ ! -d "$(dirname "$VIASH_PAR_FASTQ_1")" ]; then
mkdir -p "$(dirname "$VIASH_PAR_FASTQ_1")"
fi
if [ ! -z "$VIASH_PAR_FASTQ_2" ] && [ ! -d "$(dirname "$VIASH_PAR_FASTQ_2")" ]; then
mkdir -p "$(dirname "$VIASH_PAR_FASTQ_2")"
fi
if [ ! -z "$VIASH_PAR_SAM2BAM" ] && [ ! -d "$(dirname "$VIASH_PAR_SAM2BAM")" ]; then
mkdir -p "$(dirname "$VIASH_PAR_SAM2BAM")"
fi
if [ ! -z "$VIASH_PAR_SCAFSTATS" ] && [ ! -d "$(dirname "$VIASH_PAR_SCAFSTATS")" ]; then
mkdir -p "$(dirname "$VIASH_PAR_SCAFSTATS")"
fi
if [ ! -z "$VIASH_PAR_REFSTATS" ] && [ ! -d "$(dirname "$VIASH_PAR_REFSTATS")" ]; then
mkdir -p "$(dirname "$VIASH_PAR_REFSTATS")"
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_REF" ]; then
VIASH_TEST_REF=()
IFS=';'
for var in $VIASH_PAR_REF; do
unset IFS
VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$var")" )
var=$(ViashDockerAutodetectMount "$var")
VIASH_TEST_REF+=( "$var" )
done
VIASH_PAR_REF=$(IFS=';' ; echo "${VIASH_TEST_REF[*]}")
fi
if [ ! -z "$VIASH_PAR_BUILD" ]; then
VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$VIASH_PAR_BUILD")" )
VIASH_PAR_BUILD=$(ViashDockerAutodetectMount "$VIASH_PAR_BUILD")
fi
if [ ! -z "$VIASH_PAR_INDEX" ]; then
VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$VIASH_PAR_INDEX")" )
VIASH_PAR_INDEX=$(ViashDockerAutodetectMount "$VIASH_PAR_INDEX")
VIASH_CHOWN_VARS+=( "$VIASH_PAR_INDEX" )
fi
if [ ! -z "$VIASH_PAR_FASTQ_1" ]; then
VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$VIASH_PAR_FASTQ_1")" )
VIASH_PAR_FASTQ_1=$(ViashDockerAutodetectMount "$VIASH_PAR_FASTQ_1")
VIASH_CHOWN_VARS+=( "$VIASH_PAR_FASTQ_1" )
fi
if [ ! -z "$VIASH_PAR_FASTQ_2" ]; then
VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$VIASH_PAR_FASTQ_2")" )
VIASH_PAR_FASTQ_2=$(ViashDockerAutodetectMount "$VIASH_PAR_FASTQ_2")
VIASH_CHOWN_VARS+=( "$VIASH_PAR_FASTQ_2" )
fi
if [ ! -z "$VIASH_PAR_SAM2BAM" ]; then
VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$VIASH_PAR_SAM2BAM")" )
VIASH_PAR_SAM2BAM=$(ViashDockerAutodetectMount "$VIASH_PAR_SAM2BAM")
VIASH_CHOWN_VARS+=( "$VIASH_PAR_SAM2BAM" )
fi
if [ ! -z "$VIASH_PAR_SCAFSTATS" ]; then
VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$VIASH_PAR_SCAFSTATS")" )
VIASH_PAR_SCAFSTATS=$(ViashDockerAutodetectMount "$VIASH_PAR_SCAFSTATS")
VIASH_CHOWN_VARS+=( "$VIASH_PAR_SCAFSTATS" )
fi
if [ ! -z "$VIASH_PAR_REFSTATS" ]; then
VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$VIASH_PAR_REFSTATS")" )
VIASH_PAR_REFSTATS=$(ViashDockerAutodetectMount "$VIASH_PAR_REFSTATS")
VIASH_CHOWN_VARS+=( "$VIASH_PAR_REFSTATS" )
fi
if [ ! -z "$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-bbmap_bbsplit-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 ${VIASH_PAR_ID+x} ]; then echo "${VIASH_PAR_ID}" | sed "s#'#'\"'\"'#g;s#.*#par_id='&'#" ; else echo "# par_id="; 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 ${VIASH_PAR_INPUT+x} ]; then echo "${VIASH_PAR_INPUT}" | sed "s#'#'\"'\"'#g;s#.*#par_input='&'#" ; else echo "# par_input="; fi )
$( if [ ! -z ${VIASH_PAR_REF+x} ]; then echo "${VIASH_PAR_REF}" | sed "s#'#'\"'\"'#g;s#.*#par_ref='&'#" ; else echo "# par_ref="; fi )
$( if [ ! -z ${VIASH_PAR_ONLY_BUILD_INDEX+x} ]; then echo "${VIASH_PAR_ONLY_BUILD_INDEX}" | sed "s#'#'\"'\"'#g;s#.*#par_only_build_index='&'#" ; else echo "# par_only_build_index="; fi )
$( if [ ! -z ${VIASH_PAR_BUILD+x} ]; then echo "${VIASH_PAR_BUILD}" | sed "s#'#'\"'\"'#g;s#.*#par_build='&'#" ; else echo "# par_build="; fi )
$( if [ ! -z ${VIASH_PAR_QIN+x} ]; then echo "${VIASH_PAR_QIN}" | sed "s#'#'\"'\"'#g;s#.*#par_qin='&'#" ; else echo "# par_qin="; fi )
$( if [ ! -z ${VIASH_PAR_INTERLEAVED+x} ]; then echo "${VIASH_PAR_INTERLEAVED}" | sed "s#'#'\"'\"'#g;s#.*#par_interleaved='&'#" ; else echo "# par_interleaved="; fi )
$( if [ ! -z ${VIASH_PAR_MAXINDEL+x} ]; then echo "${VIASH_PAR_MAXINDEL}" | sed "s#'#'\"'\"'#g;s#.*#par_maxindel='&'#" ; else echo "# par_maxindel="; fi )
$( if [ ! -z ${VIASH_PAR_MINRATIO+x} ]; then echo "${VIASH_PAR_MINRATIO}" | sed "s#'#'\"'\"'#g;s#.*#par_minratio='&'#" ; else echo "# par_minratio="; fi )
$( if [ ! -z ${VIASH_PAR_MINHITS+x} ]; then echo "${VIASH_PAR_MINHITS}" | sed "s#'#'\"'\"'#g;s#.*#par_minhits='&'#" ; else echo "# par_minhits="; fi )
$( if [ ! -z ${VIASH_PAR_AMBIGUOUS+x} ]; then echo "${VIASH_PAR_AMBIGUOUS}" | sed "s#'#'\"'\"'#g;s#.*#par_ambiguous='&'#" ; else echo "# par_ambiguous="; fi )
$( if [ ! -z ${VIASH_PAR_AMBIGUOUS2+x} ]; then echo "${VIASH_PAR_AMBIGUOUS2}" | sed "s#'#'\"'\"'#g;s#.*#par_ambiguous2='&'#" ; else echo "# par_ambiguous2="; fi )
$( if [ ! -z ${VIASH_PAR_QTRIM+x} ]; then echo "${VIASH_PAR_QTRIM}" | sed "s#'#'\"'\"'#g;s#.*#par_qtrim='&'#" ; else echo "# par_qtrim="; fi )
$( if [ ! -z ${VIASH_PAR_UNTRIM+x} ]; then echo "${VIASH_PAR_UNTRIM}" | sed "s#'#'\"'\"'#g;s#.*#par_untrim='&'#" ; else echo "# par_untrim="; fi )
$( if [ ! -z ${VIASH_PAR_INDEX+x} ]; then echo "${VIASH_PAR_INDEX}" | sed "s#'#'\"'\"'#g;s#.*#par_index='&'#" ; else echo "# par_index="; fi )
$( if [ ! -z ${VIASH_PAR_FASTQ_1+x} ]; then echo "${VIASH_PAR_FASTQ_1}" | sed "s#'#'\"'\"'#g;s#.*#par_fastq_1='&'#" ; else echo "# par_fastq_1="; fi )
$( if [ ! -z ${VIASH_PAR_FASTQ_2+x} ]; then echo "${VIASH_PAR_FASTQ_2}" | sed "s#'#'\"'\"'#g;s#.*#par_fastq_2='&'#" ; else echo "# par_fastq_2="; fi )
$( if [ ! -z ${VIASH_PAR_SAM2BAM+x} ]; then echo "${VIASH_PAR_SAM2BAM}" | sed "s#'#'\"'\"'#g;s#.*#par_sam2bam='&'#" ; else echo "# par_sam2bam="; fi )
$( if [ ! -z ${VIASH_PAR_SCAFSTATS+x} ]; then echo "${VIASH_PAR_SCAFSTATS}" | sed "s#'#'\"'\"'#g;s#.*#par_scafstats='&'#" ; else echo "# par_scafstats="; fi )
$( if [ ! -z ${VIASH_PAR_REFSTATS+x} ]; then echo "${VIASH_PAR_REFSTATS}" | sed "s#'#'\"'\"'#g;s#.*#par_refstats='&'#" ; else echo "# par_refstats="; fi )
$( if [ ! -z ${VIASH_PAR_NZO+x} ]; then echo "${VIASH_PAR_NZO}" | sed "s#'#'\"'\"'#g;s#.*#par_nzo='&'#" ; else echo "# par_nzo="; fi )
$( if [ ! -z ${VIASH_PAR_BBMAP_ARGS+x} ]; then echo "${VIASH_PAR_BBMAP_ARGS}" | sed "s#'#'\"'\"'#g;s#.*#par_bbmap_args='&'#" ; else echo "# par_bbmap_args="; 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
function clean_up {
rm -rf "\$tmpdir"
}
trap clean_up EXIT
unset_if_false=( par_paired par_only_build_index par_interleaved par_untrim par_nzo)
for var in "\${unset_if_false[@]}"; do
if [ -z "\${!var}" ]; then
unset \$var
fi
done
if [ ! -d "\$par_build" ]; then
IFS=";" read -ra ref_files <<< "\$par_ref"
primary_ref="\${ref_files[0]}"
refs=()
for file in "\${ref_files[@]:1}"
do
name=\$(basename "\$file" | sed 's/\\.[^.]*\$//')
refs+=("ref_\$name=\$file")
done
fi
if \$par_only_build_index; then
if [ "\${#refs[@]}" -gt 1 ]; then
bbsplit.sh \\
--ref_primary="\$primary_ref" \\
"\${refs[@]}" \\
path=\$par_index
else
echo "ERROR: Please specify at least two reference fasta files."
fi
else
IFS=";" read -ra input <<< "\$par_input"
tmpdir=\$(mktemp -d "\$meta_temp_dir/\$meta_name-XXXXXXXX")
index_files=''
if [ -d "\$par_build" ]; then
index_files="path=\$par_build"
elif [ \${#refs[@]} -gt 0 ]; then
index_files="--ref_primary=\$primary_ref \${refs[*]}"
else
echo "ERROR: Please either specify a BBSplit index as input or at least two reference fasta files."
fi
extra_args=""
if [ -f "\$par_refstats" ]; then extra_args+=" --refstats \$par_refstats"; fi
if [ -n "\$par_ambiguous" ]; then extra_args+=" --ambiguous \$par_ambiguous"; fi
if [ -n "\$par_ambiguous2" ]; then extra_args+=" --ambiguous2 \$par_ambiguous2"; fi
if [ -n "\$par_minratio" ]; then extra_args+=" --minratio \$par_minratio"; fi
if [ -n "\$par_minhits" ]; then extra_args+=" --minhits \$par_minhits"; fi
if [ -n "\$par_maxindel" ]; then extra_args+=" --maxindel \$par_maxindel"; fi
if [ -n "\$par_qin" ]; then extra_args+=" --qin \$par_qin"; fi
if [ -n "\$par_qtrim" ]; then extra_args+=" --qtrim \$par_qtrim"; fi
if [ "\$par_interleaved" = true ]; then extra_args+=" --interleaved"; fi
if [ "\$par_untrim" = true ]; then extra_args+=" --untrim"; fi
if [ "\$par_nzo" = true ]; then extra_args+=" --nzo"; fi
if [ -n "\$par_bbmap_args" ]; then extra_args+=" \$par_bbmap_args"; fi
if \$par_paired; then
bbsplit.sh \\
\$index_files \\
in=\${input[0]} \\
in2=\${input[1]} \\
basename=\${tmpdir}/%_#.fastq \\
\$extra_args
read1=\$(find \$tmpdir/ -iname primary_1*)
read2=\$(find \$tmpdir/ -iname primary_2*)
cp \$read1 \$par_fastq_1
cp \$read2 \$par_fastq_2
else
bbsplit.sh \\
\$index_files \\
in=\${input[0]} \\
basename=\${tmpdir}/%.fastq \\
\$extra_args
read1=\$(find \$tmpdir/ -iname primary*)
cp \$read1 \$par_fastq_1
fi
fi
exit 0
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_REF" ]; then
unset VIASH_TEST_REF
IFS=';'
for var in $VIASH_PAR_REF; do
unset IFS
if [ -z "$VIASH_TEST_REF" ]; then
VIASH_TEST_REF="$(ViashDockerStripAutomount "$var")"
else
VIASH_TEST_REF="$VIASH_TEST_REF;""$(ViashDockerStripAutomount "$var")"
fi
done
VIASH_PAR_REF="$VIASH_TEST_REF"
fi
if [ ! -z "$VIASH_PAR_BUILD" ]; then
VIASH_PAR_BUILD=$(ViashDockerStripAutomount "$VIASH_PAR_BUILD")
fi
if [ ! -z "$VIASH_PAR_INDEX" ]; then
VIASH_PAR_INDEX=$(ViashDockerStripAutomount "$VIASH_PAR_INDEX")
fi
if [ ! -z "$VIASH_PAR_FASTQ_1" ]; then
VIASH_PAR_FASTQ_1=$(ViashDockerStripAutomount "$VIASH_PAR_FASTQ_1")
fi
if [ ! -z "$VIASH_PAR_FASTQ_2" ]; then
VIASH_PAR_FASTQ_2=$(ViashDockerStripAutomount "$VIASH_PAR_FASTQ_2")
fi
if [ ! -z "$VIASH_PAR_SAM2BAM" ]; then
VIASH_PAR_SAM2BAM=$(ViashDockerStripAutomount "$VIASH_PAR_SAM2BAM")
fi
if [ ! -z "$VIASH_PAR_SCAFSTATS" ]; then
VIASH_PAR_SCAFSTATS=$(ViashDockerStripAutomount "$VIASH_PAR_SCAFSTATS")
fi
if [ ! -z "$VIASH_PAR_REFSTATS" ]; then
VIASH_PAR_REFSTATS=$(ViashDockerStripAutomount "$VIASH_PAR_REFSTATS")
fi
if [ ! -z "$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_INDEX" ] && [ ! -e "$VIASH_PAR_INDEX" ]; then
ViashError "Output file '$VIASH_PAR_INDEX' does not exist."
exit 1
fi
if [ ! -z "$VIASH_PAR_FASTQ_1" ] && [ ! -e "$VIASH_PAR_FASTQ_1" ]; then
ViashError "Output file '$VIASH_PAR_FASTQ_1' does not exist."
exit 1
fi
if [ ! -z "$VIASH_PAR_FASTQ_2" ] && [ ! -e "$VIASH_PAR_FASTQ_2" ]; then
ViashError "Output file '$VIASH_PAR_FASTQ_2' does not exist."
exit 1
fi
if [ ! -z "$VIASH_PAR_SAM2BAM" ] && [ ! -e "$VIASH_PAR_SAM2BAM" ]; then
ViashError "Output file '$VIASH_PAR_SAM2BAM' does not exist."
exit 1
fi
if [ ! -z "$VIASH_PAR_SCAFSTATS" ] && [ ! -e "$VIASH_PAR_SCAFSTATS" ]; then
ViashError "Output file '$VIASH_PAR_SCAFSTATS' does not exist."
exit 1
fi
if [ ! -z "$VIASH_PAR_REFSTATS" ] && [ ! -e "$VIASH_PAR_REFSTATS" ]; then
ViashError "Output file '$VIASH_PAR_REFSTATS' does not exist."
exit 1
fi
exit 0
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