vsh/biobox
1
0
Fork 0
Code Issues Pull Requests Actions Packages Projects Releases Wiki Activity
Files
7bfa6ba6a3e2f74d48dbdf7d8167f0f706e0d1f2
biobox/target/executable/lofreq/lofreq_call/lofreq_call
CI 7bfa6ba6a3 Build branch qualimap with version qualimap (d476dee) 
Build pipeline: viash-hub.biobox.qualimap-vm78f

Source commit: d476dee6bd

Source message: fix doi
2024-08-20 21:22:30 +00:00

2001 lines
89 KiB
Bash
Executable File
Raw Blame History

#!/usr/bin/env bash
# lofreq_call qualimap
#
# This wrapper script is auto-generated by viash 0.9.0-RC6 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:
# * Kai Waldrant (author, maintainer)
set -e
if [ -z "$VIASH_TEMP" ]; then
VIASH_TEMP=${VIASH_TEMP:-$VIASH_TMPDIR}
VIASH_TEMP=${VIASH_TEMP:-$VIASH_TEMPDIR}
VIASH_TEMP=${VIASH_TEMP:-$VIASH_TMP}
VIASH_TEMP=${VIASH_TEMP:-$TMPDIR}
VIASH_TEMP=${VIASH_TEMP:-$TMP}
VIASH_TEMP=${VIASH_TEMP:-$TEMPDIR}
VIASH_TEMP=${VIASH_TEMP:-$TEMP}
VIASH_TEMP=${VIASH_TEMP:-/tmp}
fi
# define helper functions
# ViashQuote: put quotes around non flag values
# $1 : unquoted string
# return : possibly quoted string
# examples:
# ViashQuote --foo # returns --foo
# ViashQuote bar # returns 'bar'
# Viashquote --foo=bar # returns --foo='bar'
function ViashQuote {
if [[ "$1" =~ ^-+[a-zA-Z0-9_\-]+=.+$ ]]; then
echo "$1" | sed "s#=\(.*\)#='\1'#"
elif [[ "$1" =~ ^-+[a-zA-Z0-9_\-]+$ ]]; then
echo "$1"
else
echo "'$1'"
fi
}
# ViashRemoveFlags: Remove leading flag
# $1 : string with a possible leading flag
# return : string without possible leading flag
# examples:
# ViashRemoveFlags --foo=bar # returns bar
function ViashRemoveFlags {
echo "$1" | sed 's/^--*[a-zA-Z0-9_\-]*=//'
}
# ViashSourceDir: return the path of a bash file, following symlinks
# usage : ViashSourceDir ${BASH_SOURCE[0]}
# $1 : Should always be set to ${BASH_SOURCE[0]}
# returns : The absolute path of the bash file
function ViashSourceDir {
SOURCE="$1"
while [ -h "$SOURCE" ]; do
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 {
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 $VIASH_META_RESOURCES_DIR`
# define meta fields
VIASH_META_NAME="lofreq_call"
VIASH_META_FUNCTIONALITY_NAME="lofreq_call"
VIASH_META_EXECUTABLE="$VIASH_META_RESOURCES_DIR/$VIASH_META_NAME"
VIASH_META_CONFIG="$VIASH_META_RESOURCES_DIR/.config.vsh.yaml"
VIASH_META_TEMP_DIR="$VIASH_TEMP"
# ViashHelp: Display helpful explanation about this executable
function ViashHelp {
echo "lofreq_call qualimap"
echo ""
echo "Call variants from a BAM file."
echo ""
echo "LoFreq* (i.e. LoFreq version 2) is a fast and sensitive variant-caller for"
echo "inferring SNVs and indels from next-generation sequencing data. It makes full"
echo "use of base-call qualities and other sources of errors inherent in sequencing"
echo "(e.g. mapping or base/indel alignment uncertainty), which are usually ignored by"
echo "other methods or only used for filtering."
echo ""
echo "LoFreq* can run on almost any type of aligned sequencing data (e.g. Illumina,"
echo "IonTorrent or Pacbio) since no machine- or sequencing-technology dependent"
echo "thresholds are used. It automatically adapts to changes in coverage and"
echo "sequencing quality and can therefore be applied to a variety of data-sets e.g."
echo "viral/quasispecies, bacterial, metagenomics or somatic data."
echo ""
echo "LoFreq* is very sensitive; most notably, it is able to predict variants below"
echo "the average base-call quality (i.e. sequencing error rate). Each variant call is"
echo "assigned a p-value which allows for rigorous false positive control. Even though"
echo "it uses no approximations or heuristics, it is very efficient due to several"
echo "runtime optimizations and also provides a (pseudo-)parallel implementation."
echo "LoFreq* is generic and fast enough to be applied to high-coverage data and large"
echo "genomes. On a single processor it takes a minute to analyze Dengue genome"
echo "sequencing data with nearly 4000X coverage, roughly one hour to call SNVs on a"
echo "600X coverage E.coli genome and also roughly an hour to run on a 100X coverage"
echo "human exome dataset."
echo ""
echo "Inputs:"
echo " --input"
echo " type: file, required parameter, file must exist"
echo " example: normal.bam"
echo " Input BAM file."
echo ""
echo " --input_bai"
echo " type: file, required parameter, file must exist"
echo " example: normal.bai"
echo " Index file for the input BAM file."
echo ""
echo " -f, --ref"
echo " type: file, required parameter, file must exist"
echo " example: reference.fasta"
echo " Indexed reference fasta file (gzip supported). Default: none."
echo ""
echo "Outputs:"
echo " -o, --out"
echo " type: file, required parameter, output, file must exist"
echo " example: output.vcf"
echo " Vcf output file. Default: stdout."
echo ""
echo "Arguments:"
echo " -r, --region"
echo " type: string"
echo " example: chr1:1000-2000"
echo " Limit calls to this region (chrom:start-end). Default: none."
echo ""
echo " -l, --bed"
echo " type: file, file must exist"
echo " example: regions.bed"
echo " List of positions (chr pos) or regions (BED). Default: none."
echo ""
echo " -q, --min_bq"
echo " type: integer"
echo " example: 6"
echo " Skip any base with baseQ smaller than INT. Default: 6."
echo ""
echo " -Q, --min_alt_bq"
echo " type: integer"
echo " example: 6"
echo " Skip alternate bases with baseQ smaller than INT. Default: 6."
echo ""
echo " -R, --def_alt_bq"
echo " type: integer"
echo " example: 0"
echo " Overwrite baseQs of alternate bases (that passed bq filter) with this"
echo " value (-1: use median ref-bq; 0: keep). Default: 0."
echo ""
echo " -j, --min_jq"
echo " type: integer"
echo " example: 0"
echo " Skip any base with joinedQ smaller than INT. Default: 0."
echo ""
echo " -J, --min_alt_jq"
echo " type: integer"
echo " example: 0"
echo " Skip alternate bases with joinedQ smaller than INT. Default: 0."
echo ""
echo " -K, --def_alt_jq"
echo " type: integer"
echo " example: 0"
echo " Overwrite joinedQs of alternate bases (that passed jq filter) with this"
echo " value (-1: use median ref-bq; 0: keep). Default: 0."
echo ""
echo " -B, --no_baq"
echo " type: boolean_true"
echo " Disable use of base-alignment quality (BAQ)."
echo ""
echo " -A, --no_idaq"
echo " type: boolean_true"
echo " Don't use IDAQ values (NOT recommended under ANY circumstances other"
echo " than debugging)."
echo ""
echo " -D, --del_baq"
echo " type: boolean_true"
echo " Delete pre-existing BAQ values, i.e. compute even if already present in"
echo " BAM."
echo ""
echo " -e, --no_ext_baq"
echo " type: boolean_true"
echo " Use 'normal' BAQ (samtools default) instead of extended BAQ (both"
echo " computed on the fly if not already present in lb tag)."
echo ""
echo " -m, --min_mq"
echo " type: integer"
echo " example: 0"
echo " Skip reads with mapping quality smaller than INT. Default: 0."
echo ""
echo " -M, --max_mq"
echo " type: integer"
echo " example: 255"
echo " Cap mapping quality at INT. Default: 255."
echo ""
echo " -N, --no_mq"
echo " type: boolean_true"
echo " Don't merge mapping quality in LoFreq's model."
echo ""
echo " --call_indels"
echo " type: boolean_true"
echo " Enable indel calls (note: preprocess your file to include indel"
echo " alignment qualities!)."
echo ""
echo " --only_indels"
echo " type: boolean_true"
echo " Only call indels; no SNVs."
echo ""
echo " -s, --src_qual"
echo " type: boolean_true"
echo " Enable computation of source quality."
echo ""
echo " -S, --ign_vcf"
echo " type: file, file must exist"
echo " example: variants.vcf"
echo " Ignore variants in this vcf file for source quality computation."
echo " Multiple files can be given separated by commas."
echo ""
echo " -T, --def_nm_q"
echo " type: integer"
echo " example: -1"
echo " If >= 0, then replace non-match base qualities with this default value."
echo " Default: -1."
echo ""
echo " -a, --sig"
echo " type: double"
echo " example: 0.01"
echo " P-Value cutoff / significance level. Default: 0.010000."
echo ""
echo " -b, --bonf"
echo " type: string"
echo " example: dynamic"
echo " Bonferroni factor. 'dynamic' (increase per actually performed test) or"
echo " INT. Default: Dynamic."
echo ""
echo " -C, --min_cov"
echo " type: integer"
echo " example: 1"
echo " Test only positions having at least this coverage. Default: 1."
echo " (note: without --no-default-filter default filters (incl. coverage) kick"
echo " in after predictions are done)."
echo ""
echo " -d, --max_depth"
echo " type: integer"
echo " example: 1000000"
echo " Cap coverage at this depth. Default: 1000000."
echo ""
echo " --illumina_13"
echo " type: boolean_true"
echo " Assume the quality is Illumina-1.3-1.7/ASCII+64 encoded."
echo ""
echo " --use_orphan"
echo " type: boolean_true"
echo " Count anomalous read pairs (i.e. where mate is not aligned properly)."
echo ""
echo " --plp_summary_only"
echo " type: boolean_true"
echo " No variant calling. Just output pileup summary per column."
echo ""
echo " --no_default_filter"
echo " type: boolean_true"
echo " Don't run default 'lofreq filter' automatically after calling variants."
echo ""
echo " --force_overwrite"
echo " type: boolean_true"
echo " Overwrite any existing output."
echo ""
echo " --verbose"
echo " type: boolean_true"
echo " Be verbose."
echo ""
echo " --debug"
echo " type: boolean_true"
echo " Enable debugging."
}
# 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"
save=$-; set +e
docker_version=$(docker version --format '{{.Client.APIVersion}}' 2> /dev/null)
out=$?
[[ $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 $1 && return 0 || return 1
else
save=$-; set +e
docker pull $1 2> /dev/null > /dev/null
out=$?
[[ $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 '$1'"
save=$-; set +e
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
#
# $1 : image identifier with format `[registry/]image[:tag]`
# ViashDockerBuild : a Bash function which builds a docker image, takes image identifier as argument.
# examples:
# ViashDockerPullElseBuild mynewcomponent
function ViashDockerPullElseBuild {
save=$-; set +e
ViashDockerPull $1
out=$?
[[ $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/lofreq:2.1.5--py38h794fc9e_10
ENTRYPOINT []
RUN version=$(lofreq version | grep 'version' | sed 's/version: //') && \
echo "lofreq: $version" > /var/software_versions.txt
LABEL org.opencontainers.image.authors="Kai Waldrant"
LABEL org.opencontainers.image.description="Companion container for running component lofreq lofreq_call"
LABEL org.opencontainers.image.created="2024-08-20T21:04:58Z"
LABEL org.opencontainers.image.source="https://github.com/viash-hub/biobox"
LABEL org.opencontainers.image.revision="d476dee6bdcf7ee5444385acbfa0d1d3ae06557e"
LABEL org.opencontainers.image.version="qualimap"
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
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
# $VIASH_DIRECTORY_MOUNTS : Added another parameter to be passed to docker
# examples:
# ViashDockerAutodetectMount /path/to/bar # returns '/viash_automount/path/to/bar'
# ViashDockerAutodetectMountArg /path/to/bar # returns '--volume="/path/to:/viash_automount/path/to"'
function ViashDockerAutodetectMount {
abs_path=$(ViashAbsolutePath "$1")
if [ -d "$abs_path" ]; then
mount_source="$abs_path"
base_name=""
else
mount_source=`dirname "$abs_path"`
base_name=`basename "$abs_path"`
fi
mount_target="/viash_automount$mount_source"
if [ -z "$base_name" ]; then
echo "$mount_target"
else
echo "$mount_target/$base_name"
fi
}
function ViashDockerAutodetectMountArg {
abs_path=$(ViashAbsolutePath "$1")
if [ -d "$abs_path" ]; then
mount_source="$abs_path"
base_name=""
else
mount_source=`dirname "$abs_path"`
base_name=`basename "$abs_path"`
fi
mount_target="/viash_automount$mount_source"
ViashDebug "ViashDockerAutodetectMountArg $1 -> $mount_source -> $mount_target"
echo "--volume=\"$mount_source:$mount_target\""
}
function ViashDockerStripAutomount {
abs_path=$(ViashAbsolutePath "$1")
echo "${abs_path#/viash_automount}"
}
# initialise variables
VIASH_DIRECTORY_MOUNTS=()
# initialise docker variables
VIASH_DOCKER_RUN_ARGS=(-i --rm)
# initialise array
VIASH_POSITIONAL_ARGS=''
while [[ $# -gt 0 ]]; do
case "$1" in
-h|--help)
ViashHelp
exit
;;
---v|---verbose)
let "VIASH_VERBOSITY=VIASH_VERBOSITY+1"
shift 1
;;
---verbosity)
VIASH_VERBOSITY="$2"
shift 2
;;
---verbosity=*)
VIASH_VERBOSITY="$(ViashRemoveFlags "$1")"
shift 1
;;
--version)
echo "lofreq_call qualimap"
exit
;;
--input)
[ -n "$VIASH_PAR_INPUT" ] && ViashError Bad arguments for option \'--input\': \'$VIASH_PAR_INPUT\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
VIASH_PAR_INPUT="$2"
[ $# -lt 2 ] && ViashError Not enough arguments passed to --input. Use "--help" to get more information on the parameters. && exit 1
shift 2
;;
--input=*)
[ -n "$VIASH_PAR_INPUT" ] && ViashError Bad arguments for option \'--input=*\': \'$VIASH_PAR_INPUT\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
VIASH_PAR_INPUT=$(ViashRemoveFlags "$1")
shift 1
;;
--input_bai)
[ -n "$VIASH_PAR_INPUT_BAI" ] && ViashError Bad arguments for option \'--input_bai\': \'$VIASH_PAR_INPUT_BAI\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
VIASH_PAR_INPUT_BAI="$2"
[ $# -lt 2 ] && ViashError Not enough arguments passed to --input_bai. Use "--help" to get more information on the parameters. && exit 1
shift 2
;;
--input_bai=*)
[ -n "$VIASH_PAR_INPUT_BAI" ] && ViashError Bad arguments for option \'--input_bai=*\': \'$VIASH_PAR_INPUT_BAI\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
VIASH_PAR_INPUT_BAI=$(ViashRemoveFlags "$1")
shift 1
;;
--ref)
[ -n "$VIASH_PAR_REF" ] && ViashError Bad arguments for option \'--ref\': \'$VIASH_PAR_REF\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
VIASH_PAR_REF="$2"
[ $# -lt 2 ] && ViashError Not enough arguments passed to --ref. Use "--help" to get more information on the parameters. && exit 1
shift 2
;;
--ref=*)
[ -n "$VIASH_PAR_REF" ] && ViashError Bad arguments for option \'--ref=*\': \'$VIASH_PAR_REF\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
VIASH_PAR_REF=$(ViashRemoveFlags "$1")
shift 1
;;
-f)
[ -n "$VIASH_PAR_REF" ] && ViashError Bad arguments for option \'-f\': \'$VIASH_PAR_REF\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
VIASH_PAR_REF="$2"
[ $# -lt 2 ] && ViashError Not enough arguments passed to -f. Use "--help" to get more information on the parameters. && exit 1
shift 2
;;
--out)
[ -n "$VIASH_PAR_OUT" ] && ViashError Bad arguments for option \'--out\': \'$VIASH_PAR_OUT\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
VIASH_PAR_OUT="$2"
[ $# -lt 2 ] && ViashError Not enough arguments passed to --out. Use "--help" to get more information on the parameters. && exit 1
shift 2
;;
--out=*)
[ -n "$VIASH_PAR_OUT" ] && ViashError Bad arguments for option \'--out=*\': \'$VIASH_PAR_OUT\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
VIASH_PAR_OUT=$(ViashRemoveFlags "$1")
shift 1
;;
-o)
[ -n "$VIASH_PAR_OUT" ] && ViashError Bad arguments for option \'-o\': \'$VIASH_PAR_OUT\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
VIASH_PAR_OUT="$2"
[ $# -lt 2 ] && ViashError Not enough arguments passed to -o. Use "--help" to get more information on the parameters. && exit 1
shift 2
;;
--region)
[ -n "$VIASH_PAR_REGION" ] && ViashError Bad arguments for option \'--region\': \'$VIASH_PAR_REGION\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
VIASH_PAR_REGION="$2"
[ $# -lt 2 ] && ViashError Not enough arguments passed to --region. Use "--help" to get more information on the parameters. && exit 1
shift 2
;;
--region=*)
[ -n "$VIASH_PAR_REGION" ] && ViashError Bad arguments for option \'--region=*\': \'$VIASH_PAR_REGION\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
VIASH_PAR_REGION=$(ViashRemoveFlags "$1")
shift 1
;;
-r)
[ -n "$VIASH_PAR_REGION" ] && ViashError Bad arguments for option \'-r\': \'$VIASH_PAR_REGION\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
VIASH_PAR_REGION="$2"
[ $# -lt 2 ] && ViashError Not enough arguments passed to -r. Use "--help" to get more information on the parameters. && exit 1
shift 2
;;
--bed)
[ -n "$VIASH_PAR_BED" ] && ViashError Bad arguments for option \'--bed\': \'$VIASH_PAR_BED\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
VIASH_PAR_BED="$2"
[ $# -lt 2 ] && ViashError Not enough arguments passed to --bed. Use "--help" to get more information on the parameters. && exit 1
shift 2
;;
--bed=*)
[ -n "$VIASH_PAR_BED" ] && ViashError Bad arguments for option \'--bed=*\': \'$VIASH_PAR_BED\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
VIASH_PAR_BED=$(ViashRemoveFlags "$1")
shift 1
;;
-l)
[ -n "$VIASH_PAR_BED" ] && ViashError Bad arguments for option \'-l\': \'$VIASH_PAR_BED\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
VIASH_PAR_BED="$2"
[ $# -lt 2 ] && ViashError Not enough arguments passed to -l. Use "--help" to get more information on the parameters. && exit 1
shift 2
;;
--min_bq)
[ -n "$VIASH_PAR_MIN_BQ" ] && ViashError Bad arguments for option \'--min_bq\': \'$VIASH_PAR_MIN_BQ\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
VIASH_PAR_MIN_BQ="$2"
[ $# -lt 2 ] && ViashError Not enough arguments passed to --min_bq. Use "--help" to get more information on the parameters. && exit 1
shift 2
;;
--min_bq=*)
[ -n "$VIASH_PAR_MIN_BQ" ] && ViashError Bad arguments for option \'--min_bq=*\': \'$VIASH_PAR_MIN_BQ\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
VIASH_PAR_MIN_BQ=$(ViashRemoveFlags "$1")
shift 1
;;
-q)
[ -n "$VIASH_PAR_MIN_BQ" ] && ViashError Bad arguments for option \'-q\': \'$VIASH_PAR_MIN_BQ\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
VIASH_PAR_MIN_BQ="$2"
[ $# -lt 2 ] && ViashError Not enough arguments passed to -q. Use "--help" to get more information on the parameters. && exit 1
shift 2
;;
--min_alt_bq)
[ -n "$VIASH_PAR_MIN_ALT_BQ" ] && ViashError Bad arguments for option \'--min_alt_bq\': \'$VIASH_PAR_MIN_ALT_BQ\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
VIASH_PAR_MIN_ALT_BQ="$2"
[ $# -lt 2 ] && ViashError Not enough arguments passed to --min_alt_bq. Use "--help" to get more information on the parameters. && exit 1
shift 2
;;
--min_alt_bq=*)
[ -n "$VIASH_PAR_MIN_ALT_BQ" ] && ViashError Bad arguments for option \'--min_alt_bq=*\': \'$VIASH_PAR_MIN_ALT_BQ\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
VIASH_PAR_MIN_ALT_BQ=$(ViashRemoveFlags "$1")
shift 1
;;
-Q)
[ -n "$VIASH_PAR_MIN_ALT_BQ" ] && ViashError Bad arguments for option \'-Q\': \'$VIASH_PAR_MIN_ALT_BQ\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
VIASH_PAR_MIN_ALT_BQ="$2"
[ $# -lt 2 ] && ViashError Not enough arguments passed to -Q. Use "--help" to get more information on the parameters. && exit 1
shift 2
;;
--def_alt_bq)
[ -n "$VIASH_PAR_DEF_ALT_BQ" ] && ViashError Bad arguments for option \'--def_alt_bq\': \'$VIASH_PAR_DEF_ALT_BQ\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
VIASH_PAR_DEF_ALT_BQ="$2"
[ $# -lt 2 ] && ViashError Not enough arguments passed to --def_alt_bq. Use "--help" to get more information on the parameters. && exit 1
shift 2
;;
--def_alt_bq=*)
[ -n "$VIASH_PAR_DEF_ALT_BQ" ] && ViashError Bad arguments for option \'--def_alt_bq=*\': \'$VIASH_PAR_DEF_ALT_BQ\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
VIASH_PAR_DEF_ALT_BQ=$(ViashRemoveFlags "$1")
shift 1
;;
-R)
[ -n "$VIASH_PAR_DEF_ALT_BQ" ] && ViashError Bad arguments for option \'-R\': \'$VIASH_PAR_DEF_ALT_BQ\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
VIASH_PAR_DEF_ALT_BQ="$2"
[ $# -lt 2 ] && ViashError Not enough arguments passed to -R. Use "--help" to get more information on the parameters. && exit 1
shift 2
;;
--min_jq)
[ -n "$VIASH_PAR_MIN_JQ" ] && ViashError Bad arguments for option \'--min_jq\': \'$VIASH_PAR_MIN_JQ\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
VIASH_PAR_MIN_JQ="$2"
[ $# -lt 2 ] && ViashError Not enough arguments passed to --min_jq. Use "--help" to get more information on the parameters. && exit 1
shift 2
;;
--min_jq=*)
[ -n "$VIASH_PAR_MIN_JQ" ] && ViashError Bad arguments for option \'--min_jq=*\': \'$VIASH_PAR_MIN_JQ\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
VIASH_PAR_MIN_JQ=$(ViashRemoveFlags "$1")
shift 1
;;
-j)
[ -n "$VIASH_PAR_MIN_JQ" ] && ViashError Bad arguments for option \'-j\': \'$VIASH_PAR_MIN_JQ\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
VIASH_PAR_MIN_JQ="$2"
[ $# -lt 2 ] && ViashError Not enough arguments passed to -j. Use "--help" to get more information on the parameters. && exit 1
shift 2
;;
--min_alt_jq)
[ -n "$VIASH_PAR_MIN_ALT_JQ" ] && ViashError Bad arguments for option \'--min_alt_jq\': \'$VIASH_PAR_MIN_ALT_JQ\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
VIASH_PAR_MIN_ALT_JQ="$2"
[ $# -lt 2 ] && ViashError Not enough arguments passed to --min_alt_jq. Use "--help" to get more information on the parameters. && exit 1
shift 2
;;
--min_alt_jq=*)
[ -n "$VIASH_PAR_MIN_ALT_JQ" ] && ViashError Bad arguments for option \'--min_alt_jq=*\': \'$VIASH_PAR_MIN_ALT_JQ\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
VIASH_PAR_MIN_ALT_JQ=$(ViashRemoveFlags "$1")
shift 1
;;
-J)
[ -n "$VIASH_PAR_MIN_ALT_JQ" ] && ViashError Bad arguments for option \'-J\': \'$VIASH_PAR_MIN_ALT_JQ\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
VIASH_PAR_MIN_ALT_JQ="$2"
[ $# -lt 2 ] && ViashError Not enough arguments passed to -J. Use "--help" to get more information on the parameters. && exit 1
shift 2
;;
--def_alt_jq)
[ -n "$VIASH_PAR_DEF_ALT_JQ" ] && ViashError Bad arguments for option \'--def_alt_jq\': \'$VIASH_PAR_DEF_ALT_JQ\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
VIASH_PAR_DEF_ALT_JQ="$2"
[ $# -lt 2 ] && ViashError Not enough arguments passed to --def_alt_jq. Use "--help" to get more information on the parameters. && exit 1
shift 2
;;
--def_alt_jq=*)
[ -n "$VIASH_PAR_DEF_ALT_JQ" ] && ViashError Bad arguments for option \'--def_alt_jq=*\': \'$VIASH_PAR_DEF_ALT_JQ\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
VIASH_PAR_DEF_ALT_JQ=$(ViashRemoveFlags "$1")
shift 1
;;
-K)
[ -n "$VIASH_PAR_DEF_ALT_JQ" ] && ViashError Bad arguments for option \'-K\': \'$VIASH_PAR_DEF_ALT_JQ\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
VIASH_PAR_DEF_ALT_JQ="$2"
[ $# -lt 2 ] && ViashError Not enough arguments passed to -K. Use "--help" to get more information on the parameters. && exit 1
shift 2
;;
--no_baq)
[ -n "$VIASH_PAR_NO_BAQ" ] && ViashError Bad arguments for option \'--no_baq\': \'$VIASH_PAR_NO_BAQ\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
VIASH_PAR_NO_BAQ=true
shift 1
;;
-B)
[ -n "$VIASH_PAR_NO_BAQ" ] && ViashError Bad arguments for option \'-B\': \'$VIASH_PAR_NO_BAQ\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
VIASH_PAR_NO_BAQ=true
shift 1
;;
--no_idaq)
[ -n "$VIASH_PAR_NO_IDAQ" ] && ViashError Bad arguments for option \'--no_idaq\': \'$VIASH_PAR_NO_IDAQ\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
VIASH_PAR_NO_IDAQ=true
shift 1
;;
-A)
[ -n "$VIASH_PAR_NO_IDAQ" ] && ViashError Bad arguments for option \'-A\': \'$VIASH_PAR_NO_IDAQ\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
VIASH_PAR_NO_IDAQ=true
shift 1
;;
--del_baq)
[ -n "$VIASH_PAR_DEL_BAQ" ] && ViashError Bad arguments for option \'--del_baq\': \'$VIASH_PAR_DEL_BAQ\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
VIASH_PAR_DEL_BAQ=true
shift 1
;;
-D)
[ -n "$VIASH_PAR_DEL_BAQ" ] && ViashError Bad arguments for option \'-D\': \'$VIASH_PAR_DEL_BAQ\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
VIASH_PAR_DEL_BAQ=true
shift 1
;;
--no_ext_baq)
[ -n "$VIASH_PAR_NO_EXT_BAQ" ] && ViashError Bad arguments for option \'--no_ext_baq\': \'$VIASH_PAR_NO_EXT_BAQ\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
VIASH_PAR_NO_EXT_BAQ=true
shift 1
;;
-e)
[ -n "$VIASH_PAR_NO_EXT_BAQ" ] && ViashError Bad arguments for option \'-e\': \'$VIASH_PAR_NO_EXT_BAQ\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
VIASH_PAR_NO_EXT_BAQ=true
shift 1
;;
--min_mq)
[ -n "$VIASH_PAR_MIN_MQ" ] && ViashError Bad arguments for option \'--min_mq\': \'$VIASH_PAR_MIN_MQ\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
VIASH_PAR_MIN_MQ="$2"
[ $# -lt 2 ] && ViashError Not enough arguments passed to --min_mq. Use "--help" to get more information on the parameters. && exit 1
shift 2
;;
--min_mq=*)
[ -n "$VIASH_PAR_MIN_MQ" ] && ViashError Bad arguments for option \'--min_mq=*\': \'$VIASH_PAR_MIN_MQ\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
VIASH_PAR_MIN_MQ=$(ViashRemoveFlags "$1")
shift 1
;;
-m)
[ -n "$VIASH_PAR_MIN_MQ" ] && ViashError Bad arguments for option \'-m\': \'$VIASH_PAR_MIN_MQ\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
VIASH_PAR_MIN_MQ="$2"
[ $# -lt 2 ] && ViashError Not enough arguments passed to -m. Use "--help" to get more information on the parameters. && exit 1
shift 2
;;
--max_mq)
[ -n "$VIASH_PAR_MAX_MQ" ] && ViashError Bad arguments for option \'--max_mq\': \'$VIASH_PAR_MAX_MQ\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
VIASH_PAR_MAX_MQ="$2"
[ $# -lt 2 ] && ViashError Not enough arguments passed to --max_mq. Use "--help" to get more information on the parameters. && exit 1
shift 2
;;
--max_mq=*)
[ -n "$VIASH_PAR_MAX_MQ" ] && ViashError Bad arguments for option \'--max_mq=*\': \'$VIASH_PAR_MAX_MQ\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
VIASH_PAR_MAX_MQ=$(ViashRemoveFlags "$1")
shift 1
;;
-M)
[ -n "$VIASH_PAR_MAX_MQ" ] && ViashError Bad arguments for option \'-M\': \'$VIASH_PAR_MAX_MQ\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
VIASH_PAR_MAX_MQ="$2"
[ $# -lt 2 ] && ViashError Not enough arguments passed to -M. Use "--help" to get more information on the parameters. && exit 1
shift 2
;;
--no_mq)
[ -n "$VIASH_PAR_NO_MQ" ] && ViashError Bad arguments for option \'--no_mq\': \'$VIASH_PAR_NO_MQ\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
VIASH_PAR_NO_MQ=true
shift 1
;;
-N)
[ -n "$VIASH_PAR_NO_MQ" ] && ViashError Bad arguments for option \'-N\': \'$VIASH_PAR_NO_MQ\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
VIASH_PAR_NO_MQ=true
shift 1
;;
--call_indels)
[ -n "$VIASH_PAR_CALL_INDELS" ] && ViashError Bad arguments for option \'--call_indels\': \'$VIASH_PAR_CALL_INDELS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
VIASH_PAR_CALL_INDELS=true
shift 1
;;
--only_indels)
[ -n "$VIASH_PAR_ONLY_INDELS" ] && ViashError Bad arguments for option \'--only_indels\': \'$VIASH_PAR_ONLY_INDELS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
VIASH_PAR_ONLY_INDELS=true
shift 1
;;
--src_qual)
[ -n "$VIASH_PAR_SRC_QUAL" ] && ViashError Bad arguments for option \'--src_qual\': \'$VIASH_PAR_SRC_QUAL\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
VIASH_PAR_SRC_QUAL=true
shift 1
;;
-s)
[ -n "$VIASH_PAR_SRC_QUAL" ] && ViashError Bad arguments for option \'-s\': \'$VIASH_PAR_SRC_QUAL\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
VIASH_PAR_SRC_QUAL=true
shift 1
;;
--ign_vcf)
[ -n "$VIASH_PAR_IGN_VCF" ] && ViashError Bad arguments for option \'--ign_vcf\': \'$VIASH_PAR_IGN_VCF\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
VIASH_PAR_IGN_VCF="$2"
[ $# -lt 2 ] && ViashError Not enough arguments passed to --ign_vcf. Use "--help" to get more information on the parameters. && exit 1
shift 2
;;
--ign_vcf=*)
[ -n "$VIASH_PAR_IGN_VCF" ] && ViashError Bad arguments for option \'--ign_vcf=*\': \'$VIASH_PAR_IGN_VCF\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
VIASH_PAR_IGN_VCF=$(ViashRemoveFlags "$1")
shift 1
;;
-S)
[ -n "$VIASH_PAR_IGN_VCF" ] && ViashError Bad arguments for option \'-S\': \'$VIASH_PAR_IGN_VCF\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
VIASH_PAR_IGN_VCF="$2"
[ $# -lt 2 ] && ViashError Not enough arguments passed to -S. Use "--help" to get more information on the parameters. && exit 1
shift 2
;;
--def_nm_q)
[ -n "$VIASH_PAR_DEF_NM_Q" ] && ViashError Bad arguments for option \'--def_nm_q\': \'$VIASH_PAR_DEF_NM_Q\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
VIASH_PAR_DEF_NM_Q="$2"
[ $# -lt 2 ] && ViashError Not enough arguments passed to --def_nm_q. Use "--help" to get more information on the parameters. && exit 1
shift 2
;;
--def_nm_q=*)
[ -n "$VIASH_PAR_DEF_NM_Q" ] && ViashError Bad arguments for option \'--def_nm_q=*\': \'$VIASH_PAR_DEF_NM_Q\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
VIASH_PAR_DEF_NM_Q=$(ViashRemoveFlags "$1")
shift 1
;;
-T)
[ -n "$VIASH_PAR_DEF_NM_Q" ] && ViashError Bad arguments for option \'-T\': \'$VIASH_PAR_DEF_NM_Q\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
VIASH_PAR_DEF_NM_Q="$2"
[ $# -lt 2 ] && ViashError Not enough arguments passed to -T. Use "--help" to get more information on the parameters. && exit 1
shift 2
;;
--sig)
[ -n "$VIASH_PAR_SIG" ] && ViashError Bad arguments for option \'--sig\': \'$VIASH_PAR_SIG\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
VIASH_PAR_SIG="$2"
[ $# -lt 2 ] && ViashError Not enough arguments passed to --sig. Use "--help" to get more information on the parameters. && exit 1
shift 2
;;
--sig=*)
[ -n "$VIASH_PAR_SIG" ] && ViashError Bad arguments for option \'--sig=*\': \'$VIASH_PAR_SIG\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
VIASH_PAR_SIG=$(ViashRemoveFlags "$1")
shift 1
;;
-a)
[ -n "$VIASH_PAR_SIG" ] && ViashError Bad arguments for option \'-a\': \'$VIASH_PAR_SIG\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
VIASH_PAR_SIG="$2"
[ $# -lt 2 ] && ViashError Not enough arguments passed to -a. Use "--help" to get more information on the parameters. && exit 1
shift 2
;;
--bonf)
[ -n "$VIASH_PAR_BONF" ] && ViashError Bad arguments for option \'--bonf\': \'$VIASH_PAR_BONF\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
VIASH_PAR_BONF="$2"
[ $# -lt 2 ] && ViashError Not enough arguments passed to --bonf. Use "--help" to get more information on the parameters. && exit 1
shift 2
;;
--bonf=*)
[ -n "$VIASH_PAR_BONF" ] && ViashError Bad arguments for option \'--bonf=*\': \'$VIASH_PAR_BONF\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
VIASH_PAR_BONF=$(ViashRemoveFlags "$1")
shift 1
;;
-b)
[ -n "$VIASH_PAR_BONF" ] && ViashError Bad arguments for option \'-b\': \'$VIASH_PAR_BONF\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
VIASH_PAR_BONF="$2"
[ $# -lt 2 ] && ViashError Not enough arguments passed to -b. Use "--help" to get more information on the parameters. && exit 1
shift 2
;;
--min_cov)
[ -n "$VIASH_PAR_MIN_COV" ] && ViashError Bad arguments for option \'--min_cov\': \'$VIASH_PAR_MIN_COV\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
VIASH_PAR_MIN_COV="$2"
[ $# -lt 2 ] && ViashError Not enough arguments passed to --min_cov. Use "--help" to get more information on the parameters. && exit 1
shift 2
;;
--min_cov=*)
[ -n "$VIASH_PAR_MIN_COV" ] && ViashError Bad arguments for option \'--min_cov=*\': \'$VIASH_PAR_MIN_COV\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
VIASH_PAR_MIN_COV=$(ViashRemoveFlags "$1")
shift 1
;;
-C)
[ -n "$VIASH_PAR_MIN_COV" ] && ViashError Bad arguments for option \'-C\': \'$VIASH_PAR_MIN_COV\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
VIASH_PAR_MIN_COV="$2"
[ $# -lt 2 ] && ViashError Not enough arguments passed to -C. Use "--help" to get more information on the parameters. && exit 1
shift 2
;;
--max_depth)
[ -n "$VIASH_PAR_MAX_DEPTH" ] && ViashError Bad arguments for option \'--max_depth\': \'$VIASH_PAR_MAX_DEPTH\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
VIASH_PAR_MAX_DEPTH="$2"
[ $# -lt 2 ] && ViashError Not enough arguments passed to --max_depth. Use "--help" to get more information on the parameters. && exit 1
shift 2
;;
--max_depth=*)
[ -n "$VIASH_PAR_MAX_DEPTH" ] && ViashError Bad arguments for option \'--max_depth=*\': \'$VIASH_PAR_MAX_DEPTH\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
VIASH_PAR_MAX_DEPTH=$(ViashRemoveFlags "$1")
shift 1
;;
-d)
[ -n "$VIASH_PAR_MAX_DEPTH" ] && ViashError Bad arguments for option \'-d\': \'$VIASH_PAR_MAX_DEPTH\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
VIASH_PAR_MAX_DEPTH="$2"
[ $# -lt 2 ] && ViashError Not enough arguments passed to -d. Use "--help" to get more information on the parameters. && exit 1
shift 2
;;
--illumina_13)
[ -n "$VIASH_PAR_ILLUMINA_13" ] && ViashError Bad arguments for option \'--illumina_13\': \'$VIASH_PAR_ILLUMINA_13\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
VIASH_PAR_ILLUMINA_13=true
shift 1
;;
--use_orphan)
[ -n "$VIASH_PAR_USE_ORPHAN" ] && ViashError Bad arguments for option \'--use_orphan\': \'$VIASH_PAR_USE_ORPHAN\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
VIASH_PAR_USE_ORPHAN=true
shift 1
;;
--plp_summary_only)
[ -n "$VIASH_PAR_PLP_SUMMARY_ONLY" ] && ViashError Bad arguments for option \'--plp_summary_only\': \'$VIASH_PAR_PLP_SUMMARY_ONLY\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
VIASH_PAR_PLP_SUMMARY_ONLY=true
shift 1
;;
--no_default_filter)
[ -n "$VIASH_PAR_NO_DEFAULT_FILTER" ] && ViashError Bad arguments for option \'--no_default_filter\': \'$VIASH_PAR_NO_DEFAULT_FILTER\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
VIASH_PAR_NO_DEFAULT_FILTER=true
shift 1
;;
--force_overwrite)
[ -n "$VIASH_PAR_FORCE_OVERWRITE" ] && ViashError Bad arguments for option \'--force_overwrite\': \'$VIASH_PAR_FORCE_OVERWRITE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
VIASH_PAR_FORCE_OVERWRITE=true
shift 1
;;
--verbose)
[ -n "$VIASH_PAR_VERBOSE" ] && ViashError Bad arguments for option \'--verbose\': \'$VIASH_PAR_VERBOSE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
VIASH_PAR_VERBOSE=true
shift 1
;;
--debug)
[ -n "$VIASH_PAR_DEBUG" ] && ViashError Bad arguments for option \'--debug\': \'$VIASH_PAR_DEBUG\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
VIASH_PAR_DEBUG=true
shift 1
;;
---engine)
VIASH_ENGINE_ID="$2"
shift 2
;;
---engine=*)
VIASH_ENGINE_ID="$(ViashRemoveFlags "$1")"
shift 1
;;
---setup)
VIASH_MODE='setup'
VIASH_SETUP_STRATEGY="$2"
shift 2
;;
---setup=*)
VIASH_MODE='setup'
VIASH_SETUP_STRATEGY="$(ViashRemoveFlags "$1")"
shift 1
;;
---dockerfile)
VIASH_MODE='dockerfile'
shift 1
;;
---debug)
VIASH_MODE='debug'
shift 1
;;
---cpus)
[ -n "$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/lofreq/lofreq_call:qualimap'
fi
# print dockerfile
if [ "$VIASH_MODE" == "dockerfile" ]; then
ViashDockerfile "$VIASH_ENGINE_ID"
exit 0
# enter docker container
elif [[ "$VIASH_MODE" == "debug" ]]; then
VIASH_CMD="docker run --entrypoint=bash ${VIASH_DOCKER_RUN_ARGS[@]} -v '$(pwd)':/pwd --workdir /pwd -t $VIASH_DOCKER_IMAGE_ID"
ViashNotice "+ $VIASH_CMD"
eval $VIASH_CMD
exit
# build docker image
elif [ "$VIASH_MODE" == "setup" ]; then
ViashDockerSetup "$VIASH_DOCKER_IMAGE_ID" "$VIASH_SETUP_STRATEGY"
ViashDockerCheckCommands "$VIASH_DOCKER_IMAGE_ID" 'ps' 'bash'
exit 0
fi
# check if docker image exists
ViashDockerSetup "$VIASH_DOCKER_IMAGE_ID" ifneedbepullelsecachedbuild
ViashDockerCheckCommands "$VIASH_DOCKER_IMAGE_ID" 'ps' 'bash'
fi
# setting computational defaults
# helper function for parsing memory strings
function ViashMemoryAsBytes {
local memory=`echo "$1" | tr '[:upper:]' '[:lower:]' | tr -d '[:space:]'`
local memory_regex='^([0-9]+)([kmgtp]i?b?|b)$'
if [[ $memory =~ $memory_regex ]]; then
local number=${memory/[^0-9]*/}
local symbol=${memory/*[0-9]/}
case $symbol in
b) memory_b=$number ;;
kb|k) memory_b=$(( $number * 1000 )) ;;
mb|m) memory_b=$(( $number * 1000 * 1000 )) ;;
gb|g) memory_b=$(( $number * 1000 * 1000 * 1000 )) ;;
tb|t) memory_b=$(( $number * 1000 * 1000 * 1000 * 1000 )) ;;
pb|p) memory_b=$(( $number * 1000 * 1000 * 1000 * 1000 * 1000 )) ;;
kib|ki) memory_b=$(( $number * 1024 )) ;;
mib|mi) memory_b=$(( $number * 1024 * 1024 )) ;;
gib|gi) memory_b=$(( $number * 1024 * 1024 * 1024 )) ;;
tib|ti) memory_b=$(( $number * 1024 * 1024 * 1024 * 1024 )) ;;
pib|pi) memory_b=$(( $number * 1024 * 1024 * 1024 * 1024 * 1024 )) ;;
esac
echo "$memory_b"
fi
}
# compute memory in different units
if [ ! -z ${VIASH_META_MEMORY+x} ]; then
VIASH_META_MEMORY_B=`ViashMemoryAsBytes $VIASH_META_MEMORY`
# do not define other variables if memory_b is an empty string
if [ ! -z "$VIASH_META_MEMORY_B" ]; then
VIASH_META_MEMORY_KB=$(( ($VIASH_META_MEMORY_B+999) / 1000 ))
VIASH_META_MEMORY_MB=$(( ($VIASH_META_MEMORY_KB+999) / 1000 ))
VIASH_META_MEMORY_GB=$(( ($VIASH_META_MEMORY_MB+999) / 1000 ))
VIASH_META_MEMORY_TB=$(( ($VIASH_META_MEMORY_GB+999) / 1000 ))
VIASH_META_MEMORY_PB=$(( ($VIASH_META_MEMORY_TB+999) / 1000 ))
VIASH_META_MEMORY_KIB=$(( ($VIASH_META_MEMORY_B+1023) / 1024 ))
VIASH_META_MEMORY_MIB=$(( ($VIASH_META_MEMORY_KIB+1023) / 1024 ))
VIASH_META_MEMORY_GIB=$(( ($VIASH_META_MEMORY_MIB+1023) / 1024 ))
VIASH_META_MEMORY_TIB=$(( ($VIASH_META_MEMORY_GIB+1023) / 1024 ))
VIASH_META_MEMORY_PIB=$(( ($VIASH_META_MEMORY_TIB+1023) / 1024 ))
else
# unset memory if string is empty
unset $VIASH_META_MEMORY_B
fi
fi
# unset nproc if string is empty
if [ -z "$VIASH_META_CPUS" ]; then
unset $VIASH_META_CPUS
fi
# check whether required parameters exist
if [ -z ${VIASH_PAR_INPUT+x} ]; then
ViashError '--input' is a required argument. Use "--help" to get more information on the parameters.
exit 1
fi
if [ -z ${VIASH_PAR_INPUT_BAI+x} ]; then
ViashError '--input_bai' is a required argument. Use "--help" to get more information on the parameters.
exit 1
fi
if [ -z ${VIASH_PAR_REF+x} ]; then
ViashError '--ref' is a required argument. Use "--help" to get more information on the parameters.
exit 1
fi
if [ -z ${VIASH_PAR_OUT+x} ]; then
ViashError '--out' 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_NO_BAQ+x} ]; then
VIASH_PAR_NO_BAQ="false"
fi
if [ -z ${VIASH_PAR_NO_IDAQ+x} ]; then
VIASH_PAR_NO_IDAQ="false"
fi
if [ -z ${VIASH_PAR_DEL_BAQ+x} ]; then
VIASH_PAR_DEL_BAQ="false"
fi
if [ -z ${VIASH_PAR_NO_EXT_BAQ+x} ]; then
VIASH_PAR_NO_EXT_BAQ="false"
fi
if [ -z ${VIASH_PAR_NO_MQ+x} ]; then
VIASH_PAR_NO_MQ="false"
fi
if [ -z ${VIASH_PAR_CALL_INDELS+x} ]; then
VIASH_PAR_CALL_INDELS="false"
fi
if [ -z ${VIASH_PAR_ONLY_INDELS+x} ]; then
VIASH_PAR_ONLY_INDELS="false"
fi
if [ -z ${VIASH_PAR_SRC_QUAL+x} ]; then
VIASH_PAR_SRC_QUAL="false"
fi
if [ -z ${VIASH_PAR_ILLUMINA_13+x} ]; then
VIASH_PAR_ILLUMINA_13="false"
fi
if [ -z ${VIASH_PAR_USE_ORPHAN+x} ]; then
VIASH_PAR_USE_ORPHAN="false"
fi
if [ -z ${VIASH_PAR_PLP_SUMMARY_ONLY+x} ]; then
VIASH_PAR_PLP_SUMMARY_ONLY="false"
fi
if [ -z ${VIASH_PAR_NO_DEFAULT_FILTER+x} ]; then
VIASH_PAR_NO_DEFAULT_FILTER="false"
fi
if [ -z ${VIASH_PAR_FORCE_OVERWRITE+x} ]; then
VIASH_PAR_FORCE_OVERWRITE="false"
fi
if [ -z ${VIASH_PAR_VERBOSE+x} ]; then
VIASH_PAR_VERBOSE="false"
fi
if [ -z ${VIASH_PAR_DEBUG+x} ]; then
VIASH_PAR_DEBUG="false"
fi
# check whether required files exist
if [ ! -z "$VIASH_PAR_INPUT" ] && [ ! -e "$VIASH_PAR_INPUT" ]; then
ViashError "Input file '$VIASH_PAR_INPUT' does not exist."
exit 1
fi
if [ ! -z "$VIASH_PAR_INPUT_BAI" ] && [ ! -e "$VIASH_PAR_INPUT_BAI" ]; then
ViashError "Input file '$VIASH_PAR_INPUT_BAI' does not exist."
exit 1
fi
if [ ! -z "$VIASH_PAR_REF" ] && [ ! -e "$VIASH_PAR_REF" ]; then
ViashError "Input file '$VIASH_PAR_REF' does not exist."
exit 1
fi
if [ ! -z "$VIASH_PAR_BED" ] && [ ! -e "$VIASH_PAR_BED" ]; then
ViashError "Input file '$VIASH_PAR_BED' does not exist."
exit 1
fi
if [ ! -z "$VIASH_PAR_IGN_VCF" ] && [ ! -e "$VIASH_PAR_IGN_VCF" ]; then
ViashError "Input file '$VIASH_PAR_IGN_VCF' does not exist."
exit 1
fi
# check whether parameters values are of the right type
if [[ -n "$VIASH_PAR_MIN_BQ" ]]; then
if ! [[ "$VIASH_PAR_MIN_BQ" =~ ^[-+]?[0-9]+$ ]]; then
ViashError '--min_bq' has to be an integer. Use "--help" to get more information on the parameters.
exit 1
fi
fi
if [[ -n "$VIASH_PAR_MIN_ALT_BQ" ]]; then
if ! [[ "$VIASH_PAR_MIN_ALT_BQ" =~ ^[-+]?[0-9]+$ ]]; then
ViashError '--min_alt_bq' has to be an integer. Use "--help" to get more information on the parameters.
exit 1
fi
fi
if [[ -n "$VIASH_PAR_DEF_ALT_BQ" ]]; then
if ! [[ "$VIASH_PAR_DEF_ALT_BQ" =~ ^[-+]?[0-9]+$ ]]; then
ViashError '--def_alt_bq' has to be an integer. Use "--help" to get more information on the parameters.
exit 1
fi
fi
if [[ -n "$VIASH_PAR_MIN_JQ" ]]; then
if ! [[ "$VIASH_PAR_MIN_JQ" =~ ^[-+]?[0-9]+$ ]]; then
ViashError '--min_jq' has to be an integer. Use "--help" to get more information on the parameters.
exit 1
fi
fi
if [[ -n "$VIASH_PAR_MIN_ALT_JQ" ]]; then
if ! [[ "$VIASH_PAR_MIN_ALT_JQ" =~ ^[-+]?[0-9]+$ ]]; then
ViashError '--min_alt_jq' has to be an integer. Use "--help" to get more information on the parameters.
exit 1
fi
fi
if [[ -n "$VIASH_PAR_DEF_ALT_JQ" ]]; then
if ! [[ "$VIASH_PAR_DEF_ALT_JQ" =~ ^[-+]?[0-9]+$ ]]; then
ViashError '--def_alt_jq' has to be an integer. Use "--help" to get more information on the parameters.
exit 1
fi
fi
if [[ -n "$VIASH_PAR_NO_BAQ" ]]; then
if ! [[ "$VIASH_PAR_NO_BAQ" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then
ViashError '--no_baq' has to be a boolean_true. Use "--help" to get more information on the parameters.
exit 1
fi
fi
if [[ -n "$VIASH_PAR_NO_IDAQ" ]]; then
if ! [[ "$VIASH_PAR_NO_IDAQ" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then
ViashError '--no_idaq' has to be a boolean_true. Use "--help" to get more information on the parameters.
exit 1
fi
fi
if [[ -n "$VIASH_PAR_DEL_BAQ" ]]; then
if ! [[ "$VIASH_PAR_DEL_BAQ" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then
ViashError '--del_baq' has to be a boolean_true. Use "--help" to get more information on the parameters.
exit 1
fi
fi
if [[ -n "$VIASH_PAR_NO_EXT_BAQ" ]]; then
if ! [[ "$VIASH_PAR_NO_EXT_BAQ" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then
ViashError '--no_ext_baq' has to be a boolean_true. Use "--help" to get more information on the parameters.
exit 1
fi
fi
if [[ -n "$VIASH_PAR_MIN_MQ" ]]; then
if ! [[ "$VIASH_PAR_MIN_MQ" =~ ^[-+]?[0-9]+$ ]]; then
ViashError '--min_mq' has to be an integer. Use "--help" to get more information on the parameters.
exit 1
fi
fi
if [[ -n "$VIASH_PAR_MAX_MQ" ]]; then
if ! [[ "$VIASH_PAR_MAX_MQ" =~ ^[-+]?[0-9]+$ ]]; then
ViashError '--max_mq' has to be an integer. Use "--help" to get more information on the parameters.
exit 1
fi
fi
if [[ -n "$VIASH_PAR_NO_MQ" ]]; then
if ! [[ "$VIASH_PAR_NO_MQ" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then
ViashError '--no_mq' has to be a boolean_true. Use "--help" to get more information on the parameters.
exit 1
fi
fi
if [[ -n "$VIASH_PAR_CALL_INDELS" ]]; then
if ! [[ "$VIASH_PAR_CALL_INDELS" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then
ViashError '--call_indels' has to be a boolean_true. Use "--help" to get more information on the parameters.
exit 1
fi
fi
if [[ -n "$VIASH_PAR_ONLY_INDELS" ]]; then
if ! [[ "$VIASH_PAR_ONLY_INDELS" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then
ViashError '--only_indels' has to be a boolean_true. Use "--help" to get more information on the parameters.
exit 1
fi
fi
if [[ -n "$VIASH_PAR_SRC_QUAL" ]]; then
if ! [[ "$VIASH_PAR_SRC_QUAL" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then
ViashError '--src_qual' has to be a boolean_true. Use "--help" to get more information on the parameters.
exit 1
fi
fi
if [[ -n "$VIASH_PAR_DEF_NM_Q" ]]; then
if ! [[ "$VIASH_PAR_DEF_NM_Q" =~ ^[-+]?[0-9]+$ ]]; then
ViashError '--def_nm_q' has to be an integer. Use "--help" to get more information on the parameters.
exit 1
fi
fi
if [[ -n "$VIASH_PAR_SIG" ]]; then
if ! [[ "$VIASH_PAR_SIG" =~ ^[-+]?(\.[0-9]+|[0-9]+(\.[0-9]*)?)([eE][-+]?[0-9]+)?$ ]]; then
ViashError '--sig' has to be a double. Use "--help" to get more information on the parameters.
exit 1
fi
fi
if [[ -n "$VIASH_PAR_MIN_COV" ]]; then
if ! [[ "$VIASH_PAR_MIN_COV" =~ ^[-+]?[0-9]+$ ]]; then
ViashError '--min_cov' has to be an integer. Use "--help" to get more information on the parameters.
exit 1
fi
fi
if [[ -n "$VIASH_PAR_MAX_DEPTH" ]]; then
if ! [[ "$VIASH_PAR_MAX_DEPTH" =~ ^[-+]?[0-9]+$ ]]; then
ViashError '--max_depth' has to be an integer. Use "--help" to get more information on the parameters.
exit 1
fi
fi
if [[ -n "$VIASH_PAR_ILLUMINA_13" ]]; then
if ! [[ "$VIASH_PAR_ILLUMINA_13" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then
ViashError '--illumina_13' has to be a boolean_true. Use "--help" to get more information on the parameters.
exit 1
fi
fi
if [[ -n "$VIASH_PAR_USE_ORPHAN" ]]; then
if ! [[ "$VIASH_PAR_USE_ORPHAN" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then
ViashError '--use_orphan' has to be a boolean_true. Use "--help" to get more information on the parameters.
exit 1
fi
fi
if [[ -n "$VIASH_PAR_PLP_SUMMARY_ONLY" ]]; then
if ! [[ "$VIASH_PAR_PLP_SUMMARY_ONLY" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then
ViashError '--plp_summary_only' has to be a boolean_true. Use "--help" to get more information on the parameters.
exit 1
fi
fi
if [[ -n "$VIASH_PAR_NO_DEFAULT_FILTER" ]]; then
if ! [[ "$VIASH_PAR_NO_DEFAULT_FILTER" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then
ViashError '--no_default_filter' has to be a boolean_true. Use "--help" to get more information on the parameters.
exit 1
fi
fi
if [[ -n "$VIASH_PAR_FORCE_OVERWRITE" ]]; then
if ! [[ "$VIASH_PAR_FORCE_OVERWRITE" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then
ViashError '--force_overwrite' has to be a boolean_true. Use "--help" to get more information on the parameters.
exit 1
fi
fi
if [[ -n "$VIASH_PAR_VERBOSE" ]]; then
if ! [[ "$VIASH_PAR_VERBOSE" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then
ViashError '--verbose' has to be a boolean_true. Use "--help" to get more information on the parameters.
exit 1
fi
fi
if [[ -n "$VIASH_PAR_DEBUG" ]]; then
if ! [[ "$VIASH_PAR_DEBUG" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then
ViashError '--debug' 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
# create parent directories of output files, if so desired
if [ ! -z "$VIASH_PAR_OUT" ] && [ ! -d "$(dirname "$VIASH_PAR_OUT")" ]; then
mkdir -p "$(dirname "$VIASH_PAR_OUT")"
fi
if [ "$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 "$VIASH_PAR_INPUT" ]; then
VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$VIASH_PAR_INPUT")" )
VIASH_PAR_INPUT=$(ViashDockerAutodetectMount "$VIASH_PAR_INPUT")
fi
if [ ! -z "$VIASH_PAR_INPUT_BAI" ]; then
VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$VIASH_PAR_INPUT_BAI")" )
VIASH_PAR_INPUT_BAI=$(ViashDockerAutodetectMount "$VIASH_PAR_INPUT_BAI")
fi
if [ ! -z "$VIASH_PAR_REF" ]; then
VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$VIASH_PAR_REF")" )
VIASH_PAR_REF=$(ViashDockerAutodetectMount "$VIASH_PAR_REF")
fi
if [ ! -z "$VIASH_PAR_OUT" ]; then
VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$VIASH_PAR_OUT")" )
VIASH_PAR_OUT=$(ViashDockerAutodetectMount "$VIASH_PAR_OUT")
VIASH_CHOWN_VARS+=( "$VIASH_PAR_OUT" )
fi
if [ ! -z "$VIASH_PAR_BED" ]; then
VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$VIASH_PAR_BED")" )
VIASH_PAR_BED=$(ViashDockerAutodetectMount "$VIASH_PAR_BED")
fi
if [ ! -z "$VIASH_PAR_IGN_VCF" ]; then
VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$VIASH_PAR_IGN_VCF")" )
VIASH_PAR_IGN_VCF=$(ViashDockerAutodetectMount "$VIASH_PAR_IGN_VCF")
fi
if [ ! -z "$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-lofreq_call-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 ${VIASH_PAR_INPUT_BAI+x} ]; then echo "${VIASH_PAR_INPUT_BAI}" | sed "s#'#'\"'\"'#g;s#.*#par_input_bai='&'#" ; else echo "# par_input_bai="; 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 ${VIASH_PAR_OUT+x} ]; then echo "${VIASH_PAR_OUT}" | sed "s#'#'\"'\"'#g;s#.*#par_out='&'#" ; else echo "# par_out="; fi )
$( if [ ! -z ${VIASH_PAR_REGION+x} ]; then echo "${VIASH_PAR_REGION}" | sed "s#'#'\"'\"'#g;s#.*#par_region='&'#" ; else echo "# par_region="; fi )
$( if [ ! -z ${VIASH_PAR_BED+x} ]; then echo "${VIASH_PAR_BED}" | sed "s#'#'\"'\"'#g;s#.*#par_bed='&'#" ; else echo "# par_bed="; fi )
$( if [ ! -z ${VIASH_PAR_MIN_BQ+x} ]; then echo "${VIASH_PAR_MIN_BQ}" | sed "s#'#'\"'\"'#g;s#.*#par_min_bq='&'#" ; else echo "# par_min_bq="; fi )
$( if [ ! -z ${VIASH_PAR_MIN_ALT_BQ+x} ]; then echo "${VIASH_PAR_MIN_ALT_BQ}" | sed "s#'#'\"'\"'#g;s#.*#par_min_alt_bq='&'#" ; else echo "# par_min_alt_bq="; fi )
$( if [ ! -z ${VIASH_PAR_DEF_ALT_BQ+x} ]; then echo "${VIASH_PAR_DEF_ALT_BQ}" | sed "s#'#'\"'\"'#g;s#.*#par_def_alt_bq='&'#" ; else echo "# par_def_alt_bq="; fi )
$( if [ ! -z ${VIASH_PAR_MIN_JQ+x} ]; then echo "${VIASH_PAR_MIN_JQ}" | sed "s#'#'\"'\"'#g;s#.*#par_min_jq='&'#" ; else echo "# par_min_jq="; fi )
$( if [ ! -z ${VIASH_PAR_MIN_ALT_JQ+x} ]; then echo "${VIASH_PAR_MIN_ALT_JQ}" | sed "s#'#'\"'\"'#g;s#.*#par_min_alt_jq='&'#" ; else echo "# par_min_alt_jq="; fi )
$( if [ ! -z ${VIASH_PAR_DEF_ALT_JQ+x} ]; then echo "${VIASH_PAR_DEF_ALT_JQ}" | sed "s#'#'\"'\"'#g;s#.*#par_def_alt_jq='&'#" ; else echo "# par_def_alt_jq="; fi )
$( if [ ! -z ${VIASH_PAR_NO_BAQ+x} ]; then echo "${VIASH_PAR_NO_BAQ}" | sed "s#'#'\"'\"'#g;s#.*#par_no_baq='&'#" ; else echo "# par_no_baq="; fi )
$( if [ ! -z ${VIASH_PAR_NO_IDAQ+x} ]; then echo "${VIASH_PAR_NO_IDAQ}" | sed "s#'#'\"'\"'#g;s#.*#par_no_idaq='&'#" ; else echo "# par_no_idaq="; fi )
$( if [ ! -z ${VIASH_PAR_DEL_BAQ+x} ]; then echo "${VIASH_PAR_DEL_BAQ}" | sed "s#'#'\"'\"'#g;s#.*#par_del_baq='&'#" ; else echo "# par_del_baq="; fi )
$( if [ ! -z ${VIASH_PAR_NO_EXT_BAQ+x} ]; then echo "${VIASH_PAR_NO_EXT_BAQ}" | sed "s#'#'\"'\"'#g;s#.*#par_no_ext_baq='&'#" ; else echo "# par_no_ext_baq="; fi )
$( if [ ! -z ${VIASH_PAR_MIN_MQ+x} ]; then echo "${VIASH_PAR_MIN_MQ}" | sed "s#'#'\"'\"'#g;s#.*#par_min_mq='&'#" ; else echo "# par_min_mq="; fi )
$( if [ ! -z ${VIASH_PAR_MAX_MQ+x} ]; then echo "${VIASH_PAR_MAX_MQ}" | sed "s#'#'\"'\"'#g;s#.*#par_max_mq='&'#" ; else echo "# par_max_mq="; fi )
$( if [ ! -z ${VIASH_PAR_NO_MQ+x} ]; then echo "${VIASH_PAR_NO_MQ}" | sed "s#'#'\"'\"'#g;s#.*#par_no_mq='&'#" ; else echo "# par_no_mq="; fi )
$( if [ ! -z ${VIASH_PAR_CALL_INDELS+x} ]; then echo "${VIASH_PAR_CALL_INDELS}" | sed "s#'#'\"'\"'#g;s#.*#par_call_indels='&'#" ; else echo "# par_call_indels="; fi )
$( if [ ! -z ${VIASH_PAR_ONLY_INDELS+x} ]; then echo "${VIASH_PAR_ONLY_INDELS}" | sed "s#'#'\"'\"'#g;s#.*#par_only_indels='&'#" ; else echo "# par_only_indels="; fi )
$( if [ ! -z ${VIASH_PAR_SRC_QUAL+x} ]; then echo "${VIASH_PAR_SRC_QUAL}" | sed "s#'#'\"'\"'#g;s#.*#par_src_qual='&'#" ; else echo "# par_src_qual="; fi )
$( if [ ! -z ${VIASH_PAR_IGN_VCF+x} ]; then echo "${VIASH_PAR_IGN_VCF}" | sed "s#'#'\"'\"'#g;s#.*#par_ign_vcf='&'#" ; else echo "# par_ign_vcf="; fi )
$( if [ ! -z ${VIASH_PAR_DEF_NM_Q+x} ]; then echo "${VIASH_PAR_DEF_NM_Q}" | sed "s#'#'\"'\"'#g;s#.*#par_def_nm_q='&'#" ; else echo "# par_def_nm_q="; fi )
$( if [ ! -z ${VIASH_PAR_SIG+x} ]; then echo "${VIASH_PAR_SIG}" | sed "s#'#'\"'\"'#g;s#.*#par_sig='&'#" ; else echo "# par_sig="; fi )
$( if [ ! -z ${VIASH_PAR_BONF+x} ]; then echo "${VIASH_PAR_BONF}" | sed "s#'#'\"'\"'#g;s#.*#par_bonf='&'#" ; else echo "# par_bonf="; fi )
$( if [ ! -z ${VIASH_PAR_MIN_COV+x} ]; then echo "${VIASH_PAR_MIN_COV}" | sed "s#'#'\"'\"'#g;s#.*#par_min_cov='&'#" ; else echo "# par_min_cov="; fi )
$( if [ ! -z ${VIASH_PAR_MAX_DEPTH+x} ]; then echo "${VIASH_PAR_MAX_DEPTH}" | sed "s#'#'\"'\"'#g;s#.*#par_max_depth='&'#" ; else echo "# par_max_depth="; fi )
$( if [ ! -z ${VIASH_PAR_ILLUMINA_13+x} ]; then echo "${VIASH_PAR_ILLUMINA_13}" | sed "s#'#'\"'\"'#g;s#.*#par_illumina_13='&'#" ; else echo "# par_illumina_13="; fi )
$( if [ ! -z ${VIASH_PAR_USE_ORPHAN+x} ]; then echo "${VIASH_PAR_USE_ORPHAN}" | sed "s#'#'\"'\"'#g;s#.*#par_use_orphan='&'#" ; else echo "# par_use_orphan="; fi )
$( if [ ! -z ${VIASH_PAR_PLP_SUMMARY_ONLY+x} ]; then echo "${VIASH_PAR_PLP_SUMMARY_ONLY}" | sed "s#'#'\"'\"'#g;s#.*#par_plp_summary_only='&'#" ; else echo "# par_plp_summary_only="; fi )
$( if [ ! -z ${VIASH_PAR_NO_DEFAULT_FILTER+x} ]; then echo "${VIASH_PAR_NO_DEFAULT_FILTER}" | sed "s#'#'\"'\"'#g;s#.*#par_no_default_filter='&'#" ; else echo "# par_no_default_filter="; fi )
$( if [ ! -z ${VIASH_PAR_FORCE_OVERWRITE+x} ]; then echo "${VIASH_PAR_FORCE_OVERWRITE}" | sed "s#'#'\"'\"'#g;s#.*#par_force_overwrite='&'#" ; else echo "# par_force_overwrite="; fi )
$( if [ ! -z ${VIASH_PAR_VERBOSE+x} ]; then echo "${VIASH_PAR_VERBOSE}" | sed "s#'#'\"'\"'#g;s#.*#par_verbose='&'#" ; else echo "# par_verbose="; fi )
$( if [ ! -z ${VIASH_PAR_DEBUG+x} ]; then echo "${VIASH_PAR_DEBUG}" | sed "s#'#'\"'\"'#g;s#.*#par_debug='&'#" ; else echo "# par_debug="; fi )
$( if [ ! -z ${VIASH_META_NAME+x} ]; then echo "${VIASH_META_NAME}" | sed "s#'#'\"'\"'#g;s#.*#meta_name='&'#" ; else echo "# meta_name="; fi )
$( if [ ! -z ${VIASH_META_FUNCTIONALITY_NAME+x} ]; then echo "${VIASH_META_FUNCTIONALITY_NAME}" | sed "s#'#'\"'\"'#g;s#.*#meta_functionality_name='&'#" ; else echo "# meta_functionality_name="; fi )
$( if [ ! -z ${VIASH_META_RESOURCES_DIR+x} ]; then echo "${VIASH_META_RESOURCES_DIR}" | sed "s#'#'\"'\"'#g;s#.*#meta_resources_dir='&'#" ; else echo "# meta_resources_dir="; fi )
$( if [ ! -z ${VIASH_META_EXECUTABLE+x} ]; then echo "${VIASH_META_EXECUTABLE}" | sed "s#'#'\"'\"'#g;s#.*#meta_executable='&'#" ; else echo "# meta_executable="; fi )
$( if [ ! -z ${VIASH_META_CONFIG+x} ]; then echo "${VIASH_META_CONFIG}" | sed "s#'#'\"'\"'#g;s#.*#meta_config='&'#" ; else echo "# meta_config="; fi )
$( if [ ! -z ${VIASH_META_TEMP_DIR+x} ]; then echo "${VIASH_META_TEMP_DIR}" | sed "s#'#'\"'\"'#g;s#.*#meta_temp_dir='&'#" ; else echo "# meta_temp_dir="; fi )
$( if [ ! -z ${VIASH_META_CPUS+x} ]; then echo "${VIASH_META_CPUS}" | sed "s#'#'\"'\"'#g;s#.*#meta_cpus='&'#" ; else echo "# meta_cpus="; fi )
$( if [ ! -z ${VIASH_META_MEMORY_B+x} ]; then echo "${VIASH_META_MEMORY_B}" | sed "s#'#'\"'\"'#g;s#.*#meta_memory_b='&'#" ; else echo "# meta_memory_b="; fi )
$( if [ ! -z ${VIASH_META_MEMORY_KB+x} ]; then echo "${VIASH_META_MEMORY_KB}" | sed "s#'#'\"'\"'#g;s#.*#meta_memory_kb='&'#" ; else echo "# meta_memory_kb="; fi )
$( if [ ! -z ${VIASH_META_MEMORY_MB+x} ]; then echo "${VIASH_META_MEMORY_MB}" | sed "s#'#'\"'\"'#g;s#.*#meta_memory_mb='&'#" ; else echo "# meta_memory_mb="; fi )
$( if [ ! -z ${VIASH_META_MEMORY_GB+x} ]; then echo "${VIASH_META_MEMORY_GB}" | sed "s#'#'\"'\"'#g;s#.*#meta_memory_gb='&'#" ; else echo "# meta_memory_gb="; fi )
$( if [ ! -z ${VIASH_META_MEMORY_TB+x} ]; then echo "${VIASH_META_MEMORY_TB}" | sed "s#'#'\"'\"'#g;s#.*#meta_memory_tb='&'#" ; else echo "# meta_memory_tb="; fi )
$( if [ ! -z ${VIASH_META_MEMORY_PB+x} ]; then echo "${VIASH_META_MEMORY_PB}" | sed "s#'#'\"'\"'#g;s#.*#meta_memory_pb='&'#" ; else echo "# meta_memory_pb="; fi )
$( if [ ! -z ${VIASH_META_MEMORY_KIB+x} ]; then echo "${VIASH_META_MEMORY_KIB}" | sed "s#'#'\"'\"'#g;s#.*#meta_memory_kib='&'#" ; else echo "# meta_memory_kib="; fi )
$( if [ ! -z ${VIASH_META_MEMORY_MIB+x} ]; then echo "${VIASH_META_MEMORY_MIB}" | sed "s#'#'\"'\"'#g;s#.*#meta_memory_mib='&'#" ; else echo "# meta_memory_mib="; fi )
$( if [ ! -z ${VIASH_META_MEMORY_GIB+x} ]; then echo "${VIASH_META_MEMORY_GIB}" | sed "s#'#'\"'\"'#g;s#.*#meta_memory_gib='&'#" ; else echo "# meta_memory_gib="; fi )
$( if [ ! -z ${VIASH_META_MEMORY_TIB+x} ]; then echo "${VIASH_META_MEMORY_TIB}" | sed "s#'#'\"'\"'#g;s#.*#meta_memory_tib='&'#" ; else echo "# meta_memory_tib="; fi )
$( if [ ! -z ${VIASH_META_MEMORY_PIB+x} ]; then echo "${VIASH_META_MEMORY_PIB}" | sed "s#'#'\"'\"'#g;s#.*#meta_memory_pib='&'#" ; else echo "# meta_memory_pib="; fi )
## VIASH END
# Unset all parameters that are set to "false"
unset_if_false=(
par_no_baq
par_no_idaq
par_del_baq
par_no_ext_baq
par_no_mq
par_call_indels
par_only_indels
par_src_qual
par_illumina_13
par_use_orphan
par_plp_summary_only
par_no_default_filter
par_force_overwrite
par_verbose
par_debug
)
for par in \${unset_if_false[@]}; do
test_val="\${!par}"
[[ "\$test_val" == "false" ]] && unset \$par
done
# Run lofreq call
lofreq call \\
-f "\$par_ref" \\
-o "\$par_out" \\
\${par_region:+-r "\${par_region}"} \\
\${par_bed:+-l "\${par_bed}"} \\
\${par_min_bq:+-q "\${par_min_bq}"} \\
\${par_min_alt_bq:+-Q "\${par_min_alt_bq}"} \\
\${par_def_alt_bq:+-R "\${par_def_alt_bq}"} \\
\${par_min_jq:+-j "\${par_min_jq}"} \\
\${par_alt_jq:+-K "\${par_alt_jq}"} \\
\${par_no_baq:+-B} \\
\${par_no_idaq:+-A} \\
\${par_del_baq:+-D} \\
\${par_no_ext_baq:+-e} \\
\${par_min_mq:+-m "\${par_min_mq}"} \\
\${par_max_mq:+-M "\${par_max_mq}"} \\
\${par_no_mq:+-N} \\
\${par_call_indels:+--call-indels} \\
\${par_only_indels:+--only-indels} \\
\${par_src_qual:+-s} \\
\${par_ign_vcf:+-S "\${par_ign_vcf}"} \\
\${par_def_nm_q:+-T "\${par_def_nm_q}"} \\
\${par_sig:+-a "\${par_sig}"} \\
\${par_bonf:+-b "\${par_bonf}"} \\
\${par_min_cov:+-C "\${par_min_cov}"} \\
\${par_max_depth:+-d "\${par_max_depth}"} \\
\${par_illumina_13:+--illumina-1.3} \\
\${par_use_orphan:+--use-orphan} \\
\${par_plp_summary_only:+--plp-summary-only} \\
\${par_no_default_filter:+--no-default-filter} \\
\${par_force_overwrite:+--force-overwrite} \\
\${par_verbose:+--verbose} \\
\${par_debug:+--debug} \\
"\$par_input"
VIASHMAIN
bash "\$tempscript" &
wait "\$!"
VIASHEOF
if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then
# strip viash automount from file paths
if [ ! -z "$VIASH_PAR_INPUT" ]; then
VIASH_PAR_INPUT=$(ViashDockerStripAutomount "$VIASH_PAR_INPUT")
fi
if [ ! -z "$VIASH_PAR_INPUT_BAI" ]; then
VIASH_PAR_INPUT_BAI=$(ViashDockerStripAutomount "$VIASH_PAR_INPUT_BAI")
fi
if [ ! -z "$VIASH_PAR_REF" ]; then
VIASH_PAR_REF=$(ViashDockerStripAutomount "$VIASH_PAR_REF")
fi
if [ ! -z "$VIASH_PAR_OUT" ]; then
VIASH_PAR_OUT=$(ViashDockerStripAutomount "$VIASH_PAR_OUT")
fi
if [ ! -z "$VIASH_PAR_BED" ]; then
VIASH_PAR_BED=$(ViashDockerStripAutomount "$VIASH_PAR_BED")
fi
if [ ! -z "$VIASH_PAR_IGN_VCF" ]; then
VIASH_PAR_IGN_VCF=$(ViashDockerStripAutomount "$VIASH_PAR_IGN_VCF")
fi
if [ ! -z "$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_OUT" ] && [ ! -e "$VIASH_PAR_OUT" ]; then
ViashError "Output file '$VIASH_PAR_OUT' does not exist."
exit 1
fi
exit 0
Reference in New Issue View Git Blame Copy Permalink