CI
99b76ba2a1
Build pipeline: viash-hub.biobox.main-dqhhg
Source commit: 237a2e3a22
Source message: Fixes the typo raised in issue #132 (#157)
* Fixes the typo raised in issue #132
* Add changelog entry
* fix typo, modify script
---------
Co-authored-by: jakubmajercik <jakub.majercik@gmail.com>
3924 lines
197 KiB
Bash
Executable File
3924 lines
197 KiB
Bash
Executable File
#!/usr/bin/env bash
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# salmon_quant main
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#
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# This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative
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# work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
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# Intuitive.
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#
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# The component may contain files which fall under a different license. The
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# authors of this component should specify the license in the header of such
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# files, or include a separate license file detailing the licenses of all included
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# files.
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#
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# Component authors:
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# * Sai Nirmayi Yasa (author, maintainer)
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set -e
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if [ -z "$VIASH_TEMP" ]; then
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VIASH_TEMP=${VIASH_TEMP:-$VIASH_TMPDIR}
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VIASH_TEMP=${VIASH_TEMP:-$VIASH_TEMPDIR}
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VIASH_TEMP=${VIASH_TEMP:-$VIASH_TMP}
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VIASH_TEMP=${VIASH_TEMP:-$TMPDIR}
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VIASH_TEMP=${VIASH_TEMP:-$TMP}
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VIASH_TEMP=${VIASH_TEMP:-$TEMPDIR}
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VIASH_TEMP=${VIASH_TEMP:-$TEMP}
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VIASH_TEMP=${VIASH_TEMP:-/tmp}
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fi
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# define helper functions
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# ViashQuote: put quotes around non flag values
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# $1 : unquoted string
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# return : possibly quoted string
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# examples:
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# ViashQuote --foo # returns --foo
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# ViashQuote bar # returns 'bar'
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# Viashquote --foo=bar # returns --foo='bar'
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function ViashQuote {
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if [[ "$1" =~ ^-+[a-zA-Z0-9_\-]+=.+$ ]]; then
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echo "$1" | sed "s#=\(.*\)#='\1'#"
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elif [[ "$1" =~ ^-+[a-zA-Z0-9_\-]+$ ]]; then
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echo "$1"
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else
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echo "'$1'"
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fi
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}
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# ViashRemoveFlags: Remove leading flag
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# $1 : string with a possible leading flag
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# return : string without possible leading flag
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# examples:
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# ViashRemoveFlags --foo=bar # returns bar
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function ViashRemoveFlags {
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echo "$1" | sed 's/^--*[a-zA-Z0-9_\-]*=//'
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}
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# ViashSourceDir: return the path of a bash file, following symlinks
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# usage : ViashSourceDir ${BASH_SOURCE[0]}
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# $1 : Should always be set to ${BASH_SOURCE[0]}
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# returns : The absolute path of the bash file
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function ViashSourceDir {
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local source="$1"
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while [ -h "$source" ]; do
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local dir="$( cd -P "$( dirname "$source" )" >/dev/null 2>&1 && pwd )"
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source="$(readlink "$source")"
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[[ $source != /* ]] && source="$dir/$source"
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done
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cd -P "$( dirname "$source" )" >/dev/null 2>&1 && pwd
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}
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# ViashFindTargetDir: return the path of the '.build.yaml' file, following symlinks
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# usage : ViashFindTargetDir 'ScriptPath'
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# $1 : The location from where to start the upward search
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# returns : The absolute path of the '.build.yaml' file
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function ViashFindTargetDir {
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local source="$1"
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while [[ "$source" != "" && ! -e "$source/.build.yaml" ]]; do
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source=${source%/*}
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done
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echo $source
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}
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# see https://en.wikipedia.org/wiki/Syslog#Severity_level
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VIASH_LOGCODE_EMERGENCY=0
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VIASH_LOGCODE_ALERT=1
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VIASH_LOGCODE_CRITICAL=2
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VIASH_LOGCODE_ERROR=3
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VIASH_LOGCODE_WARNING=4
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VIASH_LOGCODE_NOTICE=5
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VIASH_LOGCODE_INFO=6
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VIASH_LOGCODE_DEBUG=7
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VIASH_VERBOSITY=$VIASH_LOGCODE_NOTICE
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# ViashLog: Log events depending on the verbosity level
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# usage: ViashLog 1 alert Oh no something went wrong!
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# $1: required verbosity level
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# $2: display tag
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# $3+: messages to display
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# stdout: Your input, prepended by '[$2] '.
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function ViashLog {
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local required_level="$1"
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local display_tag="$2"
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shift 2
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if [ $VIASH_VERBOSITY -ge $required_level ]; then
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>&2 echo "[$display_tag]" "$@"
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fi
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}
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# ViashEmergency: log events when the system is unstable
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# usage: ViashEmergency Oh no something went wrong.
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# stdout: Your input, prepended by '[emergency] '.
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function ViashEmergency {
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ViashLog $VIASH_LOGCODE_EMERGENCY emergency "$@"
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}
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# ViashAlert: log events when actions must be taken immediately (e.g. corrupted system database)
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# usage: ViashAlert Oh no something went wrong.
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# stdout: Your input, prepended by '[alert] '.
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function ViashAlert {
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ViashLog $VIASH_LOGCODE_ALERT alert "$@"
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}
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# ViashCritical: log events when a critical condition occurs
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# usage: ViashCritical Oh no something went wrong.
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# stdout: Your input, prepended by '[critical] '.
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function ViashCritical {
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ViashLog $VIASH_LOGCODE_CRITICAL critical "$@"
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}
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# ViashError: log events when an error condition occurs
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# usage: ViashError Oh no something went wrong.
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# stdout: Your input, prepended by '[error] '.
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function ViashError {
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ViashLog $VIASH_LOGCODE_ERROR error "$@"
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}
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# ViashWarning: log potentially abnormal events
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# usage: ViashWarning Something may have gone wrong.
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# stdout: Your input, prepended by '[warning] '.
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function ViashWarning {
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ViashLog $VIASH_LOGCODE_WARNING warning "$@"
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}
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# ViashNotice: log significant but normal events
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# usage: ViashNotice This just happened.
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# stdout: Your input, prepended by '[notice] '.
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function ViashNotice {
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ViashLog $VIASH_LOGCODE_NOTICE notice "$@"
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}
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# ViashInfo: log normal events
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# usage: ViashInfo This just happened.
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# stdout: Your input, prepended by '[info] '.
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function ViashInfo {
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ViashLog $VIASH_LOGCODE_INFO info "$@"
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}
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# ViashDebug: log all events, for debugging purposes
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# usage: ViashDebug This just happened.
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# stdout: Your input, prepended by '[debug] '.
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function ViashDebug {
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ViashLog $VIASH_LOGCODE_DEBUG debug "$@"
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}
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# find source folder of this component
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VIASH_META_RESOURCES_DIR=`ViashSourceDir ${BASH_SOURCE[0]}`
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# find the root of the built components & dependencies
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VIASH_TARGET_DIR=`ViashFindTargetDir $VIASH_META_RESOURCES_DIR`
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# define meta fields
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VIASH_META_NAME="salmon_quant"
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VIASH_META_FUNCTIONALITY_NAME="salmon_quant"
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VIASH_META_EXECUTABLE="$VIASH_META_RESOURCES_DIR/$VIASH_META_NAME"
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VIASH_META_CONFIG="$VIASH_META_RESOURCES_DIR/.config.vsh.yaml"
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VIASH_META_TEMP_DIR="$VIASH_TEMP"
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# ViashHelp: Display helpful explanation about this executable
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function ViashHelp {
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echo "salmon_quant main"
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echo ""
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echo "Salmon is a tool for wicked-fast transcript quantification from RNA-seq data. It"
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echo "can either make use of pre-computed alignments (in the form of a SAM/BAM file)"
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echo "to the transcripts rather than the raw reads, or can be run in the mapping-based"
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echo "mode."
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echo ""
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echo "Common input options:"
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echo " -l, --lib_type"
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echo " type: string"
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echo " default: A"
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echo " choices: [ A, U, SF, SR, IU, IS, ISF, ISR, OU, OS, OSF, OSR, MU, MS,"
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echo "MSF, MSR ]"
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echo " Format string describing the library."
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echo " The library type string consists of three parts:"
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echo " 1. Relative orientation of the reads: This part is only provided if the"
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echo " library is paired-end, The possible options are"
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echo " I = inward"
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echo " O = outward"
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echo " M = matching"
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echo " 2. Strandedness of the library: This part specifies whether the protocol"
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echo " is stranded or unstranded. The options are:"
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echo " S = stranded"
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echo " U = unstranded"
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echo " 3. Directionality of the reads: If the library is stranded, the final"
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echo " part of the library string is used to specify the strand from which the"
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echo " read originates. The possible values are"
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echo " F = read 1 (or single-end read) comes from the forward strand"
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echo " R = read 1 (or single-end read) comes from the reverse strand"
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echo ""
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echo "Mapping input options:"
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echo " -i, --index"
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echo " type: file, file must exist"
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echo " example: transcriptome_index"
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echo " Salmon index."
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echo ""
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echo " -r, --unmated_reads"
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echo " type: file, multiple values allowed, file must exist"
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echo " example: sample.fq.gz"
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echo " List of files containing unmated reads of (e.g. single-end reads)."
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echo ""
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echo " -m1, --mates1"
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echo " type: file, multiple values allowed, file must exist"
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echo " example: sample_1.fq.gz"
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echo " File containing the #1 mates."
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echo ""
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echo " -m2, --mates2"
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echo " type: file, multiple values allowed, file must exist"
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echo " example: sample_2.fq.gz"
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echo " File containing the #2 mates."
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echo ""
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echo "Alignment input options:"
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echo " --discard_orphans"
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echo " type: boolean_true"
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echo " Discard orphan alignments in the input [for alignment-based mode only]."
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echo " If this flag is passed, then only paired alignments will be considered"
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echo " toward quantification estimates. The default behavior is to consider"
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echo " orphan alignments if no valid paired mappings exist."
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echo ""
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echo " -a, --alignments"
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echo " type: file, multiple values allowed, file must exist"
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echo " example: sample.fq.gz"
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echo " Input alignment (BAM) file(s)."
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echo ""
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echo " -e, --eqclasses"
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echo " type: file, file must exist"
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echo " input salmon weighted equivalence class file."
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echo ""
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echo " -t, --targets"
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echo " type: file, file must exist"
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echo " example: transcripts.fasta"
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echo " FASTA format file containing target transcripts."
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echo ""
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echo " --ont"
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echo " type: boolean_true"
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echo " Use alignment model for Oxford Nanopore long reads"
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echo ""
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echo "Output:"
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echo " -o, --output"
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echo " type: file, required parameter, output, file must exist"
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echo " example: quant_output"
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echo " Output quantification directory."
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echo ""
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echo " --quant_results"
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echo " type: file, output, file must exist"
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echo " example: quant.sf"
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echo " Salmon quantification file."
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echo ""
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echo "Basic options:"
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echo " --seq_bias"
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echo " type: boolean_true"
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echo " Perform sequence-specific bias correction."
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echo ""
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echo " --gc_bias"
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echo " type: boolean_true"
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echo " Perform fragment GC bias correction [beta for single-end reads]."
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echo ""
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echo " --pos_bias"
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echo " type: boolean_true"
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echo " Perform positional bias correction."
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echo ""
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echo " --incompat_prior"
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echo " type: double"
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echo " example: 0.0"
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echo " min: 0.0"
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echo " max: 1.0"
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echo " Set the prior probability that an alignment that disagrees with the"
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echo " specified library type (--lib_type) results from the true fragment"
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echo " origin. Setting this to 0 specifies that alignments that disagree with"
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echo " the library type should be \"impossible\", while setting it to 1 says that"
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echo " alignments that disagree with the library type are no less likely than"
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echo " those that do."
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echo ""
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echo " -g, --gene_map"
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echo " type: file, file must exist"
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echo " example: gene_map.gtf"
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echo " File containing a mapping of transcripts to genes. If this file is"
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echo " provided salmon will output both quant.sf and quant.genes.sf files,"
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echo " where the latter contains aggregated gene-level abundance estimates."
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echo " The transcript to gene mapping should be provided as either a GTF file,"
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echo " or a in a simple tab-delimited format where each line contains the name"
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echo " of a transcript and the gene to which it belongs separated by a tab. The"
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echo " extension of the file is used to determine how the file should be"
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echo " parsed. Files ending in '.gtf', '.gff' or '.gff3' are assumed to be in"
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echo " GTF format; files with any other extension are assumed to be in the"
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echo " simple format. In GTF / GFF format, the \"transcript_id\" is assumed to"
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echo " contain the transcript identifier and the \"gene_id\" is assumed to"
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echo " contain the corresponding gene identifier."
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echo ""
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echo " --aux_target_file"
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echo " type: file, file must exist"
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echo " example: auxilary_targets.txt"
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echo " A file containing a list of \"auxiliary\" targets. These are valid targets"
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echo " (i.e., not decoys) to which fragments are allowed to map and be"
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echo " assigned, and which will be quantified, but for which auxiliary models"
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echo " like sequence-specific and fragment-GC bias correction should not be"
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echo " applied."
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echo ""
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echo " --meta"
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echo " type: boolean_true"
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echo " If you're using Salmon on a metagenomic dataset, consider setting this"
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echo " flag to disable parts of the abundance estimation model that make less"
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echo " sense for metagenomic data."
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echo ""
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echo " --score_exp"
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echo " type: double"
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echo " example: 1.0"
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echo " The factor by which sub-optimal alignment scores are downweighted to"
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echo " produce a probability. If the best alignment score for the current read"
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echo " is S, and the score for a particular alignment is w, then the"
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echo " probability will be computed porportional to exp( - scoreExp * (S-w) )."
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echo ""
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echo "Options specific to mapping mode:"
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echo " --discard_orphans_quasi"
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echo " type: boolean_true"
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echo " [selective-alignment mode only]"
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echo " Discard orphan mappings in selective-alignment mode. If this flag is"
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echo " passed then only paired mappings will be considered toward"
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echo " quantification estimates. The default behavior is to consider orphan"
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echo " mappings if no valid paired mappings exist. This flag is independent of"
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echo " the option to write the orphaned mappings to file (--writeOrphanLinks)."
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echo ""
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echo " --consensus_slack"
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echo " type: double"
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echo " example: 0.35"
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echo " min: 0.0"
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echo " max: 0.999999999"
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echo " [selective-alignment mode only]"
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echo " The amount of slack allowed in the selective-alignment filtering"
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echo " mechanism. If this is set to a fraction, X, greater than 0 (and in"
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echo " [0,1)), then uniMEM chains with scores below (100 * X)% of the best"
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echo " chain score for a read, and read pairs with a sum of chain scores below"
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echo " (100 * X)% of the best chain score for a read pair will be discounted as"
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echo " a mapping candidates. The default value of this option is 0.35."
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echo ""
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echo " --pre_merge_chain_sub_thresh"
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echo " type: double"
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echo " example: 0.75"
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echo " min: 0.0"
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echo " max: 1.0"
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echo " [selective-alignment mode only]"
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echo " The threshold of sub-optimal chains, compared to the best chain on a"
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echo " given target, that will be retained and passed to the next phase of"
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echo " mapping. Specifically, if the best chain for a read (or read-end in"
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echo " paired-end mode) to target t has score X_t, then all chains for this"
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echo " read with score >= X_t * preMergeChainSubThresh will be retained and"
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echo " passed to subsequent mapping phases. This value must be in the range"
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echo " [0, 1]."
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echo ""
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echo " --post_merge_chain_sub_thresh"
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echo " type: double"
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echo " example: 0.9"
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echo " min: 0.0"
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echo " max: 1.0"
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echo " [selective-alignment mode only]"
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echo " The threshold of sub-optimal chains, compared to the best chain on a"
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echo " given target, that will be retained and passed to the next phase of"
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echo " mapping. This is different than post_merge_chain_sub_thresh, because"
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echo " this is applied to pairs of chains (from the ends of paired-end reads)"
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echo " after merging (i.e. after checking concordancy constraints etc.)."
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echo " Specifically, if the best chain pair to target t has score X_t, then all"
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echo " chain pairs for this read pair with score >= X_t *"
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echo " post_merge_chain_sub_thresh will be retained and passed to subsequent"
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echo " mapping phases. This value must be in the range [0, 1]. Note: This"
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echo " option is only meaningful for paired-end libraries, and is ignored for"
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echo " single-end libraries."
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echo ""
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echo " --orphan_chain_sub_thresh"
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echo " type: double"
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echo " example: 0.95"
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echo " min: 0.0"
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echo " max: 1.0"
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echo " [selective-alignment mode only]"
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echo " This threshold sets a global sub-optimality threshold for chains"
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echo " corresponding to orphan mappings. That is, if the merging procedure"
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echo " results in no concordant mappings then only orphan mappings with a chain"
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echo " score >= orphan_chain_sub_thresh * bestChainScore will be retained and"
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echo " passed to subsequent mapping phases. This value must be in the range [0,"
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echo " 1]. Note: This option is only meaningful for paired-end libraries, and"
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echo " is ignored for single-end libraries."
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echo ""
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echo " --min_score_fraction"
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echo " type: double"
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echo " example: 0.65"
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echo " min: 1.0E-9"
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echo " max: 1.0"
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echo " [selective-alignment mode only]"
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echo " The fraction of the optimal possible alignment score that a mapping must"
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echo " achieve in order to be considered \"valid\" --- should be in (0,1]."
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echo " Default 0.65"
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echo ""
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echo " --mismatch_seed_skip"
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echo " type: integer"
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echo " example: 3"
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echo " [selective-alignment mode only]"
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echo " After a k-mer hit is extended to a uni-MEM, the uni-MEM extension can"
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echo " terminate for one of 3 reasons; the end of the read, the end of the"
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echo " unitig, or a mismatch. If the extension ends because of a mismatch, this"
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echo " is likely the result of a sequencing error. To avoid looking up many"
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echo " k-mers that will likely fail to be located in the index, the search"
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echo " procedure skips by a factor of mismatch_seed_skip until it either (1)"
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echo " finds another match or (2) is k-bases past the mismatch position. This"
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echo " value controls that skip length. A smaller value can increase"
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echo " sensitivity, while a larger value can speed up seeding."
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echo ""
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echo " --disable_chaining_heuristic"
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echo " type: boolean_true"
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echo " [selective-alignment mode only]"
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echo " By default, the heuristic of (Li 2018) is implemented, which terminates"
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echo " the chaining DP once a given number of valid backpointers are found."
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echo " This speeds up the seed (MEM) chaining step, but may result in"
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echo " sub-optimal chains in complex situations (e.g. sequences with many"
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echo " repeats and overlapping repeats). Passing this flag will disable the"
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echo " chaining heuristic, and perform the full chaining dynamic program,"
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echo " guaranteeing the optimal chain is found in this step."
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echo ""
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echo " --decoy_threshold"
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echo " type: double"
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echo " example: 1.0"
|
|
echo " min: 0.0"
|
|
echo " max: 1.0"
|
|
echo " [selective-alignment mode only]"
|
|
echo " For an alignemnt to an annotated transcript to be considered invalid, it"
|
|
echo " must have an alignment score < (decoy_threshold * bestDecoyScore). A"
|
|
echo " value of 1.0 means that any alignment strictly worse than the best decoy"
|
|
echo " alignment will be discarded. A smaller value will allow reads to be"
|
|
echo " allocated to transcripts even if they strictly align better to the decoy"
|
|
echo " sequence."
|
|
echo ""
|
|
echo " --ma"
|
|
echo " type: integer"
|
|
echo " example: 2"
|
|
echo " [selective-alignment mode only]"
|
|
echo " The value given to a match between read and reference nucleotides in an"
|
|
echo " alignment."
|
|
echo ""
|
|
echo " --mp"
|
|
echo " type: integer"
|
|
echo " example: -4"
|
|
echo " [selective-alignment mode only]"
|
|
echo " The value given to a mis-match between read and reference nucleotides in"
|
|
echo " an alignment."
|
|
echo ""
|
|
echo " --go"
|
|
echo " type: integer"
|
|
echo " example: 6"
|
|
echo " [selective-alignment mode only]"
|
|
echo " The value given to a gap opening in an alignment."
|
|
echo ""
|
|
echo " --ge"
|
|
echo " type: integer"
|
|
echo " example: 2"
|
|
echo " [selective-alignment mode only]"
|
|
echo " The value given to a gap extension in an alignment."
|
|
echo ""
|
|
echo " --bandwidth"
|
|
echo " type: integer"
|
|
echo " example: 15"
|
|
echo " [selective-alignment mode only]"
|
|
echo " The value used for the bandwidth passed to ksw2. A smaller bandwidth can"
|
|
echo " make the alignment verification run more quickly, but could possibly"
|
|
echo " miss valid alignments."
|
|
echo ""
|
|
echo " --allow_dovetail"
|
|
echo " type: boolean_true"
|
|
echo " [selective-alignment mode only]"
|
|
echo " Allow dovetailing mappings."
|
|
echo ""
|
|
echo " --recover_orphans"
|
|
echo " type: boolean_true"
|
|
echo " [selective-alignment mode only]"
|
|
echo " Attempt to recover the mates of orphaned reads. This uses edlib for"
|
|
echo " orphan recovery, and so introduces some computational overhead, but it"
|
|
echo " can improve sensitivity."
|
|
echo ""
|
|
echo " --mimicBT2"
|
|
echo " type: boolean_true"
|
|
echo " [selective-alignment mode only]"
|
|
echo " Set flags to mimic parameters similar to Bowtie2 with --no-discordant"
|
|
echo " and --no-mixed flags. This increases disallows dovetailing reads, and"
|
|
echo " discards orphans. Note, this does not impose the very strict parameters"
|
|
echo " assumed by RSEM+Bowtie2, like gapless alignments. For that behavior, use"
|
|
echo " the --mimic_strictBT2 flag below."
|
|
echo ""
|
|
echo " --mimic_strictBT2"
|
|
echo " type: boolean_true"
|
|
echo " [selective-alignment mode only]"
|
|
echo " Set flags to mimic the very strict parameters used by RSEM+Bowtie2. This"
|
|
echo " increases --min_score_fraction to 0.8, disallows dovetailing reads,"
|
|
echo " discards orphans, and disallows gaps in alignments."
|
|
echo ""
|
|
echo " --softclip"
|
|
echo " type: boolean_true"
|
|
echo " [selective-alignment mode only]"
|
|
echo " Allos soft-clipping of reads during selective-alignment. If this option"
|
|
echo " is provided, then regions at the beginning or end of the read can be"
|
|
echo " withheld from alignment without any effect on the resulting score (i.e."
|
|
echo " neither adding nor removing from the score). This will drastically"
|
|
echo " reduce the penalty if there are mismatches at the beginning or end of"
|
|
echo " the read due to e.g. low-quality bases or adapters. NOTE: Even with"
|
|
echo " soft-clipping enabled, the read must still achieve a score of at least"
|
|
echo " min_score_fraction * maximum achievable score, where the maximum"
|
|
echo " achievable score is computed based on the full (un-clipped) read length."
|
|
echo ""
|
|
echo " --softclip_overhangs"
|
|
echo " type: boolean_true"
|
|
echo " [selective-alignment mode only]"
|
|
echo " Allow soft-clipping of reads that overhang the beginning or ends of the"
|
|
echo " transcript. In this case, the overhaning section of the read will simply"
|
|
echo " be unaligned, and will not contribute or detract from the alignment"
|
|
echo " score. The default policy is to force an end-to-end alignment of the"
|
|
echo " entire read, so that overhanings will result in some deletion of"
|
|
echo " nucleotides from the read."
|
|
echo ""
|
|
echo " --full_length_alignment"
|
|
echo " type: boolean_true"
|
|
echo " [selective-alignment mode only]"
|
|
echo " Perform selective alignment over the full length of the read, beginning"
|
|
echo " from the (approximate) initial mapping location and using extension"
|
|
echo " alignment. This is in contrast with the default behavior which is to"
|
|
echo " only perform alignment between the MEMs in the optimal chain (and before"
|
|
echo " the first and after the last MEM if applicable). The default strategy"
|
|
echo " forces the MEMs to belong to the alignment, but has the benefit that it"
|
|
echo " can discover indels prior to the first hit shared between the read and"
|
|
echo " reference. Except in very rare circumstances, the default mode should be"
|
|
echo " more accurate."
|
|
echo ""
|
|
echo " --hard_filter"
|
|
echo " type: boolean_true"
|
|
echo " [selective-alignment mode only]"
|
|
echo " Instead of weighting mappings by their alignment score, this flag will"
|
|
echo " discard any mappings with sub-optimal alignment score. The default"
|
|
echo " option of soft-filtering (i.e. weighting mappings by their alignment"
|
|
echo " score) usually yields slightly more accurate abundance estimates but"
|
|
echo " this flag may be desirable if you want more accurate 'naive' equivalence"
|
|
echo " classes, rather than range factorized equivalence classes."
|
|
echo ""
|
|
echo " --min_aln_prob"
|
|
echo " type: double"
|
|
echo " example: 1.0E-5"
|
|
echo " The minimum number of fragments that must be assigned to the"
|
|
echo " transcriptome for quantification to proceed."
|
|
echo ""
|
|
echo " -z, --write_mappings"
|
|
echo " type: boolean_true"
|
|
echo " If this option is provided, then the selective-alignment results will be"
|
|
echo " written out in SAM-compatible format. By default, output will be"
|
|
echo " directed to stdout, but an alternative file name can be provided"
|
|
echo " instead."
|
|
echo ""
|
|
echo " --mapping_sam"
|
|
echo " type: file, output, file must exist"
|
|
echo " example: mappings.sam"
|
|
echo " Path to file that should output the selective-alignment results in"
|
|
echo " SAM-compatible format. This option must be provided while using"
|
|
echo " --write_mappings"
|
|
echo ""
|
|
echo " --write_qualities"
|
|
echo " type: boolean_true"
|
|
echo " This flag only has meaning if mappings are being written (with"
|
|
echo " --write_mappings/-z). If this flag is provided, then the output SAM file"
|
|
echo " will contain quality strings as well as read sequences. Note that this"
|
|
echo " can greatly increase the size of the output file."
|
|
echo ""
|
|
echo " --hit_filter_policy"
|
|
echo " type: string"
|
|
echo " example: AFTER"
|
|
echo " choices: [ BEFORE, AFTER, BOTH, NONE ]"
|
|
echo " [selective-alignment mode only]"
|
|
echo " Determines the policy by which hits are filtered in selective alignment."
|
|
echo " Filtering hits after chaining (the default) is more sensitive, but more"
|
|
echo " computationally intensive, because it performs the chaining dynamic"
|
|
echo " program for all hits. Filtering before chaining is faster, but some true"
|
|
echo " hits may be missed. The options are BEFORE, AFTER, BOTH and NONE."
|
|
echo ""
|
|
echo "Advance options:"
|
|
echo " --alternative_init_mode"
|
|
echo " type: boolean_true"
|
|
echo " Use an alternative strategy (rather than simple interpolation between)"
|
|
echo " the online and uniform abundance estimates to initialize the EM / VBEM"
|
|
echo " algorithm."
|
|
echo ""
|
|
echo " --aux_dir"
|
|
echo " type: file, output, file must exist"
|
|
echo " example: aux_info"
|
|
echo " The sub-directory of the quantification directory where auxiliary"
|
|
echo " information e.g. bootstraps, bias parameters, etc. will be written."
|
|
echo ""
|
|
echo " --skip_quant"
|
|
echo " type: boolean_true"
|
|
echo " Skip performing the actual transcript quantification (including any"
|
|
echo " Gibbs sampling or bootstrapping)."
|
|
echo ""
|
|
echo " --dump_eq"
|
|
echo " type: boolean_true"
|
|
echo " Dump the simple equivalence class counts that were computed during"
|
|
echo " mapping or alignment."
|
|
echo ""
|
|
echo " -d, --dump_eq_weights"
|
|
echo " type: boolean_true"
|
|
echo " Dump conditional probabilities associated with transcripts when"
|
|
echo " equivalence class information is being dumped to file. Note, this will"
|
|
echo " dump the factorization that is actually used by salmon's offline phase"
|
|
echo " for inference. If you are using range-factorized equivalence classes"
|
|
echo " (the default) then the same transcript set may appear multiple times"
|
|
echo " with different associated conditional probabilities."
|
|
echo ""
|
|
echo " --min_assigned_frags"
|
|
echo " type: integer"
|
|
echo " example: 10"
|
|
echo " The minimum number of fragments that must be assigned to the"
|
|
echo " transcriptome for quantification to proceed."
|
|
echo ""
|
|
echo " --reduce_GC_memory"
|
|
echo " type: boolean_true"
|
|
echo " If this option is selected, a more memory efficient (but slightly"
|
|
echo " slower) representation is used to compute fragment GC content. Enabling"
|
|
echo " this will reduce memory usage, but can also reduce speed. However, the"
|
|
echo " results themselves will remain the same."
|
|
echo ""
|
|
echo " --bias_speed_samp"
|
|
echo " type: integer"
|
|
echo " example: 5"
|
|
echo " The value at which the fragment length PMF is down-sampled when"
|
|
echo " evaluating sequence-specific & GC fragment bias. Larger values speed up"
|
|
echo " effective length correction, but may decrease the fidelity of bias"
|
|
echo " modeling results."
|
|
echo ""
|
|
echo " --fld_max"
|
|
echo " type: integer"
|
|
echo " example: 1000"
|
|
echo " The maximum fragment length to consider when building the empirical"
|
|
echo " distribution"
|
|
echo ""
|
|
echo " --fld_mean"
|
|
echo " type: integer"
|
|
echo " example: 250"
|
|
echo " The mean used in the fragment length distribution prior"
|
|
echo ""
|
|
echo " --fld_SD"
|
|
echo " type: integer"
|
|
echo " example: 25"
|
|
echo " The standard deviation used in the fragment length distribution prior"
|
|
echo ""
|
|
echo " -f, --forgetting_factor"
|
|
echo " type: double"
|
|
echo " example: 0.65"
|
|
echo " min: 0.500000001"
|
|
echo " max: 1.0"
|
|
echo " The forgetting factor used in the online learning schedule. A"
|
|
echo " smallervalue results in quicker learning, but higher variance and may be"
|
|
echo " unstable. A larger value results in slower learning but may be more"
|
|
echo " stable. Value should be in the interval (0.5, 1.0]."
|
|
echo ""
|
|
echo " --init_uniform"
|
|
echo " type: boolean_true"
|
|
echo " Initialize the offline inference with uniform parameters, rather than"
|
|
echo " seeding with online parameters."
|
|
echo ""
|
|
echo " --max_occs_per_hit"
|
|
echo " type: integer"
|
|
echo " example: 1000"
|
|
echo " When collecting \"hits\" (MEMs), hits having more than max_occs_per_hit"
|
|
echo " occurrences won't be considered."
|
|
echo ""
|
|
echo " --max_read_occ"
|
|
echo " type: integer"
|
|
echo " example: 200"
|
|
echo " Reads \"mapping\" to more than this many places won't be considered."
|
|
echo ""
|
|
echo " --no_length_correction"
|
|
echo " type: boolean_true"
|
|
echo " Entirely disables length correction when estimating the abundance of"
|
|
echo " transcripts. This option can be used with protocols where one expects"
|
|
echo " that fragments derive from their underlying targets without regard to"
|
|
echo " that target's length (e.g. QuantSeq)"
|
|
echo ""
|
|
echo " --no_effective_length_correction"
|
|
echo " type: boolean_true"
|
|
echo " Disables effective length correction when computing the probability that"
|
|
echo " a fragment was generated from a transcript. If this flag is passed"
|
|
echo " in,the fragment length distribution is not taken into account when"
|
|
echo " computing this probability."
|
|
echo ""
|
|
echo " --no_single_frag_prob"
|
|
echo " type: boolean_true"
|
|
echo " Disables the estimation of an associated fragment length probability for"
|
|
echo " single-end reads or for orphaned mappings in paired-end libraries. The"
|
|
echo " default behavior is to consider the probability of all possible"
|
|
echo " fragment lengths associated with the retained mapping. Enabling this"
|
|
echo " flag (i.e. turning this default behavior off) will simply not attempt to"
|
|
echo " estimate a fragment length probability in such cases."
|
|
echo ""
|
|
echo " --no_frag_length_dist"
|
|
echo " type: boolean_true"
|
|
echo " Don't consider concordance with the learned fragment length distribution"
|
|
echo " when trying to determine the probability that a fragment has originated"
|
|
echo " from a specified location. Normally, Fragments with unlikely lengths"
|
|
echo " will be assigned a smaller relative probability than those with more"
|
|
echo " likely lengths. When this flag is passed in, the observed fragment"
|
|
echo " length has no effect on that fragment's a priori probability."
|
|
echo ""
|
|
echo " --no_bias_length_threshold"
|
|
echo " type: boolean_true"
|
|
echo " If this option is enabled, then no (lower) threshold will be set on how"
|
|
echo " short bias correction can make effective lengths. This can increase the"
|
|
echo " precision of bias correction, but harm robustness. The default"
|
|
echo " correction applies a threshold."
|
|
echo ""
|
|
echo " --num_bias_samples"
|
|
echo " type: integer"
|
|
echo " example: 2000000"
|
|
echo " Number of fragment mappings to use when learning the sequence-specific"
|
|
echo " bias model."
|
|
echo ""
|
|
echo " --num_aux_model_samples"
|
|
echo " type: integer"
|
|
echo " example: 5000000"
|
|
echo " The first <num_aux_model_samples> are used to train the auxiliary model"
|
|
echo " parameters (e.g. fragment length distribution, bias, etc.). After ther"
|
|
echo " first <num_aux_model_samples> observations the auxiliary model"
|
|
echo " parameters will be assumed to have converged and will be fixed."
|
|
echo ""
|
|
echo " --num_pre_aux_model_samples"
|
|
echo " type: integer"
|
|
echo " example: 5000"
|
|
echo " The first <numPreAuxModelSamples> will have their assignment likelihoods"
|
|
echo " and contributions to the transcript abundances computed without applying"
|
|
echo " any auxiliary models. The purpose of ignoring the auxiliary models for"
|
|
echo " the first <num_pre_aux_model_samples> observations is to avoid applying"
|
|
echo " these models before their parameters have been learned sufficiently"
|
|
echo " well."
|
|
echo ""
|
|
echo " --useEM"
|
|
echo " type: boolean_true"
|
|
echo " Use the traditional EM algorithm for optimization in the batch passes."
|
|
echo ""
|
|
echo " --useVBOpt"
|
|
echo " type: boolean_true"
|
|
echo " Use the Variational Bayesian EM [default]"
|
|
echo ""
|
|
echo " --range_factorization_bins"
|
|
echo " type: integer"
|
|
echo " example: 4"
|
|
echo " Factorizes the likelihood used in quantification by adopting a new"
|
|
echo " notion of equivalence classes based on the conditional probabilities"
|
|
echo " with which fragments are generated from different transcripts. This is a"
|
|
echo " more fine-grained factorization than the normal rich equivalence"
|
|
echo " classes. The default value (4) corresponds to the default used in Zakeri"
|
|
echo " et al. 2017 (doi: 10.1093/bioinformatics/btx262), and larger values"
|
|
echo " imply a more fine-grained factorization. If range factorization is"
|
|
echo " enabled, a common value to select for this parameter is 4. A value of 0"
|
|
echo " signifies the use of basic rich equivalence classes."
|
|
echo ""
|
|
echo " --num_Gibbs_samples"
|
|
echo " type: integer"
|
|
echo " example: 0"
|
|
echo " Number of Gibbs sampling rounds to perform."
|
|
echo ""
|
|
echo " --no_Gamma_draw"
|
|
echo " type: boolean_true"
|
|
echo " This switch will disable drawing transcript fractions from a Gamma"
|
|
echo " distribution during Gibbs sampling. In this case the sampler does not"
|
|
echo " account for shot-noise, but only assignment ambiguity"
|
|
echo ""
|
|
echo " --num_bootstraps"
|
|
echo " type: integer"
|
|
echo " example: 0"
|
|
echo " Number of bootstrap samples to generate. Note: This is mutually"
|
|
echo " exclusive with Gibbs sampling."
|
|
echo ""
|
|
echo " --bootstrap_reproject"
|
|
echo " type: boolean_true"
|
|
echo " This switch will learn the parameter distribution from the bootstrapped"
|
|
echo " counts for each sample, but will reproject those parameters onto the"
|
|
echo " original equivalence class counts."
|
|
echo ""
|
|
echo " --thinning_factor"
|
|
echo " type: integer"
|
|
echo " example: 16"
|
|
echo " Number of steps to discard for every sample kept from the Gibbs chain."
|
|
echo " The larger this number, the less chance that subsequent samples are"
|
|
echo " auto-correlated, but the slower sampling becomes."
|
|
echo ""
|
|
echo " -q, --quiet"
|
|
echo " type: boolean_true"
|
|
echo " Be quiet while doing quantification (don't write informative output to"
|
|
echo " the console unless something goes wrong)."
|
|
echo ""
|
|
echo " --per_transcript_prior"
|
|
echo " type: boolean_true"
|
|
echo " The prior (either the default or the argument provided via --vb_prior)"
|
|
echo " will be interpreted as a transcript-level prior (i.e. each transcript"
|
|
echo " will be given a prior read count of this value)"
|
|
echo ""
|
|
echo " --per_nucleotide_prior"
|
|
echo " type: boolean_true"
|
|
echo " The prior (either the default or the argument provided via --vb_prior)"
|
|
echo " will be interpreted as a nucleotide-level prior (i.e. each nucleotide"
|
|
echo " will be given a prior read count of this value)"
|
|
echo ""
|
|
echo " --sig_digits"
|
|
echo " type: integer"
|
|
echo " example: 3"
|
|
echo " The number of significant digits to write when outputting the"
|
|
echo " EffectiveLength and NumReads columns"
|
|
echo ""
|
|
echo " --vb_prior"
|
|
echo " type: double"
|
|
echo " example: 0.01"
|
|
echo " The prior that will be used in the VBEM algorithm. This is interpreted"
|
|
echo " as a per-transcript prior, unless the --per_nucleotide_prior flag is"
|
|
echo " also given. If the --per_nucleotide_prior flag is given, this is used as"
|
|
echo " a nucleotide-level prior. If the default is used, it will be divided by"
|
|
echo " 1000 before being used as a nucleotide-level prior, i.e. the default"
|
|
echo " per-nucleotide prior will be 1e-5."
|
|
echo ""
|
|
echo " --write_orphan_links"
|
|
echo " type: boolean_true"
|
|
echo " Write the transcripts that are linked by orphaned reads."
|
|
echo ""
|
|
echo " --write_unmapped_names"
|
|
echo " type: boolean_true"
|
|
echo " Write the names of un-mapped reads to the file unmapped_names.txt in the"
|
|
echo " auxiliary directory."
|
|
echo ""
|
|
echo "Alignment-specific options:"
|
|
echo " --no_error_model"
|
|
echo " type: boolean_true"
|
|
echo " Turn off the alignment error model, which takes into account the the"
|
|
echo " observed frequency of different types of mismatches / indels when"
|
|
echo " computing the likelihood of a given alignment. Turning this off can"
|
|
echo " speed up alignment-based salmon, but can harm quantification accuracy."
|
|
echo ""
|
|
echo " --num_error_bins"
|
|
echo " type: integer"
|
|
echo " example: 6"
|
|
echo " The number of bins into which to divide each read when learning and"
|
|
echo " applying the error model. For example, a value of 10 would mean that"
|
|
echo " effectively, a separate error model is leared and applied to each 10th"
|
|
echo " of the read, while a value of 3 would mean that a separate error model"
|
|
echo " is applied to the read beginning (first third), middle (second third)"
|
|
echo " and end (final third)."
|
|
echo ""
|
|
echo " -s, --sample_out"
|
|
echo " type: boolean_true"
|
|
echo " Write a \"postSample.bam\" file in the output directory that will sample"
|
|
echo " the input alignments according to the estimated transcript abundances."
|
|
echo " If you're going to perform downstream analysis of the alignments with"
|
|
echo " tools which don't, themselves, take fragment assignment ambiguity into"
|
|
echo " account, you should use this output."
|
|
echo ""
|
|
echo " -u, --sample_unaligned"
|
|
echo " type: boolean_true"
|
|
echo " In addition to sampling the aligned reads, also write the un-aligned"
|
|
echo " reads to \"postSample.bam\"."
|
|
echo ""
|
|
echo " --gencode"
|
|
echo " type: boolean_true"
|
|
echo " This flag will expect the input transcript fasta to be in GENCODE"
|
|
echo " format, and will split the transcript name at the first '|' character."
|
|
echo " These reduced names will be used in the output and when looking for"
|
|
echo " these transcripts in a gene to transcript GTF."
|
|
echo ""
|
|
echo " --mapping_cache_memory_limit"
|
|
echo " type: integer"
|
|
echo " example: 2000000"
|
|
echo " If the file contained fewer than this many mapped reads, then just keep"
|
|
echo " the data in memory for subsequent rounds of inference. Obviously, this"
|
|
echo " value should not be too large if you wish to keep a low memory usage,"
|
|
echo " but setting it large enough to accommodate all of the mapped read can"
|
|
echo " substantially speed up inference on \"small\" files that contain only a"
|
|
echo " few million reads."
|
|
}
|
|
|
|
# initialise variables
|
|
VIASH_MODE='run'
|
|
VIASH_ENGINE_ID='docker'
|
|
|
|
######## Helper functions for setting up Docker images for viash ########
|
|
# expects: ViashDockerBuild
|
|
|
|
# ViashDockerInstallationCheck: check whether Docker is installed correctly
|
|
#
|
|
# examples:
|
|
# ViashDockerInstallationCheck
|
|
function ViashDockerInstallationCheck {
|
|
ViashDebug "Checking whether Docker is installed"
|
|
if [ ! command -v docker &> /dev/null ]; then
|
|
ViashCritical "Docker doesn't seem to be installed. See 'https://docs.docker.com/get-docker/' for instructions."
|
|
exit 1
|
|
fi
|
|
|
|
ViashDebug "Checking whether the Docker daemon is running"
|
|
local save=$-; set +e
|
|
local docker_version=$(docker version --format '{{.Client.APIVersion}}' 2> /dev/null)
|
|
local out=$?
|
|
[[ $save =~ e ]] && set -e
|
|
if [ $out -ne 0 ]; then
|
|
ViashCritical "Docker daemon does not seem to be running. Try one of the following:"
|
|
ViashCritical "- Try running 'dockerd' in the command line"
|
|
ViashCritical "- See https://docs.docker.com/config/daemon/"
|
|
exit 1
|
|
fi
|
|
}
|
|
|
|
# ViashDockerRemoteTagCheck: check whether a Docker image is available
|
|
# on a remote. Assumes `docker login` has been performed, if relevant.
|
|
#
|
|
# $1 : image identifier with format `[registry/]image[:tag]`
|
|
# exit code $? : whether or not the image was found
|
|
# examples:
|
|
# ViashDockerRemoteTagCheck python:latest
|
|
# echo $? # returns '0'
|
|
# ViashDockerRemoteTagCheck sdaizudceahifu
|
|
# echo $? # returns '1'
|
|
function ViashDockerRemoteTagCheck {
|
|
docker manifest inspect $1 > /dev/null 2> /dev/null
|
|
}
|
|
|
|
# ViashDockerLocalTagCheck: check whether a Docker image is available locally
|
|
#
|
|
# $1 : image identifier with format `[registry/]image[:tag]`
|
|
# exit code $? : whether or not the image was found
|
|
# examples:
|
|
# docker pull python:latest
|
|
# ViashDockerLocalTagCheck python:latest
|
|
# echo $? # returns '0'
|
|
# ViashDockerLocalTagCheck sdaizudceahifu
|
|
# echo $? # returns '1'
|
|
function ViashDockerLocalTagCheck {
|
|
[ -n "$(docker images -q $1)" ]
|
|
}
|
|
|
|
# ViashDockerPull: pull a Docker image
|
|
#
|
|
# $1 : image identifier with format `[registry/]image[:tag]`
|
|
# exit code $? : whether or not the image was found
|
|
# examples:
|
|
# ViashDockerPull python:latest
|
|
# echo $? # returns '0'
|
|
# ViashDockerPull sdaizudceahifu
|
|
# echo $? # returns '1'
|
|
function ViashDockerPull {
|
|
ViashNotice "Checking if Docker image is available at '$1'"
|
|
if [ $VIASH_VERBOSITY -ge $VIASH_LOGCODE_INFO ]; then
|
|
docker pull $1 && return 0 || return 1
|
|
else
|
|
local save=$-; set +e
|
|
docker pull $1 2> /dev/null > /dev/null
|
|
local out=$?
|
|
[[ $save =~ e ]] && set -e
|
|
if [ $out -ne 0 ]; then
|
|
ViashWarning "Could not pull from '$1'. Docker image doesn't exist or is not accessible."
|
|
fi
|
|
return $out
|
|
fi
|
|
}
|
|
|
|
# ViashDockerPush: push a Docker image
|
|
#
|
|
# $1 : image identifier with format `[registry/]image[:tag]`
|
|
# exit code $? : whether or not the image was found
|
|
# examples:
|
|
# ViashDockerPush python:latest
|
|
# echo $? # returns '0'
|
|
# ViashDockerPush sdaizudceahifu
|
|
# echo $? # returns '1'
|
|
function ViashDockerPush {
|
|
ViashNotice "Pushing image to '$1'"
|
|
local save=$-; set +e
|
|
local out
|
|
if [ $VIASH_VERBOSITY -ge $VIASH_LOGCODE_INFO ]; then
|
|
docker push $1
|
|
out=$?
|
|
else
|
|
docker push $1 2> /dev/null > /dev/null
|
|
out=$?
|
|
fi
|
|
[[ $save =~ e ]] && set -e
|
|
if [ $out -eq 0 ]; then
|
|
ViashNotice "Container '$1' push succeeded."
|
|
else
|
|
ViashError "Container '$1' push errored. You might not be logged in or have the necessary permissions."
|
|
fi
|
|
return $out
|
|
}
|
|
|
|
# ViashDockerPullElseBuild: pull a Docker image, else build it
|
|
#
|
|
# $1 : image identifier with format `[registry/]image[:tag]`
|
|
# ViashDockerBuild : a Bash function which builds a docker image, takes image identifier as argument.
|
|
# examples:
|
|
# ViashDockerPullElseBuild mynewcomponent
|
|
function ViashDockerPullElseBuild {
|
|
local save=$-; set +e
|
|
ViashDockerPull $1
|
|
local out=$?
|
|
[[ $save =~ e ]] && set -e
|
|
if [ $out -ne 0 ]; then
|
|
ViashDockerBuild $@
|
|
fi
|
|
}
|
|
|
|
# ViashDockerSetup: create a Docker image, according to specified docker setup strategy
|
|
#
|
|
# $1 : image identifier with format `[registry/]image[:tag]`
|
|
# $2 : docker setup strategy, see DockerSetupStrategy.scala
|
|
# examples:
|
|
# ViashDockerSetup mynewcomponent alwaysbuild
|
|
function ViashDockerSetup {
|
|
local image_id="$1"
|
|
local setup_strategy="$2"
|
|
if [ "$setup_strategy" == "alwaysbuild" -o "$setup_strategy" == "build" -o "$setup_strategy" == "b" ]; then
|
|
ViashDockerBuild $image_id --no-cache $(ViashDockerBuildArgs "$engine_id")
|
|
elif [ "$setup_strategy" == "alwayspull" -o "$setup_strategy" == "pull" -o "$setup_strategy" == "p" ]; then
|
|
ViashDockerPull $image_id
|
|
elif [ "$setup_strategy" == "alwayspullelsebuild" -o "$setup_strategy" == "pullelsebuild" ]; then
|
|
ViashDockerPullElseBuild $image_id --no-cache $(ViashDockerBuildArgs "$engine_id")
|
|
elif [ "$setup_strategy" == "alwayspullelsecachedbuild" -o "$setup_strategy" == "pullelsecachedbuild" ]; then
|
|
ViashDockerPullElseBuild $image_id $(ViashDockerBuildArgs "$engine_id")
|
|
elif [ "$setup_strategy" == "alwayscachedbuild" -o "$setup_strategy" == "cachedbuild" -o "$setup_strategy" == "cb" ]; then
|
|
ViashDockerBuild $image_id $(ViashDockerBuildArgs "$engine_id")
|
|
elif [[ "$setup_strategy" =~ ^ifneedbe ]]; then
|
|
local save=$-; set +e
|
|
ViashDockerLocalTagCheck $image_id
|
|
local outCheck=$?
|
|
[[ $save =~ e ]] && set -e
|
|
if [ $outCheck -eq 0 ]; then
|
|
ViashInfo "Image $image_id already exists"
|
|
elif [ "$setup_strategy" == "ifneedbebuild" ]; then
|
|
ViashDockerBuild $image_id --no-cache $(ViashDockerBuildArgs "$engine_id")
|
|
elif [ "$setup_strategy" == "ifneedbecachedbuild" ]; then
|
|
ViashDockerBuild $image_id $(ViashDockerBuildArgs "$engine_id")
|
|
elif [ "$setup_strategy" == "ifneedbepull" ]; then
|
|
ViashDockerPull $image_id
|
|
elif [ "$setup_strategy" == "ifneedbepullelsebuild" ]; then
|
|
ViashDockerPullElseBuild $image_id --no-cache $(ViashDockerBuildArgs "$engine_id")
|
|
elif [ "$setup_strategy" == "ifneedbepullelsecachedbuild" ]; then
|
|
ViashDockerPullElseBuild $image_id $(ViashDockerBuildArgs "$engine_id")
|
|
else
|
|
ViashError "Unrecognised Docker strategy: $setup_strategy"
|
|
exit 1
|
|
fi
|
|
elif [ "$setup_strategy" == "push" -o "$setup_strategy" == "forcepush" -o "$setup_strategy" == "alwayspush" ]; then
|
|
ViashDockerPush "$image_id"
|
|
elif [ "$setup_strategy" == "pushifnotpresent" -o "$setup_strategy" == "gentlepush" -o "$setup_strategy" == "maybepush" ]; then
|
|
local save=$-; set +e
|
|
ViashDockerRemoteTagCheck $image_id
|
|
local outCheck=$?
|
|
[[ $save =~ e ]] && set -e
|
|
if [ $outCheck -eq 0 ]; then
|
|
ViashNotice "Container '$image_id' exists, doing nothing."
|
|
else
|
|
ViashNotice "Container '$image_id' does not yet exist."
|
|
ViashDockerPush "$image_id"
|
|
fi
|
|
elif [ "$setup_strategy" == "donothing" -o "$setup_strategy" == "meh" ]; then
|
|
ViashNotice "Skipping setup."
|
|
else
|
|
ViashError "Unrecognised Docker strategy: $setup_strategy"
|
|
exit 1
|
|
fi
|
|
}
|
|
|
|
# ViashDockerCheckCommands: Check whether a docker container has the required commands
|
|
#
|
|
# $1 : image identifier with format `[registry/]image[:tag]`
|
|
# $@ : commands to verify being present
|
|
# examples:
|
|
# ViashDockerCheckCommands bash:4.0 bash ps foo
|
|
function ViashDockerCheckCommands {
|
|
local image_id="$1"
|
|
shift 1
|
|
local commands="$@"
|
|
local save=$-; set +e
|
|
local missing # mark 'missing' as local in advance, otherwise the exit code of the command will be missing and always be '0'
|
|
missing=$(docker run --rm --entrypoint=sh "$image_id" -c "for command in $commands; do command -v \$command >/dev/null 2>&1; if [ \$? -ne 0 ]; then echo \$command; exit 1; fi; done")
|
|
local outCheck=$?
|
|
[[ $save =~ e ]] && set -e
|
|
if [ $outCheck -ne 0 ]; then
|
|
ViashError "Docker container '$image_id' does not contain command '$missing'."
|
|
exit 1
|
|
fi
|
|
}
|
|
|
|
# ViashDockerBuild: build a docker image
|
|
# $1 : image identifier with format `[registry/]image[:tag]`
|
|
# $... : additional arguments to pass to docker build
|
|
# $VIASH_META_TEMP_DIR : temporary directory to store dockerfile & optional resources in
|
|
# $VIASH_META_NAME : name of the component
|
|
# $VIASH_META_RESOURCES_DIR : directory containing the resources
|
|
# $VIASH_VERBOSITY : verbosity level
|
|
# exit code $? : whether or not the image was built successfully
|
|
function ViashDockerBuild {
|
|
local image_id="$1"
|
|
shift 1
|
|
|
|
# create temporary directory to store dockerfile & optional resources in
|
|
local tmpdir=$(mktemp -d "$VIASH_META_TEMP_DIR/dockerbuild-$VIASH_META_NAME-XXXXXX")
|
|
local dockerfile="$tmpdir/Dockerfile"
|
|
function clean_up {
|
|
rm -rf "$tmpdir"
|
|
}
|
|
trap clean_up EXIT
|
|
|
|
# store dockerfile and resources
|
|
ViashDockerfile "$VIASH_ENGINE_ID" > "$dockerfile"
|
|
|
|
# generate the build command
|
|
local docker_build_cmd="docker build -t '$image_id' $@ '$VIASH_META_RESOURCES_DIR' -f '$dockerfile'"
|
|
|
|
# build the container
|
|
ViashNotice "Building container '$image_id' with Dockerfile"
|
|
ViashInfo "$docker_build_cmd"
|
|
local save=$-; set +e
|
|
if [ $VIASH_VERBOSITY -ge $VIASH_LOGCODE_INFO ]; then
|
|
eval $docker_build_cmd
|
|
else
|
|
eval $docker_build_cmd &> "$tmpdir/docker_build.log"
|
|
fi
|
|
|
|
# check exit code
|
|
local out=$?
|
|
[[ $save =~ e ]] && set -e
|
|
if [ $out -ne 0 ]; then
|
|
ViashError "Error occurred while building container '$image_id'"
|
|
if [ $VIASH_VERBOSITY -lt $VIASH_LOGCODE_INFO ]; then
|
|
ViashError "Transcript: --------------------------------"
|
|
cat "$tmpdir/docker_build.log"
|
|
ViashError "End of transcript --------------------------"
|
|
fi
|
|
exit 1
|
|
fi
|
|
}
|
|
|
|
######## End of helper functions for setting up Docker images for viash ########
|
|
|
|
# ViashDockerFile: print the dockerfile to stdout
|
|
# $1 : engine identifier
|
|
# return : dockerfile required to run this component
|
|
# examples:
|
|
# ViashDockerFile
|
|
function ViashDockerfile {
|
|
local engine_id="$1"
|
|
|
|
if [[ "$engine_id" == "docker" ]]; then
|
|
cat << 'VIASHDOCKER'
|
|
FROM quay.io/biocontainers/salmon:1.10.2--hecfa306_0
|
|
ENTRYPOINT []
|
|
RUN salmon index -v 2>&1 | sed 's/salmon \([0-9.]*\)/salmon: \1/' > /var/software_versions.txt
|
|
|
|
LABEL org.opencontainers.image.authors="Sai Nirmayi Yasa"
|
|
LABEL org.opencontainers.image.description="Companion container for running component salmon salmon_quant"
|
|
LABEL org.opencontainers.image.created="2024-09-27T09:55:23Z"
|
|
LABEL org.opencontainers.image.source="https://github.com/COMBINE-lab/salmon"
|
|
LABEL org.opencontainers.image.revision="237a2e3a229ee589d1ebbc282526f87398e26f58"
|
|
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)
|
|
|
|
# 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 "$1")"
|
|
shift 1
|
|
;;
|
|
--version)
|
|
echo "salmon_quant main"
|
|
exit
|
|
;;
|
|
--lib_type)
|
|
[ -n "$VIASH_PAR_LIB_TYPE" ] && ViashError Bad arguments for option \'--lib_type\': \'$VIASH_PAR_LIB_TYPE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_LIB_TYPE="$2"
|
|
[ $# -lt 2 ] && ViashError Not enough arguments passed to --lib_type. Use "--help" to get more information on the parameters. && exit 1
|
|
shift 2
|
|
;;
|
|
--lib_type=*)
|
|
[ -n "$VIASH_PAR_LIB_TYPE" ] && ViashError Bad arguments for option \'--lib_type=*\': \'$VIASH_PAR_LIB_TYPE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_LIB_TYPE=$(ViashRemoveFlags "$1")
|
|
shift 1
|
|
;;
|
|
-l)
|
|
[ -n "$VIASH_PAR_LIB_TYPE" ] && ViashError Bad arguments for option \'-l\': \'$VIASH_PAR_LIB_TYPE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_LIB_TYPE="$2"
|
|
[ $# -lt 2 ] && ViashError Not enough arguments passed to -l. Use "--help" to get more information on the parameters. && exit 1
|
|
shift 2
|
|
;;
|
|
--index)
|
|
[ -n "$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="$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 "$1")
|
|
shift 1
|
|
;;
|
|
-i)
|
|
[ -n "$VIASH_PAR_INDEX" ] && ViashError Bad arguments for option \'-i\': \'$VIASH_PAR_INDEX\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_INDEX="$2"
|
|
[ $# -lt 2 ] && ViashError Not enough arguments passed to -i. Use "--help" to get more information on the parameters. && exit 1
|
|
shift 2
|
|
;;
|
|
--unmated_reads)
|
|
if [ -z "$VIASH_PAR_UNMATED_READS" ]; then
|
|
VIASH_PAR_UNMATED_READS="$2"
|
|
else
|
|
VIASH_PAR_UNMATED_READS="$VIASH_PAR_UNMATED_READS;""$2"
|
|
fi
|
|
[ $# -lt 2 ] && ViashError Not enough arguments passed to --unmated_reads. Use "--help" to get more information on the parameters. && exit 1
|
|
shift 2
|
|
;;
|
|
--unmated_reads=*)
|
|
if [ -z "$VIASH_PAR_UNMATED_READS" ]; then
|
|
VIASH_PAR_UNMATED_READS=$(ViashRemoveFlags "$1")
|
|
else
|
|
VIASH_PAR_UNMATED_READS="$VIASH_PAR_UNMATED_READS;"$(ViashRemoveFlags "$1")
|
|
fi
|
|
shift 1
|
|
;;
|
|
-r)
|
|
if [ -z "$VIASH_PAR_UNMATED_READS" ]; then
|
|
VIASH_PAR_UNMATED_READS="$2"
|
|
else
|
|
VIASH_PAR_UNMATED_READS="$VIASH_PAR_UNMATED_READS;""$2"
|
|
fi
|
|
[ $# -lt 2 ] && ViashError Not enough arguments passed to -r. Use "--help" to get more information on the parameters. && exit 1
|
|
shift 2
|
|
;;
|
|
--mates1)
|
|
if [ -z "$VIASH_PAR_MATES1" ]; then
|
|
VIASH_PAR_MATES1="$2"
|
|
else
|
|
VIASH_PAR_MATES1="$VIASH_PAR_MATES1;""$2"
|
|
fi
|
|
[ $# -lt 2 ] && ViashError Not enough arguments passed to --mates1. Use "--help" to get more information on the parameters. && exit 1
|
|
shift 2
|
|
;;
|
|
--mates1=*)
|
|
if [ -z "$VIASH_PAR_MATES1" ]; then
|
|
VIASH_PAR_MATES1=$(ViashRemoveFlags "$1")
|
|
else
|
|
VIASH_PAR_MATES1="$VIASH_PAR_MATES1;"$(ViashRemoveFlags "$1")
|
|
fi
|
|
shift 1
|
|
;;
|
|
-m1)
|
|
if [ -z "$VIASH_PAR_MATES1" ]; then
|
|
VIASH_PAR_MATES1="$2"
|
|
else
|
|
VIASH_PAR_MATES1="$VIASH_PAR_MATES1;""$2"
|
|
fi
|
|
[ $# -lt 2 ] && ViashError Not enough arguments passed to -m1. Use "--help" to get more information on the parameters. && exit 1
|
|
shift 2
|
|
;;
|
|
--mates2)
|
|
if [ -z "$VIASH_PAR_MATES2" ]; then
|
|
VIASH_PAR_MATES2="$2"
|
|
else
|
|
VIASH_PAR_MATES2="$VIASH_PAR_MATES2;""$2"
|
|
fi
|
|
[ $# -lt 2 ] && ViashError Not enough arguments passed to --mates2. Use "--help" to get more information on the parameters. && exit 1
|
|
shift 2
|
|
;;
|
|
--mates2=*)
|
|
if [ -z "$VIASH_PAR_MATES2" ]; then
|
|
VIASH_PAR_MATES2=$(ViashRemoveFlags "$1")
|
|
else
|
|
VIASH_PAR_MATES2="$VIASH_PAR_MATES2;"$(ViashRemoveFlags "$1")
|
|
fi
|
|
shift 1
|
|
;;
|
|
-m2)
|
|
if [ -z "$VIASH_PAR_MATES2" ]; then
|
|
VIASH_PAR_MATES2="$2"
|
|
else
|
|
VIASH_PAR_MATES2="$VIASH_PAR_MATES2;""$2"
|
|
fi
|
|
[ $# -lt 2 ] && ViashError Not enough arguments passed to -m2. Use "--help" to get more information on the parameters. && exit 1
|
|
shift 2
|
|
;;
|
|
--discard_orphans)
|
|
[ -n "$VIASH_PAR_DISCARD_ORPHANS" ] && ViashError Bad arguments for option \'--discard_orphans\': \'$VIASH_PAR_DISCARD_ORPHANS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_DISCARD_ORPHANS=true
|
|
shift 1
|
|
;;
|
|
--alignments)
|
|
if [ -z "$VIASH_PAR_ALIGNMENTS" ]; then
|
|
VIASH_PAR_ALIGNMENTS="$2"
|
|
else
|
|
VIASH_PAR_ALIGNMENTS="$VIASH_PAR_ALIGNMENTS;""$2"
|
|
fi
|
|
[ $# -lt 2 ] && ViashError Not enough arguments passed to --alignments. Use "--help" to get more information on the parameters. && exit 1
|
|
shift 2
|
|
;;
|
|
--alignments=*)
|
|
if [ -z "$VIASH_PAR_ALIGNMENTS" ]; then
|
|
VIASH_PAR_ALIGNMENTS=$(ViashRemoveFlags "$1")
|
|
else
|
|
VIASH_PAR_ALIGNMENTS="$VIASH_PAR_ALIGNMENTS;"$(ViashRemoveFlags "$1")
|
|
fi
|
|
shift 1
|
|
;;
|
|
-a)
|
|
if [ -z "$VIASH_PAR_ALIGNMENTS" ]; then
|
|
VIASH_PAR_ALIGNMENTS="$2"
|
|
else
|
|
VIASH_PAR_ALIGNMENTS="$VIASH_PAR_ALIGNMENTS;""$2"
|
|
fi
|
|
[ $# -lt 2 ] && ViashError Not enough arguments passed to -a. Use "--help" to get more information on the parameters. && exit 1
|
|
shift 2
|
|
;;
|
|
--eqclasses)
|
|
[ -n "$VIASH_PAR_EQCLASSES" ] && ViashError Bad arguments for option \'--eqclasses\': \'$VIASH_PAR_EQCLASSES\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_EQCLASSES="$2"
|
|
[ $# -lt 2 ] && ViashError Not enough arguments passed to --eqclasses. Use "--help" to get more information on the parameters. && exit 1
|
|
shift 2
|
|
;;
|
|
--eqclasses=*)
|
|
[ -n "$VIASH_PAR_EQCLASSES" ] && ViashError Bad arguments for option \'--eqclasses=*\': \'$VIASH_PAR_EQCLASSES\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_EQCLASSES=$(ViashRemoveFlags "$1")
|
|
shift 1
|
|
;;
|
|
-e)
|
|
[ -n "$VIASH_PAR_EQCLASSES" ] && ViashError Bad arguments for option \'-e\': \'$VIASH_PAR_EQCLASSES\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_EQCLASSES="$2"
|
|
[ $# -lt 2 ] && ViashError Not enough arguments passed to -e. Use "--help" to get more information on the parameters. && exit 1
|
|
shift 2
|
|
;;
|
|
--targets)
|
|
[ -n "$VIASH_PAR_TARGETS" ] && ViashError Bad arguments for option \'--targets\': \'$VIASH_PAR_TARGETS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_TARGETS="$2"
|
|
[ $# -lt 2 ] && ViashError Not enough arguments passed to --targets. Use "--help" to get more information on the parameters. && exit 1
|
|
shift 2
|
|
;;
|
|
--targets=*)
|
|
[ -n "$VIASH_PAR_TARGETS" ] && ViashError Bad arguments for option \'--targets=*\': \'$VIASH_PAR_TARGETS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_TARGETS=$(ViashRemoveFlags "$1")
|
|
shift 1
|
|
;;
|
|
-t)
|
|
[ -n "$VIASH_PAR_TARGETS" ] && ViashError Bad arguments for option \'-t\': \'$VIASH_PAR_TARGETS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_TARGETS="$2"
|
|
[ $# -lt 2 ] && ViashError Not enough arguments passed to -t. Use "--help" to get more information on the parameters. && exit 1
|
|
shift 2
|
|
;;
|
|
--ont)
|
|
[ -n "$VIASH_PAR_ONT" ] && ViashError Bad arguments for option \'--ont\': \'$VIASH_PAR_ONT\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_ONT=true
|
|
shift 1
|
|
;;
|
|
--output)
|
|
[ -n "$VIASH_PAR_OUTPUT" ] && ViashError Bad arguments for option \'--output\': \'$VIASH_PAR_OUTPUT\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_OUTPUT="$2"
|
|
[ $# -lt 2 ] && ViashError Not enough arguments passed to --output. Use "--help" to get more information on the parameters. && exit 1
|
|
shift 2
|
|
;;
|
|
--output=*)
|
|
[ -n "$VIASH_PAR_OUTPUT" ] && ViashError Bad arguments for option \'--output=*\': \'$VIASH_PAR_OUTPUT\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_OUTPUT=$(ViashRemoveFlags "$1")
|
|
shift 1
|
|
;;
|
|
-o)
|
|
[ -n "$VIASH_PAR_OUTPUT" ] && ViashError Bad arguments for option \'-o\': \'$VIASH_PAR_OUTPUT\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_OUTPUT="$2"
|
|
[ $# -lt 2 ] && ViashError Not enough arguments passed to -o. Use "--help" to get more information on the parameters. && exit 1
|
|
shift 2
|
|
;;
|
|
--quant_results)
|
|
[ -n "$VIASH_PAR_QUANT_RESULTS" ] && ViashError Bad arguments for option \'--quant_results\': \'$VIASH_PAR_QUANT_RESULTS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_QUANT_RESULTS="$2"
|
|
[ $# -lt 2 ] && ViashError Not enough arguments passed to --quant_results. Use "--help" to get more information on the parameters. && exit 1
|
|
shift 2
|
|
;;
|
|
--quant_results=*)
|
|
[ -n "$VIASH_PAR_QUANT_RESULTS" ] && ViashError Bad arguments for option \'--quant_results=*\': \'$VIASH_PAR_QUANT_RESULTS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_QUANT_RESULTS=$(ViashRemoveFlags "$1")
|
|
shift 1
|
|
;;
|
|
--seq_bias)
|
|
[ -n "$VIASH_PAR_SEQ_BIAS" ] && ViashError Bad arguments for option \'--seq_bias\': \'$VIASH_PAR_SEQ_BIAS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_SEQ_BIAS=true
|
|
shift 1
|
|
;;
|
|
--gc_bias)
|
|
[ -n "$VIASH_PAR_GC_BIAS" ] && ViashError Bad arguments for option \'--gc_bias\': \'$VIASH_PAR_GC_BIAS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_GC_BIAS=true
|
|
shift 1
|
|
;;
|
|
--pos_bias)
|
|
[ -n "$VIASH_PAR_POS_BIAS" ] && ViashError Bad arguments for option \'--pos_bias\': \'$VIASH_PAR_POS_BIAS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_POS_BIAS=true
|
|
shift 1
|
|
;;
|
|
--incompat_prior)
|
|
[ -n "$VIASH_PAR_INCOMPAT_PRIOR" ] && ViashError Bad arguments for option \'--incompat_prior\': \'$VIASH_PAR_INCOMPAT_PRIOR\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_INCOMPAT_PRIOR="$2"
|
|
[ $# -lt 2 ] && ViashError Not enough arguments passed to --incompat_prior. Use "--help" to get more information on the parameters. && exit 1
|
|
shift 2
|
|
;;
|
|
--incompat_prior=*)
|
|
[ -n "$VIASH_PAR_INCOMPAT_PRIOR" ] && ViashError Bad arguments for option \'--incompat_prior=*\': \'$VIASH_PAR_INCOMPAT_PRIOR\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_INCOMPAT_PRIOR=$(ViashRemoveFlags "$1")
|
|
shift 1
|
|
;;
|
|
--gene_map)
|
|
[ -n "$VIASH_PAR_GENE_MAP" ] && ViashError Bad arguments for option \'--gene_map\': \'$VIASH_PAR_GENE_MAP\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_GENE_MAP="$2"
|
|
[ $# -lt 2 ] && ViashError Not enough arguments passed to --gene_map. Use "--help" to get more information on the parameters. && exit 1
|
|
shift 2
|
|
;;
|
|
--gene_map=*)
|
|
[ -n "$VIASH_PAR_GENE_MAP" ] && ViashError Bad arguments for option \'--gene_map=*\': \'$VIASH_PAR_GENE_MAP\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_GENE_MAP=$(ViashRemoveFlags "$1")
|
|
shift 1
|
|
;;
|
|
-g)
|
|
[ -n "$VIASH_PAR_GENE_MAP" ] && ViashError Bad arguments for option \'-g\': \'$VIASH_PAR_GENE_MAP\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_GENE_MAP="$2"
|
|
[ $# -lt 2 ] && ViashError Not enough arguments passed to -g. Use "--help" to get more information on the parameters. && exit 1
|
|
shift 2
|
|
;;
|
|
--aux_target_file)
|
|
[ -n "$VIASH_PAR_AUX_TARGET_FILE" ] && ViashError Bad arguments for option \'--aux_target_file\': \'$VIASH_PAR_AUX_TARGET_FILE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_AUX_TARGET_FILE="$2"
|
|
[ $# -lt 2 ] && ViashError Not enough arguments passed to --aux_target_file. Use "--help" to get more information on the parameters. && exit 1
|
|
shift 2
|
|
;;
|
|
--aux_target_file=*)
|
|
[ -n "$VIASH_PAR_AUX_TARGET_FILE" ] && ViashError Bad arguments for option \'--aux_target_file=*\': \'$VIASH_PAR_AUX_TARGET_FILE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_AUX_TARGET_FILE=$(ViashRemoveFlags "$1")
|
|
shift 1
|
|
;;
|
|
--meta)
|
|
[ -n "$VIASH_PAR_META" ] && ViashError Bad arguments for option \'--meta\': \'$VIASH_PAR_META\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_META=true
|
|
shift 1
|
|
;;
|
|
--score_exp)
|
|
[ -n "$VIASH_PAR_SCORE_EXP" ] && ViashError Bad arguments for option \'--score_exp\': \'$VIASH_PAR_SCORE_EXP\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_SCORE_EXP="$2"
|
|
[ $# -lt 2 ] && ViashError Not enough arguments passed to --score_exp. Use "--help" to get more information on the parameters. && exit 1
|
|
shift 2
|
|
;;
|
|
--score_exp=*)
|
|
[ -n "$VIASH_PAR_SCORE_EXP" ] && ViashError Bad arguments for option \'--score_exp=*\': \'$VIASH_PAR_SCORE_EXP\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_SCORE_EXP=$(ViashRemoveFlags "$1")
|
|
shift 1
|
|
;;
|
|
--discard_orphans_quasi)
|
|
[ -n "$VIASH_PAR_DISCARD_ORPHANS_QUASI" ] && ViashError Bad arguments for option \'--discard_orphans_quasi\': \'$VIASH_PAR_DISCARD_ORPHANS_QUASI\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_DISCARD_ORPHANS_QUASI=true
|
|
shift 1
|
|
;;
|
|
--consensus_slack)
|
|
[ -n "$VIASH_PAR_CONSENSUS_SLACK" ] && ViashError Bad arguments for option \'--consensus_slack\': \'$VIASH_PAR_CONSENSUS_SLACK\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_CONSENSUS_SLACK="$2"
|
|
[ $# -lt 2 ] && ViashError Not enough arguments passed to --consensus_slack. Use "--help" to get more information on the parameters. && exit 1
|
|
shift 2
|
|
;;
|
|
--consensus_slack=*)
|
|
[ -n "$VIASH_PAR_CONSENSUS_SLACK" ] && ViashError Bad arguments for option \'--consensus_slack=*\': \'$VIASH_PAR_CONSENSUS_SLACK\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_CONSENSUS_SLACK=$(ViashRemoveFlags "$1")
|
|
shift 1
|
|
;;
|
|
--pre_merge_chain_sub_thresh)
|
|
[ -n "$VIASH_PAR_PRE_MERGE_CHAIN_SUB_THRESH" ] && ViashError Bad arguments for option \'--pre_merge_chain_sub_thresh\': \'$VIASH_PAR_PRE_MERGE_CHAIN_SUB_THRESH\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_PRE_MERGE_CHAIN_SUB_THRESH="$2"
|
|
[ $# -lt 2 ] && ViashError Not enough arguments passed to --pre_merge_chain_sub_thresh. Use "--help" to get more information on the parameters. && exit 1
|
|
shift 2
|
|
;;
|
|
--pre_merge_chain_sub_thresh=*)
|
|
[ -n "$VIASH_PAR_PRE_MERGE_CHAIN_SUB_THRESH" ] && ViashError Bad arguments for option \'--pre_merge_chain_sub_thresh=*\': \'$VIASH_PAR_PRE_MERGE_CHAIN_SUB_THRESH\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_PRE_MERGE_CHAIN_SUB_THRESH=$(ViashRemoveFlags "$1")
|
|
shift 1
|
|
;;
|
|
--post_merge_chain_sub_thresh)
|
|
[ -n "$VIASH_PAR_POST_MERGE_CHAIN_SUB_THRESH" ] && ViashError Bad arguments for option \'--post_merge_chain_sub_thresh\': \'$VIASH_PAR_POST_MERGE_CHAIN_SUB_THRESH\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_POST_MERGE_CHAIN_SUB_THRESH="$2"
|
|
[ $# -lt 2 ] && ViashError Not enough arguments passed to --post_merge_chain_sub_thresh. Use "--help" to get more information on the parameters. && exit 1
|
|
shift 2
|
|
;;
|
|
--post_merge_chain_sub_thresh=*)
|
|
[ -n "$VIASH_PAR_POST_MERGE_CHAIN_SUB_THRESH" ] && ViashError Bad arguments for option \'--post_merge_chain_sub_thresh=*\': \'$VIASH_PAR_POST_MERGE_CHAIN_SUB_THRESH\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_POST_MERGE_CHAIN_SUB_THRESH=$(ViashRemoveFlags "$1")
|
|
shift 1
|
|
;;
|
|
--orphan_chain_sub_thresh)
|
|
[ -n "$VIASH_PAR_ORPHAN_CHAIN_SUB_THRESH" ] && ViashError Bad arguments for option \'--orphan_chain_sub_thresh\': \'$VIASH_PAR_ORPHAN_CHAIN_SUB_THRESH\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_ORPHAN_CHAIN_SUB_THRESH="$2"
|
|
[ $# -lt 2 ] && ViashError Not enough arguments passed to --orphan_chain_sub_thresh. Use "--help" to get more information on the parameters. && exit 1
|
|
shift 2
|
|
;;
|
|
--orphan_chain_sub_thresh=*)
|
|
[ -n "$VIASH_PAR_ORPHAN_CHAIN_SUB_THRESH" ] && ViashError Bad arguments for option \'--orphan_chain_sub_thresh=*\': \'$VIASH_PAR_ORPHAN_CHAIN_SUB_THRESH\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_ORPHAN_CHAIN_SUB_THRESH=$(ViashRemoveFlags "$1")
|
|
shift 1
|
|
;;
|
|
--min_score_fraction)
|
|
[ -n "$VIASH_PAR_MIN_SCORE_FRACTION" ] && ViashError Bad arguments for option \'--min_score_fraction\': \'$VIASH_PAR_MIN_SCORE_FRACTION\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_MIN_SCORE_FRACTION="$2"
|
|
[ $# -lt 2 ] && ViashError Not enough arguments passed to --min_score_fraction. Use "--help" to get more information on the parameters. && exit 1
|
|
shift 2
|
|
;;
|
|
--min_score_fraction=*)
|
|
[ -n "$VIASH_PAR_MIN_SCORE_FRACTION" ] && ViashError Bad arguments for option \'--min_score_fraction=*\': \'$VIASH_PAR_MIN_SCORE_FRACTION\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_MIN_SCORE_FRACTION=$(ViashRemoveFlags "$1")
|
|
shift 1
|
|
;;
|
|
--mismatch_seed_skip)
|
|
[ -n "$VIASH_PAR_MISMATCH_SEED_SKIP" ] && ViashError Bad arguments for option \'--mismatch_seed_skip\': \'$VIASH_PAR_MISMATCH_SEED_SKIP\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_MISMATCH_SEED_SKIP="$2"
|
|
[ $# -lt 2 ] && ViashError Not enough arguments passed to --mismatch_seed_skip. Use "--help" to get more information on the parameters. && exit 1
|
|
shift 2
|
|
;;
|
|
--mismatch_seed_skip=*)
|
|
[ -n "$VIASH_PAR_MISMATCH_SEED_SKIP" ] && ViashError Bad arguments for option \'--mismatch_seed_skip=*\': \'$VIASH_PAR_MISMATCH_SEED_SKIP\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_MISMATCH_SEED_SKIP=$(ViashRemoveFlags "$1")
|
|
shift 1
|
|
;;
|
|
--disable_chaining_heuristic)
|
|
[ -n "$VIASH_PAR_DISABLE_CHAINING_HEURISTIC" ] && ViashError Bad arguments for option \'--disable_chaining_heuristic\': \'$VIASH_PAR_DISABLE_CHAINING_HEURISTIC\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_DISABLE_CHAINING_HEURISTIC=true
|
|
shift 1
|
|
;;
|
|
--decoy_threshold)
|
|
[ -n "$VIASH_PAR_DECOY_THRESHOLD" ] && ViashError Bad arguments for option \'--decoy_threshold\': \'$VIASH_PAR_DECOY_THRESHOLD\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_DECOY_THRESHOLD="$2"
|
|
[ $# -lt 2 ] && ViashError Not enough arguments passed to --decoy_threshold. Use "--help" to get more information on the parameters. && exit 1
|
|
shift 2
|
|
;;
|
|
--decoy_threshold=*)
|
|
[ -n "$VIASH_PAR_DECOY_THRESHOLD" ] && ViashError Bad arguments for option \'--decoy_threshold=*\': \'$VIASH_PAR_DECOY_THRESHOLD\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_DECOY_THRESHOLD=$(ViashRemoveFlags "$1")
|
|
shift 1
|
|
;;
|
|
--ma)
|
|
[ -n "$VIASH_PAR_MA" ] && ViashError Bad arguments for option \'--ma\': \'$VIASH_PAR_MA\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_MA="$2"
|
|
[ $# -lt 2 ] && ViashError Not enough arguments passed to --ma. Use "--help" to get more information on the parameters. && exit 1
|
|
shift 2
|
|
;;
|
|
--ma=*)
|
|
[ -n "$VIASH_PAR_MA" ] && ViashError Bad arguments for option \'--ma=*\': \'$VIASH_PAR_MA\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_MA=$(ViashRemoveFlags "$1")
|
|
shift 1
|
|
;;
|
|
--mp)
|
|
[ -n "$VIASH_PAR_MP" ] && ViashError Bad arguments for option \'--mp\': \'$VIASH_PAR_MP\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_MP="$2"
|
|
[ $# -lt 2 ] && ViashError Not enough arguments passed to --mp. Use "--help" to get more information on the parameters. && exit 1
|
|
shift 2
|
|
;;
|
|
--mp=*)
|
|
[ -n "$VIASH_PAR_MP" ] && ViashError Bad arguments for option \'--mp=*\': \'$VIASH_PAR_MP\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_MP=$(ViashRemoveFlags "$1")
|
|
shift 1
|
|
;;
|
|
--go)
|
|
[ -n "$VIASH_PAR_GO" ] && ViashError Bad arguments for option \'--go\': \'$VIASH_PAR_GO\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_GO="$2"
|
|
[ $# -lt 2 ] && ViashError Not enough arguments passed to --go. Use "--help" to get more information on the parameters. && exit 1
|
|
shift 2
|
|
;;
|
|
--go=*)
|
|
[ -n "$VIASH_PAR_GO" ] && ViashError Bad arguments for option \'--go=*\': \'$VIASH_PAR_GO\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_GO=$(ViashRemoveFlags "$1")
|
|
shift 1
|
|
;;
|
|
--ge)
|
|
[ -n "$VIASH_PAR_GE" ] && ViashError Bad arguments for option \'--ge\': \'$VIASH_PAR_GE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_GE="$2"
|
|
[ $# -lt 2 ] && ViashError Not enough arguments passed to --ge. Use "--help" to get more information on the parameters. && exit 1
|
|
shift 2
|
|
;;
|
|
--ge=*)
|
|
[ -n "$VIASH_PAR_GE" ] && ViashError Bad arguments for option \'--ge=*\': \'$VIASH_PAR_GE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_GE=$(ViashRemoveFlags "$1")
|
|
shift 1
|
|
;;
|
|
--bandwidth)
|
|
[ -n "$VIASH_PAR_BANDWIDTH" ] && ViashError Bad arguments for option \'--bandwidth\': \'$VIASH_PAR_BANDWIDTH\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_BANDWIDTH="$2"
|
|
[ $# -lt 2 ] && ViashError Not enough arguments passed to --bandwidth. Use "--help" to get more information on the parameters. && exit 1
|
|
shift 2
|
|
;;
|
|
--bandwidth=*)
|
|
[ -n "$VIASH_PAR_BANDWIDTH" ] && ViashError Bad arguments for option \'--bandwidth=*\': \'$VIASH_PAR_BANDWIDTH\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_BANDWIDTH=$(ViashRemoveFlags "$1")
|
|
shift 1
|
|
;;
|
|
--allow_dovetail)
|
|
[ -n "$VIASH_PAR_ALLOW_DOVETAIL" ] && ViashError Bad arguments for option \'--allow_dovetail\': \'$VIASH_PAR_ALLOW_DOVETAIL\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_ALLOW_DOVETAIL=true
|
|
shift 1
|
|
;;
|
|
--recover_orphans)
|
|
[ -n "$VIASH_PAR_RECOVER_ORPHANS" ] && ViashError Bad arguments for option \'--recover_orphans\': \'$VIASH_PAR_RECOVER_ORPHANS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_RECOVER_ORPHANS=true
|
|
shift 1
|
|
;;
|
|
--mimicBT2)
|
|
[ -n "$VIASH_PAR_MIMICBT2" ] && ViashError Bad arguments for option \'--mimicBT2\': \'$VIASH_PAR_MIMICBT2\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_MIMICBT2=true
|
|
shift 1
|
|
;;
|
|
--mimic_strictBT2)
|
|
[ -n "$VIASH_PAR_MIMIC_STRICTBT2" ] && ViashError Bad arguments for option \'--mimic_strictBT2\': \'$VIASH_PAR_MIMIC_STRICTBT2\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_MIMIC_STRICTBT2=true
|
|
shift 1
|
|
;;
|
|
--softclip)
|
|
[ -n "$VIASH_PAR_SOFTCLIP" ] && ViashError Bad arguments for option \'--softclip\': \'$VIASH_PAR_SOFTCLIP\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_SOFTCLIP=true
|
|
shift 1
|
|
;;
|
|
--softclip_overhangs)
|
|
[ -n "$VIASH_PAR_SOFTCLIP_OVERHANGS" ] && ViashError Bad arguments for option \'--softclip_overhangs\': \'$VIASH_PAR_SOFTCLIP_OVERHANGS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_SOFTCLIP_OVERHANGS=true
|
|
shift 1
|
|
;;
|
|
--full_length_alignment)
|
|
[ -n "$VIASH_PAR_FULL_LENGTH_ALIGNMENT" ] && ViashError Bad arguments for option \'--full_length_alignment\': \'$VIASH_PAR_FULL_LENGTH_ALIGNMENT\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_FULL_LENGTH_ALIGNMENT=true
|
|
shift 1
|
|
;;
|
|
--hard_filter)
|
|
[ -n "$VIASH_PAR_HARD_FILTER" ] && ViashError Bad arguments for option \'--hard_filter\': \'$VIASH_PAR_HARD_FILTER\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_HARD_FILTER=true
|
|
shift 1
|
|
;;
|
|
--min_aln_prob)
|
|
[ -n "$VIASH_PAR_MIN_ALN_PROB" ] && ViashError Bad arguments for option \'--min_aln_prob\': \'$VIASH_PAR_MIN_ALN_PROB\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_MIN_ALN_PROB="$2"
|
|
[ $# -lt 2 ] && ViashError Not enough arguments passed to --min_aln_prob. Use "--help" to get more information on the parameters. && exit 1
|
|
shift 2
|
|
;;
|
|
--min_aln_prob=*)
|
|
[ -n "$VIASH_PAR_MIN_ALN_PROB" ] && ViashError Bad arguments for option \'--min_aln_prob=*\': \'$VIASH_PAR_MIN_ALN_PROB\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_MIN_ALN_PROB=$(ViashRemoveFlags "$1")
|
|
shift 1
|
|
;;
|
|
--write_mappings)
|
|
[ -n "$VIASH_PAR_WRITE_MAPPINGS" ] && ViashError Bad arguments for option \'--write_mappings\': \'$VIASH_PAR_WRITE_MAPPINGS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_WRITE_MAPPINGS=true
|
|
shift 1
|
|
;;
|
|
-z)
|
|
[ -n "$VIASH_PAR_WRITE_MAPPINGS" ] && ViashError Bad arguments for option \'-z\': \'$VIASH_PAR_WRITE_MAPPINGS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_WRITE_MAPPINGS=true
|
|
shift 1
|
|
;;
|
|
--mapping_sam)
|
|
[ -n "$VIASH_PAR_MAPPING_SAM" ] && ViashError Bad arguments for option \'--mapping_sam\': \'$VIASH_PAR_MAPPING_SAM\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_MAPPING_SAM="$2"
|
|
[ $# -lt 2 ] && ViashError Not enough arguments passed to --mapping_sam. Use "--help" to get more information on the parameters. && exit 1
|
|
shift 2
|
|
;;
|
|
--mapping_sam=*)
|
|
[ -n "$VIASH_PAR_MAPPING_SAM" ] && ViashError Bad arguments for option \'--mapping_sam=*\': \'$VIASH_PAR_MAPPING_SAM\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_MAPPING_SAM=$(ViashRemoveFlags "$1")
|
|
shift 1
|
|
;;
|
|
--write_qualities)
|
|
[ -n "$VIASH_PAR_WRITE_QUALITIES" ] && ViashError Bad arguments for option \'--write_qualities\': \'$VIASH_PAR_WRITE_QUALITIES\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_WRITE_QUALITIES=true
|
|
shift 1
|
|
;;
|
|
--hit_filter_policy)
|
|
[ -n "$VIASH_PAR_HIT_FILTER_POLICY" ] && ViashError Bad arguments for option \'--hit_filter_policy\': \'$VIASH_PAR_HIT_FILTER_POLICY\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_HIT_FILTER_POLICY="$2"
|
|
[ $# -lt 2 ] && ViashError Not enough arguments passed to --hit_filter_policy. Use "--help" to get more information on the parameters. && exit 1
|
|
shift 2
|
|
;;
|
|
--hit_filter_policy=*)
|
|
[ -n "$VIASH_PAR_HIT_FILTER_POLICY" ] && ViashError Bad arguments for option \'--hit_filter_policy=*\': \'$VIASH_PAR_HIT_FILTER_POLICY\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_HIT_FILTER_POLICY=$(ViashRemoveFlags "$1")
|
|
shift 1
|
|
;;
|
|
--alternative_init_mode)
|
|
[ -n "$VIASH_PAR_ALTERNATIVE_INIT_MODE" ] && ViashError Bad arguments for option \'--alternative_init_mode\': \'$VIASH_PAR_ALTERNATIVE_INIT_MODE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_ALTERNATIVE_INIT_MODE=true
|
|
shift 1
|
|
;;
|
|
--aux_dir)
|
|
[ -n "$VIASH_PAR_AUX_DIR" ] && ViashError Bad arguments for option \'--aux_dir\': \'$VIASH_PAR_AUX_DIR\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_AUX_DIR="$2"
|
|
[ $# -lt 2 ] && ViashError Not enough arguments passed to --aux_dir. Use "--help" to get more information on the parameters. && exit 1
|
|
shift 2
|
|
;;
|
|
--aux_dir=*)
|
|
[ -n "$VIASH_PAR_AUX_DIR" ] && ViashError Bad arguments for option \'--aux_dir=*\': \'$VIASH_PAR_AUX_DIR\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_AUX_DIR=$(ViashRemoveFlags "$1")
|
|
shift 1
|
|
;;
|
|
--skip_quant)
|
|
[ -n "$VIASH_PAR_SKIP_QUANT" ] && ViashError Bad arguments for option \'--skip_quant\': \'$VIASH_PAR_SKIP_QUANT\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_SKIP_QUANT=true
|
|
shift 1
|
|
;;
|
|
--dump_eq)
|
|
[ -n "$VIASH_PAR_DUMP_EQ" ] && ViashError Bad arguments for option \'--dump_eq\': \'$VIASH_PAR_DUMP_EQ\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_DUMP_EQ=true
|
|
shift 1
|
|
;;
|
|
--dump_eq_weights)
|
|
[ -n "$VIASH_PAR_DUMP_EQ_WEIGHTS" ] && ViashError Bad arguments for option \'--dump_eq_weights\': \'$VIASH_PAR_DUMP_EQ_WEIGHTS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_DUMP_EQ_WEIGHTS=true
|
|
shift 1
|
|
;;
|
|
-d)
|
|
[ -n "$VIASH_PAR_DUMP_EQ_WEIGHTS" ] && ViashError Bad arguments for option \'-d\': \'$VIASH_PAR_DUMP_EQ_WEIGHTS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_DUMP_EQ_WEIGHTS=true
|
|
shift 1
|
|
;;
|
|
--min_assigned_frags)
|
|
[ -n "$VIASH_PAR_MIN_ASSIGNED_FRAGS" ] && ViashError Bad arguments for option \'--min_assigned_frags\': \'$VIASH_PAR_MIN_ASSIGNED_FRAGS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_MIN_ASSIGNED_FRAGS="$2"
|
|
[ $# -lt 2 ] && ViashError Not enough arguments passed to --min_assigned_frags. Use "--help" to get more information on the parameters. && exit 1
|
|
shift 2
|
|
;;
|
|
--min_assigned_frags=*)
|
|
[ -n "$VIASH_PAR_MIN_ASSIGNED_FRAGS" ] && ViashError Bad arguments for option \'--min_assigned_frags=*\': \'$VIASH_PAR_MIN_ASSIGNED_FRAGS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_MIN_ASSIGNED_FRAGS=$(ViashRemoveFlags "$1")
|
|
shift 1
|
|
;;
|
|
--reduce_GC_memory)
|
|
[ -n "$VIASH_PAR_REDUCE_GC_MEMORY" ] && ViashError Bad arguments for option \'--reduce_GC_memory\': \'$VIASH_PAR_REDUCE_GC_MEMORY\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_REDUCE_GC_MEMORY=true
|
|
shift 1
|
|
;;
|
|
--bias_speed_samp)
|
|
[ -n "$VIASH_PAR_BIAS_SPEED_SAMP" ] && ViashError Bad arguments for option \'--bias_speed_samp\': \'$VIASH_PAR_BIAS_SPEED_SAMP\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_BIAS_SPEED_SAMP="$2"
|
|
[ $# -lt 2 ] && ViashError Not enough arguments passed to --bias_speed_samp. Use "--help" to get more information on the parameters. && exit 1
|
|
shift 2
|
|
;;
|
|
--bias_speed_samp=*)
|
|
[ -n "$VIASH_PAR_BIAS_SPEED_SAMP" ] && ViashError Bad arguments for option \'--bias_speed_samp=*\': \'$VIASH_PAR_BIAS_SPEED_SAMP\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_BIAS_SPEED_SAMP=$(ViashRemoveFlags "$1")
|
|
shift 1
|
|
;;
|
|
--fld_max)
|
|
[ -n "$VIASH_PAR_FLD_MAX" ] && ViashError Bad arguments for option \'--fld_max\': \'$VIASH_PAR_FLD_MAX\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_FLD_MAX="$2"
|
|
[ $# -lt 2 ] && ViashError Not enough arguments passed to --fld_max. Use "--help" to get more information on the parameters. && exit 1
|
|
shift 2
|
|
;;
|
|
--fld_max=*)
|
|
[ -n "$VIASH_PAR_FLD_MAX" ] && ViashError Bad arguments for option \'--fld_max=*\': \'$VIASH_PAR_FLD_MAX\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_FLD_MAX=$(ViashRemoveFlags "$1")
|
|
shift 1
|
|
;;
|
|
--fld_mean)
|
|
[ -n "$VIASH_PAR_FLD_MEAN" ] && ViashError Bad arguments for option \'--fld_mean\': \'$VIASH_PAR_FLD_MEAN\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_FLD_MEAN="$2"
|
|
[ $# -lt 2 ] && ViashError Not enough arguments passed to --fld_mean. Use "--help" to get more information on the parameters. && exit 1
|
|
shift 2
|
|
;;
|
|
--fld_mean=*)
|
|
[ -n "$VIASH_PAR_FLD_MEAN" ] && ViashError Bad arguments for option \'--fld_mean=*\': \'$VIASH_PAR_FLD_MEAN\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_FLD_MEAN=$(ViashRemoveFlags "$1")
|
|
shift 1
|
|
;;
|
|
--fld_SD)
|
|
[ -n "$VIASH_PAR_FLD_SD" ] && ViashError Bad arguments for option \'--fld_SD\': \'$VIASH_PAR_FLD_SD\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_FLD_SD="$2"
|
|
[ $# -lt 2 ] && ViashError Not enough arguments passed to --fld_SD. Use "--help" to get more information on the parameters. && exit 1
|
|
shift 2
|
|
;;
|
|
--fld_SD=*)
|
|
[ -n "$VIASH_PAR_FLD_SD" ] && ViashError Bad arguments for option \'--fld_SD=*\': \'$VIASH_PAR_FLD_SD\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_FLD_SD=$(ViashRemoveFlags "$1")
|
|
shift 1
|
|
;;
|
|
--forgetting_factor)
|
|
[ -n "$VIASH_PAR_FORGETTING_FACTOR" ] && ViashError Bad arguments for option \'--forgetting_factor\': \'$VIASH_PAR_FORGETTING_FACTOR\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_FORGETTING_FACTOR="$2"
|
|
[ $# -lt 2 ] && ViashError Not enough arguments passed to --forgetting_factor. Use "--help" to get more information on the parameters. && exit 1
|
|
shift 2
|
|
;;
|
|
--forgetting_factor=*)
|
|
[ -n "$VIASH_PAR_FORGETTING_FACTOR" ] && ViashError Bad arguments for option \'--forgetting_factor=*\': \'$VIASH_PAR_FORGETTING_FACTOR\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_FORGETTING_FACTOR=$(ViashRemoveFlags "$1")
|
|
shift 1
|
|
;;
|
|
-f)
|
|
[ -n "$VIASH_PAR_FORGETTING_FACTOR" ] && ViashError Bad arguments for option \'-f\': \'$VIASH_PAR_FORGETTING_FACTOR\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_FORGETTING_FACTOR="$2"
|
|
[ $# -lt 2 ] && ViashError Not enough arguments passed to -f. Use "--help" to get more information on the parameters. && exit 1
|
|
shift 2
|
|
;;
|
|
--init_uniform)
|
|
[ -n "$VIASH_PAR_INIT_UNIFORM" ] && ViashError Bad arguments for option \'--init_uniform\': \'$VIASH_PAR_INIT_UNIFORM\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_INIT_UNIFORM=true
|
|
shift 1
|
|
;;
|
|
--max_occs_per_hit)
|
|
[ -n "$VIASH_PAR_MAX_OCCS_PER_HIT" ] && ViashError Bad arguments for option \'--max_occs_per_hit\': \'$VIASH_PAR_MAX_OCCS_PER_HIT\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_MAX_OCCS_PER_HIT="$2"
|
|
[ $# -lt 2 ] && ViashError Not enough arguments passed to --max_occs_per_hit. Use "--help" to get more information on the parameters. && exit 1
|
|
shift 2
|
|
;;
|
|
--max_occs_per_hit=*)
|
|
[ -n "$VIASH_PAR_MAX_OCCS_PER_HIT" ] && ViashError Bad arguments for option \'--max_occs_per_hit=*\': \'$VIASH_PAR_MAX_OCCS_PER_HIT\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_MAX_OCCS_PER_HIT=$(ViashRemoveFlags "$1")
|
|
shift 1
|
|
;;
|
|
--max_read_occ)
|
|
[ -n "$VIASH_PAR_MAX_READ_OCC" ] && ViashError Bad arguments for option \'--max_read_occ\': \'$VIASH_PAR_MAX_READ_OCC\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_MAX_READ_OCC="$2"
|
|
[ $# -lt 2 ] && ViashError Not enough arguments passed to --max_read_occ. Use "--help" to get more information on the parameters. && exit 1
|
|
shift 2
|
|
;;
|
|
--max_read_occ=*)
|
|
[ -n "$VIASH_PAR_MAX_READ_OCC" ] && ViashError Bad arguments for option \'--max_read_occ=*\': \'$VIASH_PAR_MAX_READ_OCC\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_MAX_READ_OCC=$(ViashRemoveFlags "$1")
|
|
shift 1
|
|
;;
|
|
--no_length_correction)
|
|
[ -n "$VIASH_PAR_NO_LENGTH_CORRECTION" ] && ViashError Bad arguments for option \'--no_length_correction\': \'$VIASH_PAR_NO_LENGTH_CORRECTION\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_NO_LENGTH_CORRECTION=true
|
|
shift 1
|
|
;;
|
|
--no_effective_length_correction)
|
|
[ -n "$VIASH_PAR_NO_EFFECTIVE_LENGTH_CORRECTION" ] && ViashError Bad arguments for option \'--no_effective_length_correction\': \'$VIASH_PAR_NO_EFFECTIVE_LENGTH_CORRECTION\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_NO_EFFECTIVE_LENGTH_CORRECTION=true
|
|
shift 1
|
|
;;
|
|
--no_single_frag_prob)
|
|
[ -n "$VIASH_PAR_NO_SINGLE_FRAG_PROB" ] && ViashError Bad arguments for option \'--no_single_frag_prob\': \'$VIASH_PAR_NO_SINGLE_FRAG_PROB\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_NO_SINGLE_FRAG_PROB=true
|
|
shift 1
|
|
;;
|
|
--no_frag_length_dist)
|
|
[ -n "$VIASH_PAR_NO_FRAG_LENGTH_DIST" ] && ViashError Bad arguments for option \'--no_frag_length_dist\': \'$VIASH_PAR_NO_FRAG_LENGTH_DIST\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_NO_FRAG_LENGTH_DIST=true
|
|
shift 1
|
|
;;
|
|
--no_bias_length_threshold)
|
|
[ -n "$VIASH_PAR_NO_BIAS_LENGTH_THRESHOLD" ] && ViashError Bad arguments for option \'--no_bias_length_threshold\': \'$VIASH_PAR_NO_BIAS_LENGTH_THRESHOLD\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_NO_BIAS_LENGTH_THRESHOLD=true
|
|
shift 1
|
|
;;
|
|
--num_bias_samples)
|
|
[ -n "$VIASH_PAR_NUM_BIAS_SAMPLES" ] && ViashError Bad arguments for option \'--num_bias_samples\': \'$VIASH_PAR_NUM_BIAS_SAMPLES\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_NUM_BIAS_SAMPLES="$2"
|
|
[ $# -lt 2 ] && ViashError Not enough arguments passed to --num_bias_samples. Use "--help" to get more information on the parameters. && exit 1
|
|
shift 2
|
|
;;
|
|
--num_bias_samples=*)
|
|
[ -n "$VIASH_PAR_NUM_BIAS_SAMPLES" ] && ViashError Bad arguments for option \'--num_bias_samples=*\': \'$VIASH_PAR_NUM_BIAS_SAMPLES\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_NUM_BIAS_SAMPLES=$(ViashRemoveFlags "$1")
|
|
shift 1
|
|
;;
|
|
--num_aux_model_samples)
|
|
[ -n "$VIASH_PAR_NUM_AUX_MODEL_SAMPLES" ] && ViashError Bad arguments for option \'--num_aux_model_samples\': \'$VIASH_PAR_NUM_AUX_MODEL_SAMPLES\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_NUM_AUX_MODEL_SAMPLES="$2"
|
|
[ $# -lt 2 ] && ViashError Not enough arguments passed to --num_aux_model_samples. Use "--help" to get more information on the parameters. && exit 1
|
|
shift 2
|
|
;;
|
|
--num_aux_model_samples=*)
|
|
[ -n "$VIASH_PAR_NUM_AUX_MODEL_SAMPLES" ] && ViashError Bad arguments for option \'--num_aux_model_samples=*\': \'$VIASH_PAR_NUM_AUX_MODEL_SAMPLES\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_NUM_AUX_MODEL_SAMPLES=$(ViashRemoveFlags "$1")
|
|
shift 1
|
|
;;
|
|
--num_pre_aux_model_samples)
|
|
[ -n "$VIASH_PAR_NUM_PRE_AUX_MODEL_SAMPLES" ] && ViashError Bad arguments for option \'--num_pre_aux_model_samples\': \'$VIASH_PAR_NUM_PRE_AUX_MODEL_SAMPLES\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_NUM_PRE_AUX_MODEL_SAMPLES="$2"
|
|
[ $# -lt 2 ] && ViashError Not enough arguments passed to --num_pre_aux_model_samples. Use "--help" to get more information on the parameters. && exit 1
|
|
shift 2
|
|
;;
|
|
--num_pre_aux_model_samples=*)
|
|
[ -n "$VIASH_PAR_NUM_PRE_AUX_MODEL_SAMPLES" ] && ViashError Bad arguments for option \'--num_pre_aux_model_samples=*\': \'$VIASH_PAR_NUM_PRE_AUX_MODEL_SAMPLES\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_NUM_PRE_AUX_MODEL_SAMPLES=$(ViashRemoveFlags "$1")
|
|
shift 1
|
|
;;
|
|
--useEM)
|
|
[ -n "$VIASH_PAR_USEEM" ] && ViashError Bad arguments for option \'--useEM\': \'$VIASH_PAR_USEEM\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_USEEM=true
|
|
shift 1
|
|
;;
|
|
--useVBOpt)
|
|
[ -n "$VIASH_PAR_USEVBOPT" ] && ViashError Bad arguments for option \'--useVBOpt\': \'$VIASH_PAR_USEVBOPT\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_USEVBOPT=true
|
|
shift 1
|
|
;;
|
|
--range_factorization_bins)
|
|
[ -n "$VIASH_PAR_RANGE_FACTORIZATION_BINS" ] && ViashError Bad arguments for option \'--range_factorization_bins\': \'$VIASH_PAR_RANGE_FACTORIZATION_BINS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_RANGE_FACTORIZATION_BINS="$2"
|
|
[ $# -lt 2 ] && ViashError Not enough arguments passed to --range_factorization_bins. Use "--help" to get more information on the parameters. && exit 1
|
|
shift 2
|
|
;;
|
|
--range_factorization_bins=*)
|
|
[ -n "$VIASH_PAR_RANGE_FACTORIZATION_BINS" ] && ViashError Bad arguments for option \'--range_factorization_bins=*\': \'$VIASH_PAR_RANGE_FACTORIZATION_BINS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_RANGE_FACTORIZATION_BINS=$(ViashRemoveFlags "$1")
|
|
shift 1
|
|
;;
|
|
--num_Gibbs_samples)
|
|
[ -n "$VIASH_PAR_NUM_GIBBS_SAMPLES" ] && ViashError Bad arguments for option \'--num_Gibbs_samples\': \'$VIASH_PAR_NUM_GIBBS_SAMPLES\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_NUM_GIBBS_SAMPLES="$2"
|
|
[ $# -lt 2 ] && ViashError Not enough arguments passed to --num_Gibbs_samples. Use "--help" to get more information on the parameters. && exit 1
|
|
shift 2
|
|
;;
|
|
--num_Gibbs_samples=*)
|
|
[ -n "$VIASH_PAR_NUM_GIBBS_SAMPLES" ] && ViashError Bad arguments for option \'--num_Gibbs_samples=*\': \'$VIASH_PAR_NUM_GIBBS_SAMPLES\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_NUM_GIBBS_SAMPLES=$(ViashRemoveFlags "$1")
|
|
shift 1
|
|
;;
|
|
--no_Gamma_draw)
|
|
[ -n "$VIASH_PAR_NO_GAMMA_DRAW" ] && ViashError Bad arguments for option \'--no_Gamma_draw\': \'$VIASH_PAR_NO_GAMMA_DRAW\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_NO_GAMMA_DRAW=true
|
|
shift 1
|
|
;;
|
|
--num_bootstraps)
|
|
[ -n "$VIASH_PAR_NUM_BOOTSTRAPS" ] && ViashError Bad arguments for option \'--num_bootstraps\': \'$VIASH_PAR_NUM_BOOTSTRAPS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_NUM_BOOTSTRAPS="$2"
|
|
[ $# -lt 2 ] && ViashError Not enough arguments passed to --num_bootstraps. Use "--help" to get more information on the parameters. && exit 1
|
|
shift 2
|
|
;;
|
|
--num_bootstraps=*)
|
|
[ -n "$VIASH_PAR_NUM_BOOTSTRAPS" ] && ViashError Bad arguments for option \'--num_bootstraps=*\': \'$VIASH_PAR_NUM_BOOTSTRAPS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_NUM_BOOTSTRAPS=$(ViashRemoveFlags "$1")
|
|
shift 1
|
|
;;
|
|
--bootstrap_reproject)
|
|
[ -n "$VIASH_PAR_BOOTSTRAP_REPROJECT" ] && ViashError Bad arguments for option \'--bootstrap_reproject\': \'$VIASH_PAR_BOOTSTRAP_REPROJECT\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_BOOTSTRAP_REPROJECT=true
|
|
shift 1
|
|
;;
|
|
--thinning_factor)
|
|
[ -n "$VIASH_PAR_THINNING_FACTOR" ] && ViashError Bad arguments for option \'--thinning_factor\': \'$VIASH_PAR_THINNING_FACTOR\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_THINNING_FACTOR="$2"
|
|
[ $# -lt 2 ] && ViashError Not enough arguments passed to --thinning_factor. Use "--help" to get more information on the parameters. && exit 1
|
|
shift 2
|
|
;;
|
|
--thinning_factor=*)
|
|
[ -n "$VIASH_PAR_THINNING_FACTOR" ] && ViashError Bad arguments for option \'--thinning_factor=*\': \'$VIASH_PAR_THINNING_FACTOR\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_THINNING_FACTOR=$(ViashRemoveFlags "$1")
|
|
shift 1
|
|
;;
|
|
--quiet)
|
|
[ -n "$VIASH_PAR_QUIET" ] && ViashError Bad arguments for option \'--quiet\': \'$VIASH_PAR_QUIET\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_QUIET=true
|
|
shift 1
|
|
;;
|
|
-q)
|
|
[ -n "$VIASH_PAR_QUIET" ] && ViashError Bad arguments for option \'-q\': \'$VIASH_PAR_QUIET\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_QUIET=true
|
|
shift 1
|
|
;;
|
|
--per_transcript_prior)
|
|
[ -n "$VIASH_PAR_PER_TRANSCRIPT_PRIOR" ] && ViashError Bad arguments for option \'--per_transcript_prior\': \'$VIASH_PAR_PER_TRANSCRIPT_PRIOR\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_PER_TRANSCRIPT_PRIOR=true
|
|
shift 1
|
|
;;
|
|
--per_nucleotide_prior)
|
|
[ -n "$VIASH_PAR_PER_NUCLEOTIDE_PRIOR" ] && ViashError Bad arguments for option \'--per_nucleotide_prior\': \'$VIASH_PAR_PER_NUCLEOTIDE_PRIOR\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_PER_NUCLEOTIDE_PRIOR=true
|
|
shift 1
|
|
;;
|
|
--sig_digits)
|
|
[ -n "$VIASH_PAR_SIG_DIGITS" ] && ViashError Bad arguments for option \'--sig_digits\': \'$VIASH_PAR_SIG_DIGITS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_SIG_DIGITS="$2"
|
|
[ $# -lt 2 ] && ViashError Not enough arguments passed to --sig_digits. Use "--help" to get more information on the parameters. && exit 1
|
|
shift 2
|
|
;;
|
|
--sig_digits=*)
|
|
[ -n "$VIASH_PAR_SIG_DIGITS" ] && ViashError Bad arguments for option \'--sig_digits=*\': \'$VIASH_PAR_SIG_DIGITS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_SIG_DIGITS=$(ViashRemoveFlags "$1")
|
|
shift 1
|
|
;;
|
|
--vb_prior)
|
|
[ -n "$VIASH_PAR_VB_PRIOR" ] && ViashError Bad arguments for option \'--vb_prior\': \'$VIASH_PAR_VB_PRIOR\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_VB_PRIOR="$2"
|
|
[ $# -lt 2 ] && ViashError Not enough arguments passed to --vb_prior. Use "--help" to get more information on the parameters. && exit 1
|
|
shift 2
|
|
;;
|
|
--vb_prior=*)
|
|
[ -n "$VIASH_PAR_VB_PRIOR" ] && ViashError Bad arguments for option \'--vb_prior=*\': \'$VIASH_PAR_VB_PRIOR\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_VB_PRIOR=$(ViashRemoveFlags "$1")
|
|
shift 1
|
|
;;
|
|
--write_orphan_links)
|
|
[ -n "$VIASH_PAR_WRITE_ORPHAN_LINKS" ] && ViashError Bad arguments for option \'--write_orphan_links\': \'$VIASH_PAR_WRITE_ORPHAN_LINKS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_WRITE_ORPHAN_LINKS=true
|
|
shift 1
|
|
;;
|
|
--write_unmapped_names)
|
|
[ -n "$VIASH_PAR_WRITE_UNMAPPED_NAMES" ] && ViashError Bad arguments for option \'--write_unmapped_names\': \'$VIASH_PAR_WRITE_UNMAPPED_NAMES\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_WRITE_UNMAPPED_NAMES=true
|
|
shift 1
|
|
;;
|
|
--no_error_model)
|
|
[ -n "$VIASH_PAR_NO_ERROR_MODEL" ] && ViashError Bad arguments for option \'--no_error_model\': \'$VIASH_PAR_NO_ERROR_MODEL\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_NO_ERROR_MODEL=true
|
|
shift 1
|
|
;;
|
|
--num_error_bins)
|
|
[ -n "$VIASH_PAR_NUM_ERROR_BINS" ] && ViashError Bad arguments for option \'--num_error_bins\': \'$VIASH_PAR_NUM_ERROR_BINS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_NUM_ERROR_BINS="$2"
|
|
[ $# -lt 2 ] && ViashError Not enough arguments passed to --num_error_bins. Use "--help" to get more information on the parameters. && exit 1
|
|
shift 2
|
|
;;
|
|
--num_error_bins=*)
|
|
[ -n "$VIASH_PAR_NUM_ERROR_BINS" ] && ViashError Bad arguments for option \'--num_error_bins=*\': \'$VIASH_PAR_NUM_ERROR_BINS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_NUM_ERROR_BINS=$(ViashRemoveFlags "$1")
|
|
shift 1
|
|
;;
|
|
--sample_out)
|
|
[ -n "$VIASH_PAR_SAMPLE_OUT" ] && ViashError Bad arguments for option \'--sample_out\': \'$VIASH_PAR_SAMPLE_OUT\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_SAMPLE_OUT=true
|
|
shift 1
|
|
;;
|
|
-s)
|
|
[ -n "$VIASH_PAR_SAMPLE_OUT" ] && ViashError Bad arguments for option \'-s\': \'$VIASH_PAR_SAMPLE_OUT\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_SAMPLE_OUT=true
|
|
shift 1
|
|
;;
|
|
--sample_unaligned)
|
|
[ -n "$VIASH_PAR_SAMPLE_UNALIGNED" ] && ViashError Bad arguments for option \'--sample_unaligned\': \'$VIASH_PAR_SAMPLE_UNALIGNED\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_SAMPLE_UNALIGNED=true
|
|
shift 1
|
|
;;
|
|
-u)
|
|
[ -n "$VIASH_PAR_SAMPLE_UNALIGNED" ] && ViashError Bad arguments for option \'-u\': \'$VIASH_PAR_SAMPLE_UNALIGNED\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_SAMPLE_UNALIGNED=true
|
|
shift 1
|
|
;;
|
|
--gencode)
|
|
[ -n "$VIASH_PAR_GENCODE" ] && ViashError Bad arguments for option \'--gencode\': \'$VIASH_PAR_GENCODE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_GENCODE=true
|
|
shift 1
|
|
;;
|
|
--mapping_cache_memory_limit)
|
|
[ -n "$VIASH_PAR_MAPPING_CACHE_MEMORY_LIMIT" ] && ViashError Bad arguments for option \'--mapping_cache_memory_limit\': \'$VIASH_PAR_MAPPING_CACHE_MEMORY_LIMIT\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_MAPPING_CACHE_MEMORY_LIMIT="$2"
|
|
[ $# -lt 2 ] && ViashError Not enough arguments passed to --mapping_cache_memory_limit. Use "--help" to get more information on the parameters. && exit 1
|
|
shift 2
|
|
;;
|
|
--mapping_cache_memory_limit=*)
|
|
[ -n "$VIASH_PAR_MAPPING_CACHE_MEMORY_LIMIT" ] && ViashError Bad arguments for option \'--mapping_cache_memory_limit=*\': \'$VIASH_PAR_MAPPING_CACHE_MEMORY_LIMIT\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_MAPPING_CACHE_MEMORY_LIMIT=$(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/salmon/salmon_quant:main'
|
|
fi
|
|
|
|
# print dockerfile
|
|
if [ "$VIASH_MODE" == "dockerfile" ]; then
|
|
ViashDockerfile "$VIASH_ENGINE_ID"
|
|
exit 0
|
|
|
|
elif [ "$VIASH_MODE" == "docker_image_id" ]; then
|
|
echo "$VIASH_DOCKER_IMAGE_ID"
|
|
exit 0
|
|
|
|
# enter docker container
|
|
elif [[ "$VIASH_MODE" == "debug" ]]; then
|
|
VIASH_CMD="docker run --entrypoint=bash ${VIASH_DOCKER_RUN_ARGS[@]} -v '$(pwd)':/pwd --workdir /pwd -t $VIASH_DOCKER_IMAGE_ID"
|
|
ViashNotice "+ $VIASH_CMD"
|
|
eval $VIASH_CMD
|
|
exit
|
|
|
|
# build docker image
|
|
elif [ "$VIASH_MODE" == "setup" ]; then
|
|
ViashDockerSetup "$VIASH_DOCKER_IMAGE_ID" "$VIASH_SETUP_STRATEGY"
|
|
ViashDockerCheckCommands "$VIASH_DOCKER_IMAGE_ID" 'ps' 'bash'
|
|
exit 0
|
|
fi
|
|
|
|
# check if docker image exists
|
|
ViashDockerSetup "$VIASH_DOCKER_IMAGE_ID" ifneedbepullelsecachedbuild
|
|
ViashDockerCheckCommands "$VIASH_DOCKER_IMAGE_ID" 'ps' 'bash'
|
|
fi
|
|
|
|
# setting computational defaults
|
|
|
|
# helper function for parsing memory strings
|
|
function ViashMemoryAsBytes {
|
|
local memory=`echo "$1" | tr '[:upper:]' '[:lower:]' | tr -d '[:space:]'`
|
|
local memory_regex='^([0-9]+)([kmgtp]i?b?|b)$'
|
|
if [[ $memory =~ $memory_regex ]]; then
|
|
local number=${memory/[^0-9]*/}
|
|
local symbol=${memory/*[0-9]/}
|
|
|
|
case $symbol in
|
|
b) memory_b=$number ;;
|
|
kb|k) memory_b=$(( $number * 1000 )) ;;
|
|
mb|m) memory_b=$(( $number * 1000 * 1000 )) ;;
|
|
gb|g) memory_b=$(( $number * 1000 * 1000 * 1000 )) ;;
|
|
tb|t) memory_b=$(( $number * 1000 * 1000 * 1000 * 1000 )) ;;
|
|
pb|p) memory_b=$(( $number * 1000 * 1000 * 1000 * 1000 * 1000 )) ;;
|
|
kib|ki) memory_b=$(( $number * 1024 )) ;;
|
|
mib|mi) memory_b=$(( $number * 1024 * 1024 )) ;;
|
|
gib|gi) memory_b=$(( $number * 1024 * 1024 * 1024 )) ;;
|
|
tib|ti) memory_b=$(( $number * 1024 * 1024 * 1024 * 1024 )) ;;
|
|
pib|pi) memory_b=$(( $number * 1024 * 1024 * 1024 * 1024 * 1024 )) ;;
|
|
esac
|
|
echo "$memory_b"
|
|
fi
|
|
}
|
|
# compute memory in different units
|
|
if [ ! -z ${VIASH_META_MEMORY+x} ]; then
|
|
VIASH_META_MEMORY_B=`ViashMemoryAsBytes $VIASH_META_MEMORY`
|
|
# do not define other variables if memory_b is an empty string
|
|
if [ ! -z "$VIASH_META_MEMORY_B" ]; then
|
|
VIASH_META_MEMORY_KB=$(( ($VIASH_META_MEMORY_B+999) / 1000 ))
|
|
VIASH_META_MEMORY_MB=$(( ($VIASH_META_MEMORY_KB+999) / 1000 ))
|
|
VIASH_META_MEMORY_GB=$(( ($VIASH_META_MEMORY_MB+999) / 1000 ))
|
|
VIASH_META_MEMORY_TB=$(( ($VIASH_META_MEMORY_GB+999) / 1000 ))
|
|
VIASH_META_MEMORY_PB=$(( ($VIASH_META_MEMORY_TB+999) / 1000 ))
|
|
VIASH_META_MEMORY_KIB=$(( ($VIASH_META_MEMORY_B+1023) / 1024 ))
|
|
VIASH_META_MEMORY_MIB=$(( ($VIASH_META_MEMORY_KIB+1023) / 1024 ))
|
|
VIASH_META_MEMORY_GIB=$(( ($VIASH_META_MEMORY_MIB+1023) / 1024 ))
|
|
VIASH_META_MEMORY_TIB=$(( ($VIASH_META_MEMORY_GIB+1023) / 1024 ))
|
|
VIASH_META_MEMORY_PIB=$(( ($VIASH_META_MEMORY_TIB+1023) / 1024 ))
|
|
else
|
|
# unset memory if string is empty
|
|
unset $VIASH_META_MEMORY_B
|
|
fi
|
|
fi
|
|
# unset nproc if string is empty
|
|
if [ -z "$VIASH_META_CPUS" ]; then
|
|
unset $VIASH_META_CPUS
|
|
fi
|
|
|
|
|
|
# check whether required parameters exist
|
|
if [ -z ${VIASH_PAR_OUTPUT+x} ]; then
|
|
ViashError '--output' is a required argument. Use "--help" to get more information on the parameters.
|
|
exit 1
|
|
fi
|
|
if [ -z ${VIASH_META_NAME+x} ]; then
|
|
ViashError 'name' is a required argument. Use "--help" to get more information on the parameters.
|
|
exit 1
|
|
fi
|
|
if [ -z ${VIASH_META_FUNCTIONALITY_NAME+x} ]; then
|
|
ViashError 'functionality_name' is a required argument. Use "--help" to get more information on the parameters.
|
|
exit 1
|
|
fi
|
|
if [ -z ${VIASH_META_RESOURCES_DIR+x} ]; then
|
|
ViashError 'resources_dir' is a required argument. Use "--help" to get more information on the parameters.
|
|
exit 1
|
|
fi
|
|
if [ -z ${VIASH_META_EXECUTABLE+x} ]; then
|
|
ViashError 'executable' is a required argument. Use "--help" to get more information on the parameters.
|
|
exit 1
|
|
fi
|
|
if [ -z ${VIASH_META_CONFIG+x} ]; then
|
|
ViashError 'config' is a required argument. Use "--help" to get more information on the parameters.
|
|
exit 1
|
|
fi
|
|
if [ -z ${VIASH_META_TEMP_DIR+x} ]; then
|
|
ViashError 'temp_dir' is a required argument. Use "--help" to get more information on the parameters.
|
|
exit 1
|
|
fi
|
|
|
|
# filling in defaults
|
|
if [ -z ${VIASH_PAR_LIB_TYPE+x} ]; then
|
|
VIASH_PAR_LIB_TYPE="A"
|
|
fi
|
|
if [ -z ${VIASH_PAR_DISCARD_ORPHANS+x} ]; then
|
|
VIASH_PAR_DISCARD_ORPHANS="false"
|
|
fi
|
|
if [ -z ${VIASH_PAR_ONT+x} ]; then
|
|
VIASH_PAR_ONT="false"
|
|
fi
|
|
if [ -z ${VIASH_PAR_SEQ_BIAS+x} ]; then
|
|
VIASH_PAR_SEQ_BIAS="false"
|
|
fi
|
|
if [ -z ${VIASH_PAR_GC_BIAS+x} ]; then
|
|
VIASH_PAR_GC_BIAS="false"
|
|
fi
|
|
if [ -z ${VIASH_PAR_POS_BIAS+x} ]; then
|
|
VIASH_PAR_POS_BIAS="false"
|
|
fi
|
|
if [ -z ${VIASH_PAR_META+x} ]; then
|
|
VIASH_PAR_META="false"
|
|
fi
|
|
if [ -z ${VIASH_PAR_DISCARD_ORPHANS_QUASI+x} ]; then
|
|
VIASH_PAR_DISCARD_ORPHANS_QUASI="false"
|
|
fi
|
|
if [ -z ${VIASH_PAR_DISABLE_CHAINING_HEURISTIC+x} ]; then
|
|
VIASH_PAR_DISABLE_CHAINING_HEURISTIC="false"
|
|
fi
|
|
if [ -z ${VIASH_PAR_ALLOW_DOVETAIL+x} ]; then
|
|
VIASH_PAR_ALLOW_DOVETAIL="false"
|
|
fi
|
|
if [ -z ${VIASH_PAR_RECOVER_ORPHANS+x} ]; then
|
|
VIASH_PAR_RECOVER_ORPHANS="false"
|
|
fi
|
|
if [ -z ${VIASH_PAR_MIMICBT2+x} ]; then
|
|
VIASH_PAR_MIMICBT2="false"
|
|
fi
|
|
if [ -z ${VIASH_PAR_MIMIC_STRICTBT2+x} ]; then
|
|
VIASH_PAR_MIMIC_STRICTBT2="false"
|
|
fi
|
|
if [ -z ${VIASH_PAR_SOFTCLIP+x} ]; then
|
|
VIASH_PAR_SOFTCLIP="false"
|
|
fi
|
|
if [ -z ${VIASH_PAR_SOFTCLIP_OVERHANGS+x} ]; then
|
|
VIASH_PAR_SOFTCLIP_OVERHANGS="false"
|
|
fi
|
|
if [ -z ${VIASH_PAR_FULL_LENGTH_ALIGNMENT+x} ]; then
|
|
VIASH_PAR_FULL_LENGTH_ALIGNMENT="false"
|
|
fi
|
|
if [ -z ${VIASH_PAR_HARD_FILTER+x} ]; then
|
|
VIASH_PAR_HARD_FILTER="false"
|
|
fi
|
|
if [ -z ${VIASH_PAR_WRITE_MAPPINGS+x} ]; then
|
|
VIASH_PAR_WRITE_MAPPINGS="false"
|
|
fi
|
|
if [ -z ${VIASH_PAR_WRITE_QUALITIES+x} ]; then
|
|
VIASH_PAR_WRITE_QUALITIES="false"
|
|
fi
|
|
if [ -z ${VIASH_PAR_ALTERNATIVE_INIT_MODE+x} ]; then
|
|
VIASH_PAR_ALTERNATIVE_INIT_MODE="false"
|
|
fi
|
|
if [ -z ${VIASH_PAR_SKIP_QUANT+x} ]; then
|
|
VIASH_PAR_SKIP_QUANT="false"
|
|
fi
|
|
if [ -z ${VIASH_PAR_DUMP_EQ+x} ]; then
|
|
VIASH_PAR_DUMP_EQ="false"
|
|
fi
|
|
if [ -z ${VIASH_PAR_DUMP_EQ_WEIGHTS+x} ]; then
|
|
VIASH_PAR_DUMP_EQ_WEIGHTS="false"
|
|
fi
|
|
if [ -z ${VIASH_PAR_REDUCE_GC_MEMORY+x} ]; then
|
|
VIASH_PAR_REDUCE_GC_MEMORY="false"
|
|
fi
|
|
if [ -z ${VIASH_PAR_INIT_UNIFORM+x} ]; then
|
|
VIASH_PAR_INIT_UNIFORM="false"
|
|
fi
|
|
if [ -z ${VIASH_PAR_NO_LENGTH_CORRECTION+x} ]; then
|
|
VIASH_PAR_NO_LENGTH_CORRECTION="false"
|
|
fi
|
|
if [ -z ${VIASH_PAR_NO_EFFECTIVE_LENGTH_CORRECTION+x} ]; then
|
|
VIASH_PAR_NO_EFFECTIVE_LENGTH_CORRECTION="false"
|
|
fi
|
|
if [ -z ${VIASH_PAR_NO_SINGLE_FRAG_PROB+x} ]; then
|
|
VIASH_PAR_NO_SINGLE_FRAG_PROB="false"
|
|
fi
|
|
if [ -z ${VIASH_PAR_NO_FRAG_LENGTH_DIST+x} ]; then
|
|
VIASH_PAR_NO_FRAG_LENGTH_DIST="false"
|
|
fi
|
|
if [ -z ${VIASH_PAR_NO_BIAS_LENGTH_THRESHOLD+x} ]; then
|
|
VIASH_PAR_NO_BIAS_LENGTH_THRESHOLD="false"
|
|
fi
|
|
if [ -z ${VIASH_PAR_USEEM+x} ]; then
|
|
VIASH_PAR_USEEM="false"
|
|
fi
|
|
if [ -z ${VIASH_PAR_USEVBOPT+x} ]; then
|
|
VIASH_PAR_USEVBOPT="false"
|
|
fi
|
|
if [ -z ${VIASH_PAR_NO_GAMMA_DRAW+x} ]; then
|
|
VIASH_PAR_NO_GAMMA_DRAW="false"
|
|
fi
|
|
if [ -z ${VIASH_PAR_BOOTSTRAP_REPROJECT+x} ]; then
|
|
VIASH_PAR_BOOTSTRAP_REPROJECT="false"
|
|
fi
|
|
if [ -z ${VIASH_PAR_QUIET+x} ]; then
|
|
VIASH_PAR_QUIET="false"
|
|
fi
|
|
if [ -z ${VIASH_PAR_PER_TRANSCRIPT_PRIOR+x} ]; then
|
|
VIASH_PAR_PER_TRANSCRIPT_PRIOR="false"
|
|
fi
|
|
if [ -z ${VIASH_PAR_PER_NUCLEOTIDE_PRIOR+x} ]; then
|
|
VIASH_PAR_PER_NUCLEOTIDE_PRIOR="false"
|
|
fi
|
|
if [ -z ${VIASH_PAR_WRITE_ORPHAN_LINKS+x} ]; then
|
|
VIASH_PAR_WRITE_ORPHAN_LINKS="false"
|
|
fi
|
|
if [ -z ${VIASH_PAR_WRITE_UNMAPPED_NAMES+x} ]; then
|
|
VIASH_PAR_WRITE_UNMAPPED_NAMES="false"
|
|
fi
|
|
if [ -z ${VIASH_PAR_NO_ERROR_MODEL+x} ]; then
|
|
VIASH_PAR_NO_ERROR_MODEL="false"
|
|
fi
|
|
if [ -z ${VIASH_PAR_SAMPLE_OUT+x} ]; then
|
|
VIASH_PAR_SAMPLE_OUT="false"
|
|
fi
|
|
if [ -z ${VIASH_PAR_SAMPLE_UNALIGNED+x} ]; then
|
|
VIASH_PAR_SAMPLE_UNALIGNED="false"
|
|
fi
|
|
if [ -z ${VIASH_PAR_GENCODE+x} ]; then
|
|
VIASH_PAR_GENCODE="false"
|
|
fi
|
|
|
|
# check whether required files exist
|
|
if [ ! -z "$VIASH_PAR_INDEX" ] && [ ! -e "$VIASH_PAR_INDEX" ]; then
|
|
ViashError "Input file '$VIASH_PAR_INDEX' does not exist."
|
|
exit 1
|
|
fi
|
|
if [ ! -z "$VIASH_PAR_UNMATED_READS" ]; then
|
|
IFS=';'
|
|
set -f
|
|
for file in $VIASH_PAR_UNMATED_READS; do
|
|
unset IFS
|
|
if [ ! -e "$file" ]; then
|
|
ViashError "Input file '$file' does not exist."
|
|
exit 1
|
|
fi
|
|
done
|
|
set +f
|
|
fi
|
|
if [ ! -z "$VIASH_PAR_MATES1" ]; then
|
|
IFS=';'
|
|
set -f
|
|
for file in $VIASH_PAR_MATES1; do
|
|
unset IFS
|
|
if [ ! -e "$file" ]; then
|
|
ViashError "Input file '$file' does not exist."
|
|
exit 1
|
|
fi
|
|
done
|
|
set +f
|
|
fi
|
|
if [ ! -z "$VIASH_PAR_MATES2" ]; then
|
|
IFS=';'
|
|
set -f
|
|
for file in $VIASH_PAR_MATES2; do
|
|
unset IFS
|
|
if [ ! -e "$file" ]; then
|
|
ViashError "Input file '$file' does not exist."
|
|
exit 1
|
|
fi
|
|
done
|
|
set +f
|
|
fi
|
|
if [ ! -z "$VIASH_PAR_ALIGNMENTS" ]; then
|
|
IFS=';'
|
|
set -f
|
|
for file in $VIASH_PAR_ALIGNMENTS; do
|
|
unset IFS
|
|
if [ ! -e "$file" ]; then
|
|
ViashError "Input file '$file' does not exist."
|
|
exit 1
|
|
fi
|
|
done
|
|
set +f
|
|
fi
|
|
if [ ! -z "$VIASH_PAR_EQCLASSES" ] && [ ! -e "$VIASH_PAR_EQCLASSES" ]; then
|
|
ViashError "Input file '$VIASH_PAR_EQCLASSES' does not exist."
|
|
exit 1
|
|
fi
|
|
if [ ! -z "$VIASH_PAR_TARGETS" ] && [ ! -e "$VIASH_PAR_TARGETS" ]; then
|
|
ViashError "Input file '$VIASH_PAR_TARGETS' does not exist."
|
|
exit 1
|
|
fi
|
|
if [ ! -z "$VIASH_PAR_GENE_MAP" ] && [ ! -e "$VIASH_PAR_GENE_MAP" ]; then
|
|
ViashError "Input file '$VIASH_PAR_GENE_MAP' does not exist."
|
|
exit 1
|
|
fi
|
|
if [ ! -z "$VIASH_PAR_AUX_TARGET_FILE" ] && [ ! -e "$VIASH_PAR_AUX_TARGET_FILE" ]; then
|
|
ViashError "Input file '$VIASH_PAR_AUX_TARGET_FILE' does not exist."
|
|
exit 1
|
|
fi
|
|
|
|
# check whether parameters values are of the right type
|
|
if [[ -n "$VIASH_PAR_DISCARD_ORPHANS" ]]; then
|
|
if ! [[ "$VIASH_PAR_DISCARD_ORPHANS" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then
|
|
ViashError '--discard_orphans' has to be a boolean_true. Use "--help" to get more information on the parameters.
|
|
exit 1
|
|
fi
|
|
fi
|
|
if [[ -n "$VIASH_PAR_ONT" ]]; then
|
|
if ! [[ "$VIASH_PAR_ONT" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then
|
|
ViashError '--ont' has to be a boolean_true. Use "--help" to get more information on the parameters.
|
|
exit 1
|
|
fi
|
|
fi
|
|
if [[ -n "$VIASH_PAR_SEQ_BIAS" ]]; then
|
|
if ! [[ "$VIASH_PAR_SEQ_BIAS" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then
|
|
ViashError '--seq_bias' has to be a boolean_true. Use "--help" to get more information on the parameters.
|
|
exit 1
|
|
fi
|
|
fi
|
|
if [[ -n "$VIASH_PAR_GC_BIAS" ]]; then
|
|
if ! [[ "$VIASH_PAR_GC_BIAS" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then
|
|
ViashError '--gc_bias' has to be a boolean_true. Use "--help" to get more information on the parameters.
|
|
exit 1
|
|
fi
|
|
fi
|
|
if [[ -n "$VIASH_PAR_POS_BIAS" ]]; then
|
|
if ! [[ "$VIASH_PAR_POS_BIAS" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then
|
|
ViashError '--pos_bias' has to be a boolean_true. Use "--help" to get more information on the parameters.
|
|
exit 1
|
|
fi
|
|
fi
|
|
if [[ -n "$VIASH_PAR_INCOMPAT_PRIOR" ]]; then
|
|
if ! [[ "$VIASH_PAR_INCOMPAT_PRIOR" =~ ^[-+]?(\.[0-9]+|[0-9]+(\.[0-9]*)?)([eE][-+]?[0-9]+)?$ ]]; then
|
|
ViashError '--incompat_prior' has to be a double. Use "--help" to get more information on the parameters.
|
|
exit 1
|
|
fi
|
|
if command -v bc &> /dev/null; then
|
|
if ! [[ `echo $VIASH_PAR_INCOMPAT_PRIOR '>=' 0.0 | bc` -eq 1 ]]; then
|
|
ViashError '--incompat_prior' has be more than or equal to 0.0. Use "--help" to get more information on the parameters.
|
|
exit 1
|
|
fi
|
|
elif command -v awk &> /dev/null; then
|
|
if ! [[ `awk -v n1=$VIASH_PAR_INCOMPAT_PRIOR -v n2=0.0 'BEGIN { print (n1 >= n2) ? "1" : "0" }'` -eq 1 ]]; then
|
|
ViashError '--incompat_prior' has be more than or equal to 0.0. Use "--help" to get more information on the parameters.
|
|
exit 1
|
|
fi
|
|
else
|
|
ViashWarning '--incompat_prior' specifies a minimum value but the value was not verified as neither \'bc\' or \`awk\` are present on the system.
|
|
fi
|
|
if command -v bc &> /dev/null; then
|
|
if ! [[ `echo $VIASH_PAR_INCOMPAT_PRIOR '<=' 1.0 | bc` -eq 1 ]]; then
|
|
ViashError '--incompat_prior' has to be less than or equal to 1.0. Use "--help" to get more information on the parameters.
|
|
exit 1
|
|
fi
|
|
elif command -v awk &> /dev/null; then
|
|
if ! [[ `awk -v n1=$VIASH_PAR_INCOMPAT_PRIOR -v n2=1.0 'BEGIN { print (n1 <= n2) ? "1" : "0" }'` -eq 1 ]]; then
|
|
ViashError '--incompat_prior' has be less than or equal to 1.0. Use "--help" to get more information on the parameters.
|
|
exit 1
|
|
fi
|
|
else
|
|
ViashWarning '--incompat_prior' specifies a maximum value but the value was not verified as neither \'bc\' or \'awk\' are present on the system.
|
|
fi
|
|
fi
|
|
if [[ -n "$VIASH_PAR_META" ]]; then
|
|
if ! [[ "$VIASH_PAR_META" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then
|
|
ViashError '--meta' has to be a boolean_true. Use "--help" to get more information on the parameters.
|
|
exit 1
|
|
fi
|
|
fi
|
|
if [[ -n "$VIASH_PAR_SCORE_EXP" ]]; then
|
|
if ! [[ "$VIASH_PAR_SCORE_EXP" =~ ^[-+]?(\.[0-9]+|[0-9]+(\.[0-9]*)?)([eE][-+]?[0-9]+)?$ ]]; then
|
|
ViashError '--score_exp' has to be a double. Use "--help" to get more information on the parameters.
|
|
exit 1
|
|
fi
|
|
fi
|
|
if [[ -n "$VIASH_PAR_DISCARD_ORPHANS_QUASI" ]]; then
|
|
if ! [[ "$VIASH_PAR_DISCARD_ORPHANS_QUASI" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then
|
|
ViashError '--discard_orphans_quasi' has to be a boolean_true. Use "--help" to get more information on the parameters.
|
|
exit 1
|
|
fi
|
|
fi
|
|
if [[ -n "$VIASH_PAR_CONSENSUS_SLACK" ]]; then
|
|
if ! [[ "$VIASH_PAR_CONSENSUS_SLACK" =~ ^[-+]?(\.[0-9]+|[0-9]+(\.[0-9]*)?)([eE][-+]?[0-9]+)?$ ]]; then
|
|
ViashError '--consensus_slack' has to be a double. Use "--help" to get more information on the parameters.
|
|
exit 1
|
|
fi
|
|
if command -v bc &> /dev/null; then
|
|
if ! [[ `echo $VIASH_PAR_CONSENSUS_SLACK '>=' 0.0 | bc` -eq 1 ]]; then
|
|
ViashError '--consensus_slack' has be more than or equal to 0.0. Use "--help" to get more information on the parameters.
|
|
exit 1
|
|
fi
|
|
elif command -v awk &> /dev/null; then
|
|
if ! [[ `awk -v n1=$VIASH_PAR_CONSENSUS_SLACK -v n2=0.0 'BEGIN { print (n1 >= n2) ? "1" : "0" }'` -eq 1 ]]; then
|
|
ViashError '--consensus_slack' has be more than or equal to 0.0. Use "--help" to get more information on the parameters.
|
|
exit 1
|
|
fi
|
|
else
|
|
ViashWarning '--consensus_slack' specifies a minimum value but the value was not verified as neither \'bc\' or \`awk\` are present on the system.
|
|
fi
|
|
if command -v bc &> /dev/null; then
|
|
if ! [[ `echo $VIASH_PAR_CONSENSUS_SLACK '<=' 0.999999999 | bc` -eq 1 ]]; then
|
|
ViashError '--consensus_slack' has to be less than or equal to 0.999999999. Use "--help" to get more information on the parameters.
|
|
exit 1
|
|
fi
|
|
elif command -v awk &> /dev/null; then
|
|
if ! [[ `awk -v n1=$VIASH_PAR_CONSENSUS_SLACK -v n2=0.999999999 'BEGIN { print (n1 <= n2) ? "1" : "0" }'` -eq 1 ]]; then
|
|
ViashError '--consensus_slack' has be less than or equal to 0.999999999. Use "--help" to get more information on the parameters.
|
|
exit 1
|
|
fi
|
|
else
|
|
ViashWarning '--consensus_slack' specifies a maximum value but the value was not verified as neither \'bc\' or \'awk\' are present on the system.
|
|
fi
|
|
fi
|
|
if [[ -n "$VIASH_PAR_PRE_MERGE_CHAIN_SUB_THRESH" ]]; then
|
|
if ! [[ "$VIASH_PAR_PRE_MERGE_CHAIN_SUB_THRESH" =~ ^[-+]?(\.[0-9]+|[0-9]+(\.[0-9]*)?)([eE][-+]?[0-9]+)?$ ]]; then
|
|
ViashError '--pre_merge_chain_sub_thresh' has to be a double. Use "--help" to get more information on the parameters.
|
|
exit 1
|
|
fi
|
|
if command -v bc &> /dev/null; then
|
|
if ! [[ `echo $VIASH_PAR_PRE_MERGE_CHAIN_SUB_THRESH '>=' 0.0 | bc` -eq 1 ]]; then
|
|
ViashError '--pre_merge_chain_sub_thresh' has be more than or equal to 0.0. Use "--help" to get more information on the parameters.
|
|
exit 1
|
|
fi
|
|
elif command -v awk &> /dev/null; then
|
|
if ! [[ `awk -v n1=$VIASH_PAR_PRE_MERGE_CHAIN_SUB_THRESH -v n2=0.0 'BEGIN { print (n1 >= n2) ? "1" : "0" }'` -eq 1 ]]; then
|
|
ViashError '--pre_merge_chain_sub_thresh' has be more than or equal to 0.0. Use "--help" to get more information on the parameters.
|
|
exit 1
|
|
fi
|
|
else
|
|
ViashWarning '--pre_merge_chain_sub_thresh' specifies a minimum value but the value was not verified as neither \'bc\' or \`awk\` are present on the system.
|
|
fi
|
|
if command -v bc &> /dev/null; then
|
|
if ! [[ `echo $VIASH_PAR_PRE_MERGE_CHAIN_SUB_THRESH '<=' 1.0 | bc` -eq 1 ]]; then
|
|
ViashError '--pre_merge_chain_sub_thresh' has to be less than or equal to 1.0. Use "--help" to get more information on the parameters.
|
|
exit 1
|
|
fi
|
|
elif command -v awk &> /dev/null; then
|
|
if ! [[ `awk -v n1=$VIASH_PAR_PRE_MERGE_CHAIN_SUB_THRESH -v n2=1.0 'BEGIN { print (n1 <= n2) ? "1" : "0" }'` -eq 1 ]]; then
|
|
ViashError '--pre_merge_chain_sub_thresh' has be less than or equal to 1.0. Use "--help" to get more information on the parameters.
|
|
exit 1
|
|
fi
|
|
else
|
|
ViashWarning '--pre_merge_chain_sub_thresh' specifies a maximum value but the value was not verified as neither \'bc\' or \'awk\' are present on the system.
|
|
fi
|
|
fi
|
|
if [[ -n "$VIASH_PAR_POST_MERGE_CHAIN_SUB_THRESH" ]]; then
|
|
if ! [[ "$VIASH_PAR_POST_MERGE_CHAIN_SUB_THRESH" =~ ^[-+]?(\.[0-9]+|[0-9]+(\.[0-9]*)?)([eE][-+]?[0-9]+)?$ ]]; then
|
|
ViashError '--post_merge_chain_sub_thresh' has to be a double. Use "--help" to get more information on the parameters.
|
|
exit 1
|
|
fi
|
|
if command -v bc &> /dev/null; then
|
|
if ! [[ `echo $VIASH_PAR_POST_MERGE_CHAIN_SUB_THRESH '>=' 0.0 | bc` -eq 1 ]]; then
|
|
ViashError '--post_merge_chain_sub_thresh' has be more than or equal to 0.0. Use "--help" to get more information on the parameters.
|
|
exit 1
|
|
fi
|
|
elif command -v awk &> /dev/null; then
|
|
if ! [[ `awk -v n1=$VIASH_PAR_POST_MERGE_CHAIN_SUB_THRESH -v n2=0.0 'BEGIN { print (n1 >= n2) ? "1" : "0" }'` -eq 1 ]]; then
|
|
ViashError '--post_merge_chain_sub_thresh' has be more than or equal to 0.0. Use "--help" to get more information on the parameters.
|
|
exit 1
|
|
fi
|
|
else
|
|
ViashWarning '--post_merge_chain_sub_thresh' specifies a minimum value but the value was not verified as neither \'bc\' or \`awk\` are present on the system.
|
|
fi
|
|
if command -v bc &> /dev/null; then
|
|
if ! [[ `echo $VIASH_PAR_POST_MERGE_CHAIN_SUB_THRESH '<=' 1.0 | bc` -eq 1 ]]; then
|
|
ViashError '--post_merge_chain_sub_thresh' has to be less than or equal to 1.0. Use "--help" to get more information on the parameters.
|
|
exit 1
|
|
fi
|
|
elif command -v awk &> /dev/null; then
|
|
if ! [[ `awk -v n1=$VIASH_PAR_POST_MERGE_CHAIN_SUB_THRESH -v n2=1.0 'BEGIN { print (n1 <= n2) ? "1" : "0" }'` -eq 1 ]]; then
|
|
ViashError '--post_merge_chain_sub_thresh' has be less than or equal to 1.0. Use "--help" to get more information on the parameters.
|
|
exit 1
|
|
fi
|
|
else
|
|
ViashWarning '--post_merge_chain_sub_thresh' specifies a maximum value but the value was not verified as neither \'bc\' or \'awk\' are present on the system.
|
|
fi
|
|
fi
|
|
if [[ -n "$VIASH_PAR_ORPHAN_CHAIN_SUB_THRESH" ]]; then
|
|
if ! [[ "$VIASH_PAR_ORPHAN_CHAIN_SUB_THRESH" =~ ^[-+]?(\.[0-9]+|[0-9]+(\.[0-9]*)?)([eE][-+]?[0-9]+)?$ ]]; then
|
|
ViashError '--orphan_chain_sub_thresh' has to be a double. Use "--help" to get more information on the parameters.
|
|
exit 1
|
|
fi
|
|
if command -v bc &> /dev/null; then
|
|
if ! [[ `echo $VIASH_PAR_ORPHAN_CHAIN_SUB_THRESH '>=' 0.0 | bc` -eq 1 ]]; then
|
|
ViashError '--orphan_chain_sub_thresh' has be more than or equal to 0.0. Use "--help" to get more information on the parameters.
|
|
exit 1
|
|
fi
|
|
elif command -v awk &> /dev/null; then
|
|
if ! [[ `awk -v n1=$VIASH_PAR_ORPHAN_CHAIN_SUB_THRESH -v n2=0.0 'BEGIN { print (n1 >= n2) ? "1" : "0" }'` -eq 1 ]]; then
|
|
ViashError '--orphan_chain_sub_thresh' has be more than or equal to 0.0. Use "--help" to get more information on the parameters.
|
|
exit 1
|
|
fi
|
|
else
|
|
ViashWarning '--orphan_chain_sub_thresh' specifies a minimum value but the value was not verified as neither \'bc\' or \`awk\` are present on the system.
|
|
fi
|
|
if command -v bc &> /dev/null; then
|
|
if ! [[ `echo $VIASH_PAR_ORPHAN_CHAIN_SUB_THRESH '<=' 1.0 | bc` -eq 1 ]]; then
|
|
ViashError '--orphan_chain_sub_thresh' has to be less than or equal to 1.0. Use "--help" to get more information on the parameters.
|
|
exit 1
|
|
fi
|
|
elif command -v awk &> /dev/null; then
|
|
if ! [[ `awk -v n1=$VIASH_PAR_ORPHAN_CHAIN_SUB_THRESH -v n2=1.0 'BEGIN { print (n1 <= n2) ? "1" : "0" }'` -eq 1 ]]; then
|
|
ViashError '--orphan_chain_sub_thresh' has be less than or equal to 1.0. Use "--help" to get more information on the parameters.
|
|
exit 1
|
|
fi
|
|
else
|
|
ViashWarning '--orphan_chain_sub_thresh' specifies a maximum value but the value was not verified as neither \'bc\' or \'awk\' are present on the system.
|
|
fi
|
|
fi
|
|
if [[ -n "$VIASH_PAR_MIN_SCORE_FRACTION" ]]; then
|
|
if ! [[ "$VIASH_PAR_MIN_SCORE_FRACTION" =~ ^[-+]?(\.[0-9]+|[0-9]+(\.[0-9]*)?)([eE][-+]?[0-9]+)?$ ]]; then
|
|
ViashError '--min_score_fraction' has to be a double. Use "--help" to get more information on the parameters.
|
|
exit 1
|
|
fi
|
|
if command -v bc &> /dev/null; then
|
|
if ! [[ `echo $VIASH_PAR_MIN_SCORE_FRACTION '>=' 1.0E-9 | bc` -eq 1 ]]; then
|
|
ViashError '--min_score_fraction' has be more than or equal to 1.0E-9. Use "--help" to get more information on the parameters.
|
|
exit 1
|
|
fi
|
|
elif command -v awk &> /dev/null; then
|
|
if ! [[ `awk -v n1=$VIASH_PAR_MIN_SCORE_FRACTION -v n2=1.0E-9 'BEGIN { print (n1 >= n2) ? "1" : "0" }'` -eq 1 ]]; then
|
|
ViashError '--min_score_fraction' has be more than or equal to 1.0E-9. Use "--help" to get more information on the parameters.
|
|
exit 1
|
|
fi
|
|
else
|
|
ViashWarning '--min_score_fraction' specifies a minimum value but the value was not verified as neither \'bc\' or \`awk\` are present on the system.
|
|
fi
|
|
if command -v bc &> /dev/null; then
|
|
if ! [[ `echo $VIASH_PAR_MIN_SCORE_FRACTION '<=' 1.0 | bc` -eq 1 ]]; then
|
|
ViashError '--min_score_fraction' has to be less than or equal to 1.0. Use "--help" to get more information on the parameters.
|
|
exit 1
|
|
fi
|
|
elif command -v awk &> /dev/null; then
|
|
if ! [[ `awk -v n1=$VIASH_PAR_MIN_SCORE_FRACTION -v n2=1.0 'BEGIN { print (n1 <= n2) ? "1" : "0" }'` -eq 1 ]]; then
|
|
ViashError '--min_score_fraction' has be less than or equal to 1.0. Use "--help" to get more information on the parameters.
|
|
exit 1
|
|
fi
|
|
else
|
|
ViashWarning '--min_score_fraction' specifies a maximum value but the value was not verified as neither \'bc\' or \'awk\' are present on the system.
|
|
fi
|
|
fi
|
|
if [[ -n "$VIASH_PAR_MISMATCH_SEED_SKIP" ]]; then
|
|
if ! [[ "$VIASH_PAR_MISMATCH_SEED_SKIP" =~ ^[-+]?[0-9]+$ ]]; then
|
|
ViashError '--mismatch_seed_skip' has to be an integer. Use "--help" to get more information on the parameters.
|
|
exit 1
|
|
fi
|
|
fi
|
|
if [[ -n "$VIASH_PAR_DISABLE_CHAINING_HEURISTIC" ]]; then
|
|
if ! [[ "$VIASH_PAR_DISABLE_CHAINING_HEURISTIC" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then
|
|
ViashError '--disable_chaining_heuristic' has to be a boolean_true. Use "--help" to get more information on the parameters.
|
|
exit 1
|
|
fi
|
|
fi
|
|
if [[ -n "$VIASH_PAR_DECOY_THRESHOLD" ]]; then
|
|
if ! [[ "$VIASH_PAR_DECOY_THRESHOLD" =~ ^[-+]?(\.[0-9]+|[0-9]+(\.[0-9]*)?)([eE][-+]?[0-9]+)?$ ]]; then
|
|
ViashError '--decoy_threshold' has to be a double. Use "--help" to get more information on the parameters.
|
|
exit 1
|
|
fi
|
|
if command -v bc &> /dev/null; then
|
|
if ! [[ `echo $VIASH_PAR_DECOY_THRESHOLD '>=' 0.0 | bc` -eq 1 ]]; then
|
|
ViashError '--decoy_threshold' has be more than or equal to 0.0. Use "--help" to get more information on the parameters.
|
|
exit 1
|
|
fi
|
|
elif command -v awk &> /dev/null; then
|
|
if ! [[ `awk -v n1=$VIASH_PAR_DECOY_THRESHOLD -v n2=0.0 'BEGIN { print (n1 >= n2) ? "1" : "0" }'` -eq 1 ]]; then
|
|
ViashError '--decoy_threshold' has be more than or equal to 0.0. Use "--help" to get more information on the parameters.
|
|
exit 1
|
|
fi
|
|
else
|
|
ViashWarning '--decoy_threshold' specifies a minimum value but the value was not verified as neither \'bc\' or \`awk\` are present on the system.
|
|
fi
|
|
if command -v bc &> /dev/null; then
|
|
if ! [[ `echo $VIASH_PAR_DECOY_THRESHOLD '<=' 1.0 | bc` -eq 1 ]]; then
|
|
ViashError '--decoy_threshold' has to be less than or equal to 1.0. Use "--help" to get more information on the parameters.
|
|
exit 1
|
|
fi
|
|
elif command -v awk &> /dev/null; then
|
|
if ! [[ `awk -v n1=$VIASH_PAR_DECOY_THRESHOLD -v n2=1.0 'BEGIN { print (n1 <= n2) ? "1" : "0" }'` -eq 1 ]]; then
|
|
ViashError '--decoy_threshold' has be less than or equal to 1.0. Use "--help" to get more information on the parameters.
|
|
exit 1
|
|
fi
|
|
else
|
|
ViashWarning '--decoy_threshold' specifies a maximum value but the value was not verified as neither \'bc\' or \'awk\' are present on the system.
|
|
fi
|
|
fi
|
|
if [[ -n "$VIASH_PAR_MA" ]]; then
|
|
if ! [[ "$VIASH_PAR_MA" =~ ^[-+]?[0-9]+$ ]]; then
|
|
ViashError '--ma' has to be an integer. Use "--help" to get more information on the parameters.
|
|
exit 1
|
|
fi
|
|
fi
|
|
if [[ -n "$VIASH_PAR_MP" ]]; then
|
|
if ! [[ "$VIASH_PAR_MP" =~ ^[-+]?[0-9]+$ ]]; then
|
|
ViashError '--mp' has to be an integer. Use "--help" to get more information on the parameters.
|
|
exit 1
|
|
fi
|
|
fi
|
|
if [[ -n "$VIASH_PAR_GO" ]]; then
|
|
if ! [[ "$VIASH_PAR_GO" =~ ^[-+]?[0-9]+$ ]]; then
|
|
ViashError '--go' has to be an integer. Use "--help" to get more information on the parameters.
|
|
exit 1
|
|
fi
|
|
fi
|
|
if [[ -n "$VIASH_PAR_GE" ]]; then
|
|
if ! [[ "$VIASH_PAR_GE" =~ ^[-+]?[0-9]+$ ]]; then
|
|
ViashError '--ge' has to be an integer. Use "--help" to get more information on the parameters.
|
|
exit 1
|
|
fi
|
|
fi
|
|
if [[ -n "$VIASH_PAR_BANDWIDTH" ]]; then
|
|
if ! [[ "$VIASH_PAR_BANDWIDTH" =~ ^[-+]?[0-9]+$ ]]; then
|
|
ViashError '--bandwidth' has to be an integer. Use "--help" to get more information on the parameters.
|
|
exit 1
|
|
fi
|
|
fi
|
|
if [[ -n "$VIASH_PAR_ALLOW_DOVETAIL" ]]; then
|
|
if ! [[ "$VIASH_PAR_ALLOW_DOVETAIL" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then
|
|
ViashError '--allow_dovetail' has to be a boolean_true. Use "--help" to get more information on the parameters.
|
|
exit 1
|
|
fi
|
|
fi
|
|
if [[ -n "$VIASH_PAR_RECOVER_ORPHANS" ]]; then
|
|
if ! [[ "$VIASH_PAR_RECOVER_ORPHANS" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then
|
|
ViashError '--recover_orphans' has to be a boolean_true. Use "--help" to get more information on the parameters.
|
|
exit 1
|
|
fi
|
|
fi
|
|
if [[ -n "$VIASH_PAR_MIMICBT2" ]]; then
|
|
if ! [[ "$VIASH_PAR_MIMICBT2" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then
|
|
ViashError '--mimicBT2' has to be a boolean_true. Use "--help" to get more information on the parameters.
|
|
exit 1
|
|
fi
|
|
fi
|
|
if [[ -n "$VIASH_PAR_MIMIC_STRICTBT2" ]]; then
|
|
if ! [[ "$VIASH_PAR_MIMIC_STRICTBT2" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then
|
|
ViashError '--mimic_strictBT2' has to be a boolean_true. Use "--help" to get more information on the parameters.
|
|
exit 1
|
|
fi
|
|
fi
|
|
if [[ -n "$VIASH_PAR_SOFTCLIP" ]]; then
|
|
if ! [[ "$VIASH_PAR_SOFTCLIP" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then
|
|
ViashError '--softclip' has to be a boolean_true. Use "--help" to get more information on the parameters.
|
|
exit 1
|
|
fi
|
|
fi
|
|
if [[ -n "$VIASH_PAR_SOFTCLIP_OVERHANGS" ]]; then
|
|
if ! [[ "$VIASH_PAR_SOFTCLIP_OVERHANGS" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then
|
|
ViashError '--softclip_overhangs' has to be a boolean_true. Use "--help" to get more information on the parameters.
|
|
exit 1
|
|
fi
|
|
fi
|
|
if [[ -n "$VIASH_PAR_FULL_LENGTH_ALIGNMENT" ]]; then
|
|
if ! [[ "$VIASH_PAR_FULL_LENGTH_ALIGNMENT" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then
|
|
ViashError '--full_length_alignment' has to be a boolean_true. Use "--help" to get more information on the parameters.
|
|
exit 1
|
|
fi
|
|
fi
|
|
if [[ -n "$VIASH_PAR_HARD_FILTER" ]]; then
|
|
if ! [[ "$VIASH_PAR_HARD_FILTER" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then
|
|
ViashError '--hard_filter' has to be a boolean_true. Use "--help" to get more information on the parameters.
|
|
exit 1
|
|
fi
|
|
fi
|
|
if [[ -n "$VIASH_PAR_MIN_ALN_PROB" ]]; then
|
|
if ! [[ "$VIASH_PAR_MIN_ALN_PROB" =~ ^[-+]?(\.[0-9]+|[0-9]+(\.[0-9]*)?)([eE][-+]?[0-9]+)?$ ]]; then
|
|
ViashError '--min_aln_prob' has to be a double. Use "--help" to get more information on the parameters.
|
|
exit 1
|
|
fi
|
|
fi
|
|
if [[ -n "$VIASH_PAR_WRITE_MAPPINGS" ]]; then
|
|
if ! [[ "$VIASH_PAR_WRITE_MAPPINGS" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then
|
|
ViashError '--write_mappings' has to be a boolean_true. Use "--help" to get more information on the parameters.
|
|
exit 1
|
|
fi
|
|
fi
|
|
if [[ -n "$VIASH_PAR_WRITE_QUALITIES" ]]; then
|
|
if ! [[ "$VIASH_PAR_WRITE_QUALITIES" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then
|
|
ViashError '--write_qualities' has to be a boolean_true. Use "--help" to get more information on the parameters.
|
|
exit 1
|
|
fi
|
|
fi
|
|
if [[ -n "$VIASH_PAR_ALTERNATIVE_INIT_MODE" ]]; then
|
|
if ! [[ "$VIASH_PAR_ALTERNATIVE_INIT_MODE" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then
|
|
ViashError '--alternative_init_mode' has to be a boolean_true. Use "--help" to get more information on the parameters.
|
|
exit 1
|
|
fi
|
|
fi
|
|
if [[ -n "$VIASH_PAR_SKIP_QUANT" ]]; then
|
|
if ! [[ "$VIASH_PAR_SKIP_QUANT" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then
|
|
ViashError '--skip_quant' has to be a boolean_true. Use "--help" to get more information on the parameters.
|
|
exit 1
|
|
fi
|
|
fi
|
|
if [[ -n "$VIASH_PAR_DUMP_EQ" ]]; then
|
|
if ! [[ "$VIASH_PAR_DUMP_EQ" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then
|
|
ViashError '--dump_eq' has to be a boolean_true. Use "--help" to get more information on the parameters.
|
|
exit 1
|
|
fi
|
|
fi
|
|
if [[ -n "$VIASH_PAR_DUMP_EQ_WEIGHTS" ]]; then
|
|
if ! [[ "$VIASH_PAR_DUMP_EQ_WEIGHTS" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then
|
|
ViashError '--dump_eq_weights' has to be a boolean_true. Use "--help" to get more information on the parameters.
|
|
exit 1
|
|
fi
|
|
fi
|
|
if [[ -n "$VIASH_PAR_MIN_ASSIGNED_FRAGS" ]]; then
|
|
if ! [[ "$VIASH_PAR_MIN_ASSIGNED_FRAGS" =~ ^[-+]?[0-9]+$ ]]; then
|
|
ViashError '--min_assigned_frags' has to be an integer. Use "--help" to get more information on the parameters.
|
|
exit 1
|
|
fi
|
|
fi
|
|
if [[ -n "$VIASH_PAR_REDUCE_GC_MEMORY" ]]; then
|
|
if ! [[ "$VIASH_PAR_REDUCE_GC_MEMORY" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then
|
|
ViashError '--reduce_GC_memory' has to be a boolean_true. Use "--help" to get more information on the parameters.
|
|
exit 1
|
|
fi
|
|
fi
|
|
if [[ -n "$VIASH_PAR_BIAS_SPEED_SAMP" ]]; then
|
|
if ! [[ "$VIASH_PAR_BIAS_SPEED_SAMP" =~ ^[-+]?[0-9]+$ ]]; then
|
|
ViashError '--bias_speed_samp' has to be an integer. Use "--help" to get more information on the parameters.
|
|
exit 1
|
|
fi
|
|
fi
|
|
if [[ -n "$VIASH_PAR_FLD_MAX" ]]; then
|
|
if ! [[ "$VIASH_PAR_FLD_MAX" =~ ^[-+]?[0-9]+$ ]]; then
|
|
ViashError '--fld_max' has to be an integer. Use "--help" to get more information on the parameters.
|
|
exit 1
|
|
fi
|
|
fi
|
|
if [[ -n "$VIASH_PAR_FLD_MEAN" ]]; then
|
|
if ! [[ "$VIASH_PAR_FLD_MEAN" =~ ^[-+]?[0-9]+$ ]]; then
|
|
ViashError '--fld_mean' has to be an integer. Use "--help" to get more information on the parameters.
|
|
exit 1
|
|
fi
|
|
fi
|
|
if [[ -n "$VIASH_PAR_FLD_SD" ]]; then
|
|
if ! [[ "$VIASH_PAR_FLD_SD" =~ ^[-+]?[0-9]+$ ]]; then
|
|
ViashError '--fld_SD' has to be an integer. Use "--help" to get more information on the parameters.
|
|
exit 1
|
|
fi
|
|
fi
|
|
if [[ -n "$VIASH_PAR_FORGETTING_FACTOR" ]]; then
|
|
if ! [[ "$VIASH_PAR_FORGETTING_FACTOR" =~ ^[-+]?(\.[0-9]+|[0-9]+(\.[0-9]*)?)([eE][-+]?[0-9]+)?$ ]]; then
|
|
ViashError '--forgetting_factor' has to be a double. Use "--help" to get more information on the parameters.
|
|
exit 1
|
|
fi
|
|
if command -v bc &> /dev/null; then
|
|
if ! [[ `echo $VIASH_PAR_FORGETTING_FACTOR '>=' 0.500000001 | bc` -eq 1 ]]; then
|
|
ViashError '--forgetting_factor' has be more than or equal to 0.500000001. Use "--help" to get more information on the parameters.
|
|
exit 1
|
|
fi
|
|
elif command -v awk &> /dev/null; then
|
|
if ! [[ `awk -v n1=$VIASH_PAR_FORGETTING_FACTOR -v n2=0.500000001 'BEGIN { print (n1 >= n2) ? "1" : "0" }'` -eq 1 ]]; then
|
|
ViashError '--forgetting_factor' has be more than or equal to 0.500000001. Use "--help" to get more information on the parameters.
|
|
exit 1
|
|
fi
|
|
else
|
|
ViashWarning '--forgetting_factor' specifies a minimum value but the value was not verified as neither \'bc\' or \`awk\` are present on the system.
|
|
fi
|
|
if command -v bc &> /dev/null; then
|
|
if ! [[ `echo $VIASH_PAR_FORGETTING_FACTOR '<=' 1.0 | bc` -eq 1 ]]; then
|
|
ViashError '--forgetting_factor' has to be less than or equal to 1.0. Use "--help" to get more information on the parameters.
|
|
exit 1
|
|
fi
|
|
elif command -v awk &> /dev/null; then
|
|
if ! [[ `awk -v n1=$VIASH_PAR_FORGETTING_FACTOR -v n2=1.0 'BEGIN { print (n1 <= n2) ? "1" : "0" }'` -eq 1 ]]; then
|
|
ViashError '--forgetting_factor' has be less than or equal to 1.0. Use "--help" to get more information on the parameters.
|
|
exit 1
|
|
fi
|
|
else
|
|
ViashWarning '--forgetting_factor' specifies a maximum value but the value was not verified as neither \'bc\' or \'awk\' are present on the system.
|
|
fi
|
|
fi
|
|
if [[ -n "$VIASH_PAR_INIT_UNIFORM" ]]; then
|
|
if ! [[ "$VIASH_PAR_INIT_UNIFORM" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then
|
|
ViashError '--init_uniform' has to be a boolean_true. Use "--help" to get more information on the parameters.
|
|
exit 1
|
|
fi
|
|
fi
|
|
if [[ -n "$VIASH_PAR_MAX_OCCS_PER_HIT" ]]; then
|
|
if ! [[ "$VIASH_PAR_MAX_OCCS_PER_HIT" =~ ^[-+]?[0-9]+$ ]]; then
|
|
ViashError '--max_occs_per_hit' has to be an integer. Use "--help" to get more information on the parameters.
|
|
exit 1
|
|
fi
|
|
fi
|
|
if [[ -n "$VIASH_PAR_MAX_READ_OCC" ]]; then
|
|
if ! [[ "$VIASH_PAR_MAX_READ_OCC" =~ ^[-+]?[0-9]+$ ]]; then
|
|
ViashError '--max_read_occ' has to be an integer. Use "--help" to get more information on the parameters.
|
|
exit 1
|
|
fi
|
|
fi
|
|
if [[ -n "$VIASH_PAR_NO_LENGTH_CORRECTION" ]]; then
|
|
if ! [[ "$VIASH_PAR_NO_LENGTH_CORRECTION" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then
|
|
ViashError '--no_length_correction' has to be a boolean_true. Use "--help" to get more information on the parameters.
|
|
exit 1
|
|
fi
|
|
fi
|
|
if [[ -n "$VIASH_PAR_NO_EFFECTIVE_LENGTH_CORRECTION" ]]; then
|
|
if ! [[ "$VIASH_PAR_NO_EFFECTIVE_LENGTH_CORRECTION" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then
|
|
ViashError '--no_effective_length_correction' has to be a boolean_true. Use "--help" to get more information on the parameters.
|
|
exit 1
|
|
fi
|
|
fi
|
|
if [[ -n "$VIASH_PAR_NO_SINGLE_FRAG_PROB" ]]; then
|
|
if ! [[ "$VIASH_PAR_NO_SINGLE_FRAG_PROB" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then
|
|
ViashError '--no_single_frag_prob' has to be a boolean_true. Use "--help" to get more information on the parameters.
|
|
exit 1
|
|
fi
|
|
fi
|
|
if [[ -n "$VIASH_PAR_NO_FRAG_LENGTH_DIST" ]]; then
|
|
if ! [[ "$VIASH_PAR_NO_FRAG_LENGTH_DIST" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then
|
|
ViashError '--no_frag_length_dist' has to be a boolean_true. Use "--help" to get more information on the parameters.
|
|
exit 1
|
|
fi
|
|
fi
|
|
if [[ -n "$VIASH_PAR_NO_BIAS_LENGTH_THRESHOLD" ]]; then
|
|
if ! [[ "$VIASH_PAR_NO_BIAS_LENGTH_THRESHOLD" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then
|
|
ViashError '--no_bias_length_threshold' has to be a boolean_true. Use "--help" to get more information on the parameters.
|
|
exit 1
|
|
fi
|
|
fi
|
|
if [[ -n "$VIASH_PAR_NUM_BIAS_SAMPLES" ]]; then
|
|
if ! [[ "$VIASH_PAR_NUM_BIAS_SAMPLES" =~ ^[-+]?[0-9]+$ ]]; then
|
|
ViashError '--num_bias_samples' has to be an integer. Use "--help" to get more information on the parameters.
|
|
exit 1
|
|
fi
|
|
fi
|
|
if [[ -n "$VIASH_PAR_NUM_AUX_MODEL_SAMPLES" ]]; then
|
|
if ! [[ "$VIASH_PAR_NUM_AUX_MODEL_SAMPLES" =~ ^[-+]?[0-9]+$ ]]; then
|
|
ViashError '--num_aux_model_samples' has to be an integer. Use "--help" to get more information on the parameters.
|
|
exit 1
|
|
fi
|
|
fi
|
|
if [[ -n "$VIASH_PAR_NUM_PRE_AUX_MODEL_SAMPLES" ]]; then
|
|
if ! [[ "$VIASH_PAR_NUM_PRE_AUX_MODEL_SAMPLES" =~ ^[-+]?[0-9]+$ ]]; then
|
|
ViashError '--num_pre_aux_model_samples' has to be an integer. Use "--help" to get more information on the parameters.
|
|
exit 1
|
|
fi
|
|
fi
|
|
if [[ -n "$VIASH_PAR_USEEM" ]]; then
|
|
if ! [[ "$VIASH_PAR_USEEM" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then
|
|
ViashError '--useEM' has to be a boolean_true. Use "--help" to get more information on the parameters.
|
|
exit 1
|
|
fi
|
|
fi
|
|
if [[ -n "$VIASH_PAR_USEVBOPT" ]]; then
|
|
if ! [[ "$VIASH_PAR_USEVBOPT" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then
|
|
ViashError '--useVBOpt' has to be a boolean_true. Use "--help" to get more information on the parameters.
|
|
exit 1
|
|
fi
|
|
fi
|
|
if [[ -n "$VIASH_PAR_RANGE_FACTORIZATION_BINS" ]]; then
|
|
if ! [[ "$VIASH_PAR_RANGE_FACTORIZATION_BINS" =~ ^[-+]?[0-9]+$ ]]; then
|
|
ViashError '--range_factorization_bins' has to be an integer. Use "--help" to get more information on the parameters.
|
|
exit 1
|
|
fi
|
|
fi
|
|
if [[ -n "$VIASH_PAR_NUM_GIBBS_SAMPLES" ]]; then
|
|
if ! [[ "$VIASH_PAR_NUM_GIBBS_SAMPLES" =~ ^[-+]?[0-9]+$ ]]; then
|
|
ViashError '--num_Gibbs_samples' has to be an integer. Use "--help" to get more information on the parameters.
|
|
exit 1
|
|
fi
|
|
fi
|
|
if [[ -n "$VIASH_PAR_NO_GAMMA_DRAW" ]]; then
|
|
if ! [[ "$VIASH_PAR_NO_GAMMA_DRAW" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then
|
|
ViashError '--no_Gamma_draw' has to be a boolean_true. Use "--help" to get more information on the parameters.
|
|
exit 1
|
|
fi
|
|
fi
|
|
if [[ -n "$VIASH_PAR_NUM_BOOTSTRAPS" ]]; then
|
|
if ! [[ "$VIASH_PAR_NUM_BOOTSTRAPS" =~ ^[-+]?[0-9]+$ ]]; then
|
|
ViashError '--num_bootstraps' has to be an integer. Use "--help" to get more information on the parameters.
|
|
exit 1
|
|
fi
|
|
fi
|
|
if [[ -n "$VIASH_PAR_BOOTSTRAP_REPROJECT" ]]; then
|
|
if ! [[ "$VIASH_PAR_BOOTSTRAP_REPROJECT" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then
|
|
ViashError '--bootstrap_reproject' has to be a boolean_true. Use "--help" to get more information on the parameters.
|
|
exit 1
|
|
fi
|
|
fi
|
|
if [[ -n "$VIASH_PAR_THINNING_FACTOR" ]]; then
|
|
if ! [[ "$VIASH_PAR_THINNING_FACTOR" =~ ^[-+]?[0-9]+$ ]]; then
|
|
ViashError '--thinning_factor' has to be an integer. Use "--help" to get more information on the parameters.
|
|
exit 1
|
|
fi
|
|
fi
|
|
if [[ -n "$VIASH_PAR_QUIET" ]]; then
|
|
if ! [[ "$VIASH_PAR_QUIET" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then
|
|
ViashError '--quiet' has to be a boolean_true. Use "--help" to get more information on the parameters.
|
|
exit 1
|
|
fi
|
|
fi
|
|
if [[ -n "$VIASH_PAR_PER_TRANSCRIPT_PRIOR" ]]; then
|
|
if ! [[ "$VIASH_PAR_PER_TRANSCRIPT_PRIOR" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then
|
|
ViashError '--per_transcript_prior' has to be a boolean_true. Use "--help" to get more information on the parameters.
|
|
exit 1
|
|
fi
|
|
fi
|
|
if [[ -n "$VIASH_PAR_PER_NUCLEOTIDE_PRIOR" ]]; then
|
|
if ! [[ "$VIASH_PAR_PER_NUCLEOTIDE_PRIOR" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then
|
|
ViashError '--per_nucleotide_prior' has to be a boolean_true. Use "--help" to get more information on the parameters.
|
|
exit 1
|
|
fi
|
|
fi
|
|
if [[ -n "$VIASH_PAR_SIG_DIGITS" ]]; then
|
|
if ! [[ "$VIASH_PAR_SIG_DIGITS" =~ ^[-+]?[0-9]+$ ]]; then
|
|
ViashError '--sig_digits' has to be an integer. Use "--help" to get more information on the parameters.
|
|
exit 1
|
|
fi
|
|
fi
|
|
if [[ -n "$VIASH_PAR_VB_PRIOR" ]]; then
|
|
if ! [[ "$VIASH_PAR_VB_PRIOR" =~ ^[-+]?(\.[0-9]+|[0-9]+(\.[0-9]*)?)([eE][-+]?[0-9]+)?$ ]]; then
|
|
ViashError '--vb_prior' has to be a double. Use "--help" to get more information on the parameters.
|
|
exit 1
|
|
fi
|
|
fi
|
|
if [[ -n "$VIASH_PAR_WRITE_ORPHAN_LINKS" ]]; then
|
|
if ! [[ "$VIASH_PAR_WRITE_ORPHAN_LINKS" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then
|
|
ViashError '--write_orphan_links' has to be a boolean_true. Use "--help" to get more information on the parameters.
|
|
exit 1
|
|
fi
|
|
fi
|
|
if [[ -n "$VIASH_PAR_WRITE_UNMAPPED_NAMES" ]]; then
|
|
if ! [[ "$VIASH_PAR_WRITE_UNMAPPED_NAMES" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then
|
|
ViashError '--write_unmapped_names' has to be a boolean_true. Use "--help" to get more information on the parameters.
|
|
exit 1
|
|
fi
|
|
fi
|
|
if [[ -n "$VIASH_PAR_NO_ERROR_MODEL" ]]; then
|
|
if ! [[ "$VIASH_PAR_NO_ERROR_MODEL" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then
|
|
ViashError '--no_error_model' has to be a boolean_true. Use "--help" to get more information on the parameters.
|
|
exit 1
|
|
fi
|
|
fi
|
|
if [[ -n "$VIASH_PAR_NUM_ERROR_BINS" ]]; then
|
|
if ! [[ "$VIASH_PAR_NUM_ERROR_BINS" =~ ^[-+]?[0-9]+$ ]]; then
|
|
ViashError '--num_error_bins' has to be an integer. Use "--help" to get more information on the parameters.
|
|
exit 1
|
|
fi
|
|
fi
|
|
if [[ -n "$VIASH_PAR_SAMPLE_OUT" ]]; then
|
|
if ! [[ "$VIASH_PAR_SAMPLE_OUT" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then
|
|
ViashError '--sample_out' has to be a boolean_true. Use "--help" to get more information on the parameters.
|
|
exit 1
|
|
fi
|
|
fi
|
|
if [[ -n "$VIASH_PAR_SAMPLE_UNALIGNED" ]]; then
|
|
if ! [[ "$VIASH_PAR_SAMPLE_UNALIGNED" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then
|
|
ViashError '--sample_unaligned' has to be a boolean_true. Use "--help" to get more information on the parameters.
|
|
exit 1
|
|
fi
|
|
fi
|
|
if [[ -n "$VIASH_PAR_GENCODE" ]]; then
|
|
if ! [[ "$VIASH_PAR_GENCODE" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then
|
|
ViashError '--gencode' has to be a boolean_true. Use "--help" to get more information on the parameters.
|
|
exit 1
|
|
fi
|
|
fi
|
|
if [[ -n "$VIASH_PAR_MAPPING_CACHE_MEMORY_LIMIT" ]]; then
|
|
if ! [[ "$VIASH_PAR_MAPPING_CACHE_MEMORY_LIMIT" =~ ^[-+]?[0-9]+$ ]]; then
|
|
ViashError '--mapping_cache_memory_limit' has to be an integer. Use "--help" to get more information on the parameters.
|
|
exit 1
|
|
fi
|
|
fi
|
|
if [[ -n "$VIASH_META_CPUS" ]]; then
|
|
if ! [[ "$VIASH_META_CPUS" =~ ^[-+]?[0-9]+$ ]]; then
|
|
ViashError 'cpus' has to be an integer. Use "--help" to get more information on the parameters.
|
|
exit 1
|
|
fi
|
|
fi
|
|
if [[ -n "$VIASH_META_MEMORY_B" ]]; then
|
|
if ! [[ "$VIASH_META_MEMORY_B" =~ ^[-+]?[0-9]+$ ]]; then
|
|
ViashError 'memory_b' has to be a long. Use "--help" to get more information on the parameters.
|
|
exit 1
|
|
fi
|
|
fi
|
|
if [[ -n "$VIASH_META_MEMORY_KB" ]]; then
|
|
if ! [[ "$VIASH_META_MEMORY_KB" =~ ^[-+]?[0-9]+$ ]]; then
|
|
ViashError 'memory_kb' has to be a long. Use "--help" to get more information on the parameters.
|
|
exit 1
|
|
fi
|
|
fi
|
|
if [[ -n "$VIASH_META_MEMORY_MB" ]]; then
|
|
if ! [[ "$VIASH_META_MEMORY_MB" =~ ^[-+]?[0-9]+$ ]]; then
|
|
ViashError 'memory_mb' has to be a long. Use "--help" to get more information on the parameters.
|
|
exit 1
|
|
fi
|
|
fi
|
|
if [[ -n "$VIASH_META_MEMORY_GB" ]]; then
|
|
if ! [[ "$VIASH_META_MEMORY_GB" =~ ^[-+]?[0-9]+$ ]]; then
|
|
ViashError 'memory_gb' has to be a long. Use "--help" to get more information on the parameters.
|
|
exit 1
|
|
fi
|
|
fi
|
|
if [[ -n "$VIASH_META_MEMORY_TB" ]]; then
|
|
if ! [[ "$VIASH_META_MEMORY_TB" =~ ^[-+]?[0-9]+$ ]]; then
|
|
ViashError 'memory_tb' has to be a long. Use "--help" to get more information on the parameters.
|
|
exit 1
|
|
fi
|
|
fi
|
|
if [[ -n "$VIASH_META_MEMORY_PB" ]]; then
|
|
if ! [[ "$VIASH_META_MEMORY_PB" =~ ^[-+]?[0-9]+$ ]]; then
|
|
ViashError 'memory_pb' has to be a long. Use "--help" to get more information on the parameters.
|
|
exit 1
|
|
fi
|
|
fi
|
|
if [[ -n "$VIASH_META_MEMORY_KIB" ]]; then
|
|
if ! [[ "$VIASH_META_MEMORY_KIB" =~ ^[-+]?[0-9]+$ ]]; then
|
|
ViashError 'memory_kib' has to be a long. Use "--help" to get more information on the parameters.
|
|
exit 1
|
|
fi
|
|
fi
|
|
if [[ -n "$VIASH_META_MEMORY_MIB" ]]; then
|
|
if ! [[ "$VIASH_META_MEMORY_MIB" =~ ^[-+]?[0-9]+$ ]]; then
|
|
ViashError 'memory_mib' has to be a long. Use "--help" to get more information on the parameters.
|
|
exit 1
|
|
fi
|
|
fi
|
|
if [[ -n "$VIASH_META_MEMORY_GIB" ]]; then
|
|
if ! [[ "$VIASH_META_MEMORY_GIB" =~ ^[-+]?[0-9]+$ ]]; then
|
|
ViashError 'memory_gib' has to be a long. Use "--help" to get more information on the parameters.
|
|
exit 1
|
|
fi
|
|
fi
|
|
if [[ -n "$VIASH_META_MEMORY_TIB" ]]; then
|
|
if ! [[ "$VIASH_META_MEMORY_TIB" =~ ^[-+]?[0-9]+$ ]]; then
|
|
ViashError 'memory_tib' has to be a long. Use "--help" to get more information on the parameters.
|
|
exit 1
|
|
fi
|
|
fi
|
|
if [[ -n "$VIASH_META_MEMORY_PIB" ]]; then
|
|
if ! [[ "$VIASH_META_MEMORY_PIB" =~ ^[-+]?[0-9]+$ ]]; then
|
|
ViashError 'memory_pib' has to be a long. Use "--help" to get more information on the parameters.
|
|
exit 1
|
|
fi
|
|
fi
|
|
|
|
# check whether value is belongs to a set of choices
|
|
if [ ! -z "$VIASH_PAR_LIB_TYPE" ]; then
|
|
VIASH_PAR_LIB_TYPE_CHOICES=("A;U;SF;SR;IU;IS;ISF;ISR;OU;OS;OSF;OSR;MU;MS;MSF;MSR")
|
|
IFS=';'
|
|
set -f
|
|
if ! [[ ";${VIASH_PAR_LIB_TYPE_CHOICES[*]};" =~ ";$VIASH_PAR_LIB_TYPE;" ]]; then
|
|
ViashError '--lib_type' specified value of \'$VIASH_PAR_LIB_TYPE\' is not in the list of allowed values. Use "--help" to get more information on the parameters.
|
|
exit 1
|
|
fi
|
|
set +f
|
|
unset IFS
|
|
fi
|
|
|
|
if [ ! -z "$VIASH_PAR_HIT_FILTER_POLICY" ]; then
|
|
VIASH_PAR_HIT_FILTER_POLICY_CHOICES=("BEFORE;AFTER;BOTH;NONE")
|
|
IFS=';'
|
|
set -f
|
|
if ! [[ ";${VIASH_PAR_HIT_FILTER_POLICY_CHOICES[*]};" =~ ";$VIASH_PAR_HIT_FILTER_POLICY;" ]]; then
|
|
ViashError '--hit_filter_policy' specified value of \'$VIASH_PAR_HIT_FILTER_POLICY\' is not in the list of allowed values. Use "--help" to get more information on the parameters.
|
|
exit 1
|
|
fi
|
|
set +f
|
|
unset IFS
|
|
fi
|
|
|
|
# create parent directories of output files, if so desired
|
|
if [ ! -z "$VIASH_PAR_OUTPUT" ] && [ ! -d "$(dirname "$VIASH_PAR_OUTPUT")" ]; then
|
|
mkdir -p "$(dirname "$VIASH_PAR_OUTPUT")"
|
|
fi
|
|
if [ ! -z "$VIASH_PAR_QUANT_RESULTS" ] && [ ! -d "$(dirname "$VIASH_PAR_QUANT_RESULTS")" ]; then
|
|
mkdir -p "$(dirname "$VIASH_PAR_QUANT_RESULTS")"
|
|
fi
|
|
if [ ! -z "$VIASH_PAR_MAPPING_SAM" ] && [ ! -d "$(dirname "$VIASH_PAR_MAPPING_SAM")" ]; then
|
|
mkdir -p "$(dirname "$VIASH_PAR_MAPPING_SAM")"
|
|
fi
|
|
if [ ! -z "$VIASH_PAR_AUX_DIR" ] && [ ! -d "$(dirname "$VIASH_PAR_AUX_DIR")" ]; then
|
|
mkdir -p "$(dirname "$VIASH_PAR_AUX_DIR")"
|
|
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_INDEX" ]; then
|
|
VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$VIASH_PAR_INDEX")" )
|
|
VIASH_PAR_INDEX=$(ViashDockerAutodetectMount "$VIASH_PAR_INDEX")
|
|
fi
|
|
if [ ! -z "$VIASH_PAR_UNMATED_READS" ]; then
|
|
VIASH_TEST_UNMATED_READS=()
|
|
IFS=';'
|
|
for var in $VIASH_PAR_UNMATED_READS; do
|
|
unset IFS
|
|
VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$var")" )
|
|
var=$(ViashDockerAutodetectMount "$var")
|
|
VIASH_TEST_UNMATED_READS+=( "$var" )
|
|
done
|
|
VIASH_PAR_UNMATED_READS=$(IFS=';' ; echo "${VIASH_TEST_UNMATED_READS[*]}")
|
|
fi
|
|
if [ ! -z "$VIASH_PAR_MATES1" ]; then
|
|
VIASH_TEST_MATES1=()
|
|
IFS=';'
|
|
for var in $VIASH_PAR_MATES1; do
|
|
unset IFS
|
|
VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$var")" )
|
|
var=$(ViashDockerAutodetectMount "$var")
|
|
VIASH_TEST_MATES1+=( "$var" )
|
|
done
|
|
VIASH_PAR_MATES1=$(IFS=';' ; echo "${VIASH_TEST_MATES1[*]}")
|
|
fi
|
|
if [ ! -z "$VIASH_PAR_MATES2" ]; then
|
|
VIASH_TEST_MATES2=()
|
|
IFS=';'
|
|
for var in $VIASH_PAR_MATES2; do
|
|
unset IFS
|
|
VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$var")" )
|
|
var=$(ViashDockerAutodetectMount "$var")
|
|
VIASH_TEST_MATES2+=( "$var" )
|
|
done
|
|
VIASH_PAR_MATES2=$(IFS=';' ; echo "${VIASH_TEST_MATES2[*]}")
|
|
fi
|
|
if [ ! -z "$VIASH_PAR_ALIGNMENTS" ]; then
|
|
VIASH_TEST_ALIGNMENTS=()
|
|
IFS=';'
|
|
for var in $VIASH_PAR_ALIGNMENTS; do
|
|
unset IFS
|
|
VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$var")" )
|
|
var=$(ViashDockerAutodetectMount "$var")
|
|
VIASH_TEST_ALIGNMENTS+=( "$var" )
|
|
done
|
|
VIASH_PAR_ALIGNMENTS=$(IFS=';' ; echo "${VIASH_TEST_ALIGNMENTS[*]}")
|
|
fi
|
|
if [ ! -z "$VIASH_PAR_EQCLASSES" ]; then
|
|
VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$VIASH_PAR_EQCLASSES")" )
|
|
VIASH_PAR_EQCLASSES=$(ViashDockerAutodetectMount "$VIASH_PAR_EQCLASSES")
|
|
fi
|
|
if [ ! -z "$VIASH_PAR_TARGETS" ]; then
|
|
VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$VIASH_PAR_TARGETS")" )
|
|
VIASH_PAR_TARGETS=$(ViashDockerAutodetectMount "$VIASH_PAR_TARGETS")
|
|
fi
|
|
if [ ! -z "$VIASH_PAR_OUTPUT" ]; then
|
|
VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$VIASH_PAR_OUTPUT")" )
|
|
VIASH_PAR_OUTPUT=$(ViashDockerAutodetectMount "$VIASH_PAR_OUTPUT")
|
|
VIASH_CHOWN_VARS+=( "$VIASH_PAR_OUTPUT" )
|
|
fi
|
|
if [ ! -z "$VIASH_PAR_QUANT_RESULTS" ]; then
|
|
VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$VIASH_PAR_QUANT_RESULTS")" )
|
|
VIASH_PAR_QUANT_RESULTS=$(ViashDockerAutodetectMount "$VIASH_PAR_QUANT_RESULTS")
|
|
VIASH_CHOWN_VARS+=( "$VIASH_PAR_QUANT_RESULTS" )
|
|
fi
|
|
if [ ! -z "$VIASH_PAR_GENE_MAP" ]; then
|
|
VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$VIASH_PAR_GENE_MAP")" )
|
|
VIASH_PAR_GENE_MAP=$(ViashDockerAutodetectMount "$VIASH_PAR_GENE_MAP")
|
|
fi
|
|
if [ ! -z "$VIASH_PAR_AUX_TARGET_FILE" ]; then
|
|
VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$VIASH_PAR_AUX_TARGET_FILE")" )
|
|
VIASH_PAR_AUX_TARGET_FILE=$(ViashDockerAutodetectMount "$VIASH_PAR_AUX_TARGET_FILE")
|
|
fi
|
|
if [ ! -z "$VIASH_PAR_MAPPING_SAM" ]; then
|
|
VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$VIASH_PAR_MAPPING_SAM")" )
|
|
VIASH_PAR_MAPPING_SAM=$(ViashDockerAutodetectMount "$VIASH_PAR_MAPPING_SAM")
|
|
VIASH_CHOWN_VARS+=( "$VIASH_PAR_MAPPING_SAM" )
|
|
fi
|
|
if [ ! -z "$VIASH_PAR_AUX_DIR" ]; then
|
|
VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$VIASH_PAR_AUX_DIR")" )
|
|
VIASH_PAR_AUX_DIR=$(ViashDockerAutodetectMount "$VIASH_PAR_AUX_DIR")
|
|
VIASH_CHOWN_VARS+=( "$VIASH_PAR_AUX_DIR" )
|
|
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-salmon_quant-XXXXXX").sh
|
|
function clean_up {
|
|
rm "\$tempscript"
|
|
}
|
|
function interrupt {
|
|
echo -e "\nCTRL-C Pressed..."
|
|
exit 1
|
|
}
|
|
trap clean_up EXIT
|
|
trap interrupt INT SIGINT
|
|
cat > "\$tempscript" << 'VIASHMAIN'
|
|
#!/bin/bash
|
|
|
|
set -e
|
|
|
|
## VIASH START
|
|
# The following code has been auto-generated by Viash.
|
|
$( if [ ! -z ${VIASH_PAR_LIB_TYPE+x} ]; then echo "${VIASH_PAR_LIB_TYPE}" | sed "s#'#'\"'\"'#g;s#.*#par_lib_type='&'#" ; else echo "# par_lib_type="; 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 ${VIASH_PAR_UNMATED_READS+x} ]; then echo "${VIASH_PAR_UNMATED_READS}" | sed "s#'#'\"'\"'#g;s#.*#par_unmated_reads='&'#" ; else echo "# par_unmated_reads="; fi )
|
|
$( if [ ! -z ${VIASH_PAR_MATES1+x} ]; then echo "${VIASH_PAR_MATES1}" | sed "s#'#'\"'\"'#g;s#.*#par_mates1='&'#" ; else echo "# par_mates1="; fi )
|
|
$( if [ ! -z ${VIASH_PAR_MATES2+x} ]; then echo "${VIASH_PAR_MATES2}" | sed "s#'#'\"'\"'#g;s#.*#par_mates2='&'#" ; else echo "# par_mates2="; fi )
|
|
$( if [ ! -z ${VIASH_PAR_DISCARD_ORPHANS+x} ]; then echo "${VIASH_PAR_DISCARD_ORPHANS}" | sed "s#'#'\"'\"'#g;s#.*#par_discard_orphans='&'#" ; else echo "# par_discard_orphans="; fi )
|
|
$( if [ ! -z ${VIASH_PAR_ALIGNMENTS+x} ]; then echo "${VIASH_PAR_ALIGNMENTS}" | sed "s#'#'\"'\"'#g;s#.*#par_alignments='&'#" ; else echo "# par_alignments="; fi )
|
|
$( if [ ! -z ${VIASH_PAR_EQCLASSES+x} ]; then echo "${VIASH_PAR_EQCLASSES}" | sed "s#'#'\"'\"'#g;s#.*#par_eqclasses='&'#" ; else echo "# par_eqclasses="; fi )
|
|
$( if [ ! -z ${VIASH_PAR_TARGETS+x} ]; then echo "${VIASH_PAR_TARGETS}" | sed "s#'#'\"'\"'#g;s#.*#par_targets='&'#" ; else echo "# par_targets="; fi )
|
|
$( if [ ! -z ${VIASH_PAR_ONT+x} ]; then echo "${VIASH_PAR_ONT}" | sed "s#'#'\"'\"'#g;s#.*#par_ont='&'#" ; else echo "# par_ont="; fi )
|
|
$( if [ ! -z ${VIASH_PAR_OUTPUT+x} ]; then echo "${VIASH_PAR_OUTPUT}" | sed "s#'#'\"'\"'#g;s#.*#par_output='&'#" ; else echo "# par_output="; fi )
|
|
$( if [ ! -z ${VIASH_PAR_QUANT_RESULTS+x} ]; then echo "${VIASH_PAR_QUANT_RESULTS}" | sed "s#'#'\"'\"'#g;s#.*#par_quant_results='&'#" ; else echo "# par_quant_results="; fi )
|
|
$( if [ ! -z ${VIASH_PAR_SEQ_BIAS+x} ]; then echo "${VIASH_PAR_SEQ_BIAS}" | sed "s#'#'\"'\"'#g;s#.*#par_seq_bias='&'#" ; else echo "# par_seq_bias="; fi )
|
|
$( if [ ! -z ${VIASH_PAR_GC_BIAS+x} ]; then echo "${VIASH_PAR_GC_BIAS}" | sed "s#'#'\"'\"'#g;s#.*#par_gc_bias='&'#" ; else echo "# par_gc_bias="; fi )
|
|
$( if [ ! -z ${VIASH_PAR_POS_BIAS+x} ]; then echo "${VIASH_PAR_POS_BIAS}" | sed "s#'#'\"'\"'#g;s#.*#par_pos_bias='&'#" ; else echo "# par_pos_bias="; fi )
|
|
$( if [ ! -z ${VIASH_PAR_INCOMPAT_PRIOR+x} ]; then echo "${VIASH_PAR_INCOMPAT_PRIOR}" | sed "s#'#'\"'\"'#g;s#.*#par_incompat_prior='&'#" ; else echo "# par_incompat_prior="; fi )
|
|
$( if [ ! -z ${VIASH_PAR_GENE_MAP+x} ]; then echo "${VIASH_PAR_GENE_MAP}" | sed "s#'#'\"'\"'#g;s#.*#par_gene_map='&'#" ; else echo "# par_gene_map="; fi )
|
|
$( if [ ! -z ${VIASH_PAR_AUX_TARGET_FILE+x} ]; then echo "${VIASH_PAR_AUX_TARGET_FILE}" | sed "s#'#'\"'\"'#g;s#.*#par_aux_target_file='&'#" ; else echo "# par_aux_target_file="; fi )
|
|
$( if [ ! -z ${VIASH_PAR_META+x} ]; then echo "${VIASH_PAR_META}" | sed "s#'#'\"'\"'#g;s#.*#par_meta='&'#" ; else echo "# par_meta="; fi )
|
|
$( if [ ! -z ${VIASH_PAR_SCORE_EXP+x} ]; then echo "${VIASH_PAR_SCORE_EXP}" | sed "s#'#'\"'\"'#g;s#.*#par_score_exp='&'#" ; else echo "# par_score_exp="; fi )
|
|
$( if [ ! -z ${VIASH_PAR_DISCARD_ORPHANS_QUASI+x} ]; then echo "${VIASH_PAR_DISCARD_ORPHANS_QUASI}" | sed "s#'#'\"'\"'#g;s#.*#par_discard_orphans_quasi='&'#" ; else echo "# par_discard_orphans_quasi="; fi )
|
|
$( if [ ! -z ${VIASH_PAR_CONSENSUS_SLACK+x} ]; then echo "${VIASH_PAR_CONSENSUS_SLACK}" | sed "s#'#'\"'\"'#g;s#.*#par_consensus_slack='&'#" ; else echo "# par_consensus_slack="; fi )
|
|
$( if [ ! -z ${VIASH_PAR_PRE_MERGE_CHAIN_SUB_THRESH+x} ]; then echo "${VIASH_PAR_PRE_MERGE_CHAIN_SUB_THRESH}" | sed "s#'#'\"'\"'#g;s#.*#par_pre_merge_chain_sub_thresh='&'#" ; else echo "# par_pre_merge_chain_sub_thresh="; fi )
|
|
$( if [ ! -z ${VIASH_PAR_POST_MERGE_CHAIN_SUB_THRESH+x} ]; then echo "${VIASH_PAR_POST_MERGE_CHAIN_SUB_THRESH}" | sed "s#'#'\"'\"'#g;s#.*#par_post_merge_chain_sub_thresh='&'#" ; else echo "# par_post_merge_chain_sub_thresh="; fi )
|
|
$( if [ ! -z ${VIASH_PAR_ORPHAN_CHAIN_SUB_THRESH+x} ]; then echo "${VIASH_PAR_ORPHAN_CHAIN_SUB_THRESH}" | sed "s#'#'\"'\"'#g;s#.*#par_orphan_chain_sub_thresh='&'#" ; else echo "# par_orphan_chain_sub_thresh="; fi )
|
|
$( if [ ! -z ${VIASH_PAR_MIN_SCORE_FRACTION+x} ]; then echo "${VIASH_PAR_MIN_SCORE_FRACTION}" | sed "s#'#'\"'\"'#g;s#.*#par_min_score_fraction='&'#" ; else echo "# par_min_score_fraction="; fi )
|
|
$( if [ ! -z ${VIASH_PAR_MISMATCH_SEED_SKIP+x} ]; then echo "${VIASH_PAR_MISMATCH_SEED_SKIP}" | sed "s#'#'\"'\"'#g;s#.*#par_mismatch_seed_skip='&'#" ; else echo "# par_mismatch_seed_skip="; fi )
|
|
$( if [ ! -z ${VIASH_PAR_DISABLE_CHAINING_HEURISTIC+x} ]; then echo "${VIASH_PAR_DISABLE_CHAINING_HEURISTIC}" | sed "s#'#'\"'\"'#g;s#.*#par_disable_chaining_heuristic='&'#" ; else echo "# par_disable_chaining_heuristic="; fi )
|
|
$( if [ ! -z ${VIASH_PAR_DECOY_THRESHOLD+x} ]; then echo "${VIASH_PAR_DECOY_THRESHOLD}" | sed "s#'#'\"'\"'#g;s#.*#par_decoy_threshold='&'#" ; else echo "# par_decoy_threshold="; fi )
|
|
$( if [ ! -z ${VIASH_PAR_MA+x} ]; then echo "${VIASH_PAR_MA}" | sed "s#'#'\"'\"'#g;s#.*#par_ma='&'#" ; else echo "# par_ma="; fi )
|
|
$( if [ ! -z ${VIASH_PAR_MP+x} ]; then echo "${VIASH_PAR_MP}" | sed "s#'#'\"'\"'#g;s#.*#par_mp='&'#" ; else echo "# par_mp="; fi )
|
|
$( if [ ! -z ${VIASH_PAR_GO+x} ]; then echo "${VIASH_PAR_GO}" | sed "s#'#'\"'\"'#g;s#.*#par_go='&'#" ; else echo "# par_go="; fi )
|
|
$( if [ ! -z ${VIASH_PAR_GE+x} ]; then echo "${VIASH_PAR_GE}" | sed "s#'#'\"'\"'#g;s#.*#par_ge='&'#" ; else echo "# par_ge="; fi )
|
|
$( if [ ! -z ${VIASH_PAR_BANDWIDTH+x} ]; then echo "${VIASH_PAR_BANDWIDTH}" | sed "s#'#'\"'\"'#g;s#.*#par_bandwidth='&'#" ; else echo "# par_bandwidth="; fi )
|
|
$( if [ ! -z ${VIASH_PAR_ALLOW_DOVETAIL+x} ]; then echo "${VIASH_PAR_ALLOW_DOVETAIL}" | sed "s#'#'\"'\"'#g;s#.*#par_allow_dovetail='&'#" ; else echo "# par_allow_dovetail="; fi )
|
|
$( if [ ! -z ${VIASH_PAR_RECOVER_ORPHANS+x} ]; then echo "${VIASH_PAR_RECOVER_ORPHANS}" | sed "s#'#'\"'\"'#g;s#.*#par_recover_orphans='&'#" ; else echo "# par_recover_orphans="; fi )
|
|
$( if [ ! -z ${VIASH_PAR_MIMICBT2+x} ]; then echo "${VIASH_PAR_MIMICBT2}" | sed "s#'#'\"'\"'#g;s#.*#par_mimicBT2='&'#" ; else echo "# par_mimicBT2="; fi )
|
|
$( if [ ! -z ${VIASH_PAR_MIMIC_STRICTBT2+x} ]; then echo "${VIASH_PAR_MIMIC_STRICTBT2}" | sed "s#'#'\"'\"'#g;s#.*#par_mimic_strictBT2='&'#" ; else echo "# par_mimic_strictBT2="; fi )
|
|
$( if [ ! -z ${VIASH_PAR_SOFTCLIP+x} ]; then echo "${VIASH_PAR_SOFTCLIP}" | sed "s#'#'\"'\"'#g;s#.*#par_softclip='&'#" ; else echo "# par_softclip="; fi )
|
|
$( if [ ! -z ${VIASH_PAR_SOFTCLIP_OVERHANGS+x} ]; then echo "${VIASH_PAR_SOFTCLIP_OVERHANGS}" | sed "s#'#'\"'\"'#g;s#.*#par_softclip_overhangs='&'#" ; else echo "# par_softclip_overhangs="; fi )
|
|
$( if [ ! -z ${VIASH_PAR_FULL_LENGTH_ALIGNMENT+x} ]; then echo "${VIASH_PAR_FULL_LENGTH_ALIGNMENT}" | sed "s#'#'\"'\"'#g;s#.*#par_full_length_alignment='&'#" ; else echo "# par_full_length_alignment="; fi )
|
|
$( if [ ! -z ${VIASH_PAR_HARD_FILTER+x} ]; then echo "${VIASH_PAR_HARD_FILTER}" | sed "s#'#'\"'\"'#g;s#.*#par_hard_filter='&'#" ; else echo "# par_hard_filter="; fi )
|
|
$( if [ ! -z ${VIASH_PAR_MIN_ALN_PROB+x} ]; then echo "${VIASH_PAR_MIN_ALN_PROB}" | sed "s#'#'\"'\"'#g;s#.*#par_min_aln_prob='&'#" ; else echo "# par_min_aln_prob="; fi )
|
|
$( if [ ! -z ${VIASH_PAR_WRITE_MAPPINGS+x} ]; then echo "${VIASH_PAR_WRITE_MAPPINGS}" | sed "s#'#'\"'\"'#g;s#.*#par_write_mappings='&'#" ; else echo "# par_write_mappings="; fi )
|
|
$( if [ ! -z ${VIASH_PAR_MAPPING_SAM+x} ]; then echo "${VIASH_PAR_MAPPING_SAM}" | sed "s#'#'\"'\"'#g;s#.*#par_mapping_sam='&'#" ; else echo "# par_mapping_sam="; fi )
|
|
$( if [ ! -z ${VIASH_PAR_WRITE_QUALITIES+x} ]; then echo "${VIASH_PAR_WRITE_QUALITIES}" | sed "s#'#'\"'\"'#g;s#.*#par_write_qualities='&'#" ; else echo "# par_write_qualities="; fi )
|
|
$( if [ ! -z ${VIASH_PAR_HIT_FILTER_POLICY+x} ]; then echo "${VIASH_PAR_HIT_FILTER_POLICY}" | sed "s#'#'\"'\"'#g;s#.*#par_hit_filter_policy='&'#" ; else echo "# par_hit_filter_policy="; fi )
|
|
$( if [ ! -z ${VIASH_PAR_ALTERNATIVE_INIT_MODE+x} ]; then echo "${VIASH_PAR_ALTERNATIVE_INIT_MODE}" | sed "s#'#'\"'\"'#g;s#.*#par_alternative_init_mode='&'#" ; else echo "# par_alternative_init_mode="; fi )
|
|
$( if [ ! -z ${VIASH_PAR_AUX_DIR+x} ]; then echo "${VIASH_PAR_AUX_DIR}" | sed "s#'#'\"'\"'#g;s#.*#par_aux_dir='&'#" ; else echo "# par_aux_dir="; fi )
|
|
$( if [ ! -z ${VIASH_PAR_SKIP_QUANT+x} ]; then echo "${VIASH_PAR_SKIP_QUANT}" | sed "s#'#'\"'\"'#g;s#.*#par_skip_quant='&'#" ; else echo "# par_skip_quant="; fi )
|
|
$( if [ ! -z ${VIASH_PAR_DUMP_EQ+x} ]; then echo "${VIASH_PAR_DUMP_EQ}" | sed "s#'#'\"'\"'#g;s#.*#par_dump_eq='&'#" ; else echo "# par_dump_eq="; fi )
|
|
$( if [ ! -z ${VIASH_PAR_DUMP_EQ_WEIGHTS+x} ]; then echo "${VIASH_PAR_DUMP_EQ_WEIGHTS}" | sed "s#'#'\"'\"'#g;s#.*#par_dump_eq_weights='&'#" ; else echo "# par_dump_eq_weights="; fi )
|
|
$( if [ ! -z ${VIASH_PAR_MIN_ASSIGNED_FRAGS+x} ]; then echo "${VIASH_PAR_MIN_ASSIGNED_FRAGS}" | sed "s#'#'\"'\"'#g;s#.*#par_min_assigned_frags='&'#" ; else echo "# par_min_assigned_frags="; fi )
|
|
$( if [ ! -z ${VIASH_PAR_REDUCE_GC_MEMORY+x} ]; then echo "${VIASH_PAR_REDUCE_GC_MEMORY}" | sed "s#'#'\"'\"'#g;s#.*#par_reduce_GC_memory='&'#" ; else echo "# par_reduce_GC_memory="; fi )
|
|
$( if [ ! -z ${VIASH_PAR_BIAS_SPEED_SAMP+x} ]; then echo "${VIASH_PAR_BIAS_SPEED_SAMP}" | sed "s#'#'\"'\"'#g;s#.*#par_bias_speed_samp='&'#" ; else echo "# par_bias_speed_samp="; fi )
|
|
$( if [ ! -z ${VIASH_PAR_FLD_MAX+x} ]; then echo "${VIASH_PAR_FLD_MAX}" | sed "s#'#'\"'\"'#g;s#.*#par_fld_max='&'#" ; else echo "# par_fld_max="; fi )
|
|
$( if [ ! -z ${VIASH_PAR_FLD_MEAN+x} ]; then echo "${VIASH_PAR_FLD_MEAN}" | sed "s#'#'\"'\"'#g;s#.*#par_fld_mean='&'#" ; else echo "# par_fld_mean="; fi )
|
|
$( if [ ! -z ${VIASH_PAR_FLD_SD+x} ]; then echo "${VIASH_PAR_FLD_SD}" | sed "s#'#'\"'\"'#g;s#.*#par_fld_SD='&'#" ; else echo "# par_fld_SD="; fi )
|
|
$( if [ ! -z ${VIASH_PAR_FORGETTING_FACTOR+x} ]; then echo "${VIASH_PAR_FORGETTING_FACTOR}" | sed "s#'#'\"'\"'#g;s#.*#par_forgetting_factor='&'#" ; else echo "# par_forgetting_factor="; fi )
|
|
$( if [ ! -z ${VIASH_PAR_INIT_UNIFORM+x} ]; then echo "${VIASH_PAR_INIT_UNIFORM}" | sed "s#'#'\"'\"'#g;s#.*#par_init_uniform='&'#" ; else echo "# par_init_uniform="; fi )
|
|
$( if [ ! -z ${VIASH_PAR_MAX_OCCS_PER_HIT+x} ]; then echo "${VIASH_PAR_MAX_OCCS_PER_HIT}" | sed "s#'#'\"'\"'#g;s#.*#par_max_occs_per_hit='&'#" ; else echo "# par_max_occs_per_hit="; fi )
|
|
$( if [ ! -z ${VIASH_PAR_MAX_READ_OCC+x} ]; then echo "${VIASH_PAR_MAX_READ_OCC}" | sed "s#'#'\"'\"'#g;s#.*#par_max_read_occ='&'#" ; else echo "# par_max_read_occ="; fi )
|
|
$( if [ ! -z ${VIASH_PAR_NO_LENGTH_CORRECTION+x} ]; then echo "${VIASH_PAR_NO_LENGTH_CORRECTION}" | sed "s#'#'\"'\"'#g;s#.*#par_no_length_correction='&'#" ; else echo "# par_no_length_correction="; fi )
|
|
$( if [ ! -z ${VIASH_PAR_NO_EFFECTIVE_LENGTH_CORRECTION+x} ]; then echo "${VIASH_PAR_NO_EFFECTIVE_LENGTH_CORRECTION}" | sed "s#'#'\"'\"'#g;s#.*#par_no_effective_length_correction='&'#" ; else echo "# par_no_effective_length_correction="; fi )
|
|
$( if [ ! -z ${VIASH_PAR_NO_SINGLE_FRAG_PROB+x} ]; then echo "${VIASH_PAR_NO_SINGLE_FRAG_PROB}" | sed "s#'#'\"'\"'#g;s#.*#par_no_single_frag_prob='&'#" ; else echo "# par_no_single_frag_prob="; fi )
|
|
$( if [ ! -z ${VIASH_PAR_NO_FRAG_LENGTH_DIST+x} ]; then echo "${VIASH_PAR_NO_FRAG_LENGTH_DIST}" | sed "s#'#'\"'\"'#g;s#.*#par_no_frag_length_dist='&'#" ; else echo "# par_no_frag_length_dist="; fi )
|
|
$( if [ ! -z ${VIASH_PAR_NO_BIAS_LENGTH_THRESHOLD+x} ]; then echo "${VIASH_PAR_NO_BIAS_LENGTH_THRESHOLD}" | sed "s#'#'\"'\"'#g;s#.*#par_no_bias_length_threshold='&'#" ; else echo "# par_no_bias_length_threshold="; fi )
|
|
$( if [ ! -z ${VIASH_PAR_NUM_BIAS_SAMPLES+x} ]; then echo "${VIASH_PAR_NUM_BIAS_SAMPLES}" | sed "s#'#'\"'\"'#g;s#.*#par_num_bias_samples='&'#" ; else echo "# par_num_bias_samples="; fi )
|
|
$( if [ ! -z ${VIASH_PAR_NUM_AUX_MODEL_SAMPLES+x} ]; then echo "${VIASH_PAR_NUM_AUX_MODEL_SAMPLES}" | sed "s#'#'\"'\"'#g;s#.*#par_num_aux_model_samples='&'#" ; else echo "# par_num_aux_model_samples="; fi )
|
|
$( if [ ! -z ${VIASH_PAR_NUM_PRE_AUX_MODEL_SAMPLES+x} ]; then echo "${VIASH_PAR_NUM_PRE_AUX_MODEL_SAMPLES}" | sed "s#'#'\"'\"'#g;s#.*#par_num_pre_aux_model_samples='&'#" ; else echo "# par_num_pre_aux_model_samples="; fi )
|
|
$( if [ ! -z ${VIASH_PAR_USEEM+x} ]; then echo "${VIASH_PAR_USEEM}" | sed "s#'#'\"'\"'#g;s#.*#par_useEM='&'#" ; else echo "# par_useEM="; fi )
|
|
$( if [ ! -z ${VIASH_PAR_USEVBOPT+x} ]; then echo "${VIASH_PAR_USEVBOPT}" | sed "s#'#'\"'\"'#g;s#.*#par_useVBOpt='&'#" ; else echo "# par_useVBOpt="; fi )
|
|
$( if [ ! -z ${VIASH_PAR_RANGE_FACTORIZATION_BINS+x} ]; then echo "${VIASH_PAR_RANGE_FACTORIZATION_BINS}" | sed "s#'#'\"'\"'#g;s#.*#par_range_factorization_bins='&'#" ; else echo "# par_range_factorization_bins="; fi )
|
|
$( if [ ! -z ${VIASH_PAR_NUM_GIBBS_SAMPLES+x} ]; then echo "${VIASH_PAR_NUM_GIBBS_SAMPLES}" | sed "s#'#'\"'\"'#g;s#.*#par_num_Gibbs_samples='&'#" ; else echo "# par_num_Gibbs_samples="; fi )
|
|
$( if [ ! -z ${VIASH_PAR_NO_GAMMA_DRAW+x} ]; then echo "${VIASH_PAR_NO_GAMMA_DRAW}" | sed "s#'#'\"'\"'#g;s#.*#par_no_Gamma_draw='&'#" ; else echo "# par_no_Gamma_draw="; fi )
|
|
$( if [ ! -z ${VIASH_PAR_NUM_BOOTSTRAPS+x} ]; then echo "${VIASH_PAR_NUM_BOOTSTRAPS}" | sed "s#'#'\"'\"'#g;s#.*#par_num_bootstraps='&'#" ; else echo "# par_num_bootstraps="; fi )
|
|
$( if [ ! -z ${VIASH_PAR_BOOTSTRAP_REPROJECT+x} ]; then echo "${VIASH_PAR_BOOTSTRAP_REPROJECT}" | sed "s#'#'\"'\"'#g;s#.*#par_bootstrap_reproject='&'#" ; else echo "# par_bootstrap_reproject="; fi )
|
|
$( if [ ! -z ${VIASH_PAR_THINNING_FACTOR+x} ]; then echo "${VIASH_PAR_THINNING_FACTOR}" | sed "s#'#'\"'\"'#g;s#.*#par_thinning_factor='&'#" ; else echo "# par_thinning_factor="; fi )
|
|
$( if [ ! -z ${VIASH_PAR_QUIET+x} ]; then echo "${VIASH_PAR_QUIET}" | sed "s#'#'\"'\"'#g;s#.*#par_quiet='&'#" ; else echo "# par_quiet="; fi )
|
|
$( if [ ! -z ${VIASH_PAR_PER_TRANSCRIPT_PRIOR+x} ]; then echo "${VIASH_PAR_PER_TRANSCRIPT_PRIOR}" | sed "s#'#'\"'\"'#g;s#.*#par_per_transcript_prior='&'#" ; else echo "# par_per_transcript_prior="; fi )
|
|
$( if [ ! -z ${VIASH_PAR_PER_NUCLEOTIDE_PRIOR+x} ]; then echo "${VIASH_PAR_PER_NUCLEOTIDE_PRIOR}" | sed "s#'#'\"'\"'#g;s#.*#par_per_nucleotide_prior='&'#" ; else echo "# par_per_nucleotide_prior="; fi )
|
|
$( if [ ! -z ${VIASH_PAR_SIG_DIGITS+x} ]; then echo "${VIASH_PAR_SIG_DIGITS}" | sed "s#'#'\"'\"'#g;s#.*#par_sig_digits='&'#" ; else echo "# par_sig_digits="; fi )
|
|
$( if [ ! -z ${VIASH_PAR_VB_PRIOR+x} ]; then echo "${VIASH_PAR_VB_PRIOR}" | sed "s#'#'\"'\"'#g;s#.*#par_vb_prior='&'#" ; else echo "# par_vb_prior="; fi )
|
|
$( if [ ! -z ${VIASH_PAR_WRITE_ORPHAN_LINKS+x} ]; then echo "${VIASH_PAR_WRITE_ORPHAN_LINKS}" | sed "s#'#'\"'\"'#g;s#.*#par_write_orphan_links='&'#" ; else echo "# par_write_orphan_links="; fi )
|
|
$( if [ ! -z ${VIASH_PAR_WRITE_UNMAPPED_NAMES+x} ]; then echo "${VIASH_PAR_WRITE_UNMAPPED_NAMES}" | sed "s#'#'\"'\"'#g;s#.*#par_write_unmapped_names='&'#" ; else echo "# par_write_unmapped_names="; fi )
|
|
$( if [ ! -z ${VIASH_PAR_NO_ERROR_MODEL+x} ]; then echo "${VIASH_PAR_NO_ERROR_MODEL}" | sed "s#'#'\"'\"'#g;s#.*#par_no_error_model='&'#" ; else echo "# par_no_error_model="; fi )
|
|
$( if [ ! -z ${VIASH_PAR_NUM_ERROR_BINS+x} ]; then echo "${VIASH_PAR_NUM_ERROR_BINS}" | sed "s#'#'\"'\"'#g;s#.*#par_num_error_bins='&'#" ; else echo "# par_num_error_bins="; fi )
|
|
$( if [ ! -z ${VIASH_PAR_SAMPLE_OUT+x} ]; then echo "${VIASH_PAR_SAMPLE_OUT}" | sed "s#'#'\"'\"'#g;s#.*#par_sample_out='&'#" ; else echo "# par_sample_out="; fi )
|
|
$( if [ ! -z ${VIASH_PAR_SAMPLE_UNALIGNED+x} ]; then echo "${VIASH_PAR_SAMPLE_UNALIGNED}" | sed "s#'#'\"'\"'#g;s#.*#par_sample_unaligned='&'#" ; else echo "# par_sample_unaligned="; fi )
|
|
$( if [ ! -z ${VIASH_PAR_GENCODE+x} ]; then echo "${VIASH_PAR_GENCODE}" | sed "s#'#'\"'\"'#g;s#.*#par_gencode='&'#" ; else echo "# par_gencode="; fi )
|
|
$( if [ ! -z ${VIASH_PAR_MAPPING_CACHE_MEMORY_LIMIT+x} ]; then echo "${VIASH_PAR_MAPPING_CACHE_MEMORY_LIMIT}" | sed "s#'#'\"'\"'#g;s#.*#par_mapping_cache_memory_limit='&'#" ; else echo "# par_mapping_cache_memory_limit="; 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_if_false=(
|
|
par_discard_orphans
|
|
par_ont
|
|
par_seq_bias
|
|
par_gc_bias
|
|
par_pos_bias
|
|
par_meta
|
|
par_discard_orphans_quasi
|
|
par_disable_chaining_heuristic
|
|
par_allow_dovetail
|
|
par_recover_orphans
|
|
par_mimicBT2
|
|
par_mimic_strictBT2
|
|
par_softclip
|
|
par_softclip_overhangs
|
|
par_full_length_alignment
|
|
par_hard_filter
|
|
par_write_mappings
|
|
par_write_qualities
|
|
par_alternative_init_mode
|
|
par_skip_quant
|
|
par_dump_eq
|
|
par_dump_eq_weights
|
|
par_reduce_GC_memory
|
|
par_init_uniform
|
|
par_no_length_correction
|
|
par_no_effective_length_correction
|
|
par_no_single_frag_prob
|
|
par_no_frag_length_dist
|
|
par_no_bias_length_threshold
|
|
par_useEM
|
|
par_useVBOpt
|
|
par_no_Gamma_draw
|
|
par_bootstrap_reproject
|
|
par_quiet
|
|
par_per_transcript_prior
|
|
par_per_nucleotide_prior
|
|
par_write_orphan_links
|
|
par_write_unmapped_names
|
|
par_no_error_model
|
|
par_sample_out
|
|
par_sample_unaligned
|
|
par_gencode
|
|
)
|
|
|
|
for par in \${unset_if_false[@]}; do
|
|
test_val="\${!par}"
|
|
[[ "\$test_val" == "false" ]] && unset \$par
|
|
done
|
|
|
|
IFS=";" read -ra unmated_reads <<< \$par_unmated_reads
|
|
IFS=";" read -ra mates1 <<< \$par_mates1
|
|
IFS=";" read -ra mates2 <<< \$par_mates2
|
|
IFS=";" read -ra alignment <<< \$par_alignments
|
|
|
|
salmon quant \\
|
|
\${par_lib_type:+-l "\${par_lib_type}"} \\
|
|
\${par_index:+-i "\${par_index}"} \\
|
|
\${par_unmated_reads:+-r \${unmated_reads[*]}} \\
|
|
\${par_mates1:+-1 \${mates1[*]}} \\
|
|
\${par_mates2:+-2 \${mates2[*]}} \\
|
|
\${par_alignments:+-a \${alignment[*]}} \\
|
|
\${par_discard_orphans:+--discardOrphans} \\
|
|
\${par_eqclasses:+-e "\${par_eqclasses}"} \\
|
|
\${par_targets:+-t "\${par_targets}"} \\
|
|
\${par_ont:+--ont} \\
|
|
\${par_output:+-o "\${par_output}"} \\
|
|
\${par_seq_bias:+--seqBias} \\
|
|
\${par_gc_bias:+--gcBias} \\
|
|
\${par_pos_bias:+--posBias} \\
|
|
\${meta_cpus:+-p "\${meta_cpus}"} \\
|
|
\${par_incompat_prior:+--incompatPrior "\${par_incompat_prior}"} \\
|
|
\${par_gene_map:+-g "\${par_gene_map}"} \\
|
|
\${par_aux_target_file:+--auxTargetFile "\${par_aux_target_file}"} \\
|
|
\${par_meta:+--meta} \\
|
|
\${par_score_exp:+--scoreExp "\${par_score_exp}"} \\
|
|
\${par_discard_orphans_quasi:+--discardOrphansQuasi} \\
|
|
\${par_consensus_slack:+--consensusSlack "\${par_consensus_slack}"} \\
|
|
\${par_pre_merge_chain_sub_thresh:+--preMergeChainSubThresh "\${par_pre_merge_chain_sub_thresh}"} \\
|
|
\${par_post_merge_chain_sub_thresh:+--postMergeChainSubThresh "\${par_post_merge_chain_sub_thresh}"} \\
|
|
\${par_orphan_chain_sub_thresh:+--orphanChainSubThresh "\${par_orphan_chain_sub_thresh}"} \\
|
|
\${par_min_score_fraction:+--minScoreFraction "\${par_min_score_fraction}"} \\
|
|
\${par_mismatch_seed_skip:+--mismatchSeedSkip "\${par_mismatch_seed_skip}"} \\
|
|
\${par_disable_chaining_heuristic:+--disableChainingHeuristic} \\
|
|
\${par_decoy_threshold:+--decoyThreshold "\${par_decoy_threshold}"} \\
|
|
\${par_ma:+--ma "\${par_ma}"} \\
|
|
\${par_mp:+--mp "\${par_mp}"} \\
|
|
\${par_go:+--go "\${par_go}"} \\
|
|
\${par_ge:+--ge "\${par_ge}"} \\
|
|
\${par_bandwidth:+--bandwidth "\${par_bandwidth}"} \\
|
|
\${par_allow_dovetail:+--allowDovetail} \\
|
|
\${par_recover_orphans:+--recoverOrphans} \\
|
|
\${par_mimicBT2:+--mimicBT2} \\
|
|
\${par_mimic_strictBT2:+--mimicStrictBT2} \\
|
|
\${par_softclip:+--softclip} \\
|
|
\${par_softclip_overhangs:+--softclipOverhangs} \\
|
|
\${par_full_length_alignment:+--fullLengthAlignment} \\
|
|
\${par_hard_filter:+--hardFilter} \\
|
|
\${par_min_aln_prob:+--minAlnProb "\${par_min_aln_prob}"} \\
|
|
\${par_write_mappings:+--write_mappings="\${par_mappings_sam}"} \\
|
|
\${par_write_qualities:+--writeQualities} \\
|
|
\${par_hit_filter_policy:+--hitFilterPolicy "\${par_hit_filter_policy}"} \\
|
|
\${par_alternative_init_mode:+--alternativeInitMode} \\
|
|
\${par_aux_dir:+--auxDir "\${par_aux_dir}"} \\
|
|
\${par_skip_quant:+--skipQuant} \\
|
|
\${par_dump_eq:+--dumpEq} \\
|
|
\${par_dump_eq_weights:+-d "\${par_dump_eq_weights}"} \\
|
|
\${par_min_assigned_frags:+--minAssignedFrags "\${par_min_assigned_frags}"} \\
|
|
\${par_reduce_GC_memory:+--reduceGCMemory} \\
|
|
\${par_bias_speed_samp:+--biasSpeedSamp "\${par_bias_speed_samp}"} \\
|
|
\${par_fld_max:+--fldMax "\${par_fld_max}"} \\
|
|
\${par_fld_mean:+--fldMean "\${par_fld_mean}"} \\
|
|
\${par_fld_SD:+--fldSD "\${par_fld_SD}"} \\
|
|
\${par_forgetting_factor:+-f "\${par_forgetting_factor}"} \\
|
|
\${par_init_uniform:+--initUniform} \\
|
|
\${par_max_occs_per_hit:+--maxOccsPerHit "\${par_max_occs_per_hit}"} \\
|
|
\${par_max_read_occ:+-w "\${par_max_read_occ}"} \\
|
|
\${par_no_length_correction:+--noLengthCorrection} \\
|
|
\${par_no_effective_length_correction:+--noEffectiveLengthCorrection} \\
|
|
\${par_no_single_frag_prob:+--noSingleFragProb} \\
|
|
\${par_no_frag_length_dist:+--noFragLengthDist} \\
|
|
\${par_no_bias_length_threshold:+--noBiasLengthThreshold} \\
|
|
\${par_num_bias_samples:+--numBiasSamples "\${par_num_bias_samples}"} \\
|
|
\${par_num_aux_model_samples:+--numAuxModelSamples "\${par_num_aux_model_samples}"} \\
|
|
\${par_num_pre_aux_model_samples:+--numPreAuxModelSamples "\${par_num_pre_aux_model_samples}"} \\
|
|
\${par_useEM:+--useEM} \\
|
|
\${par_useVBOpt:+--useVBOpt} \\
|
|
\${par_range_factorization_bins:+--rangeFactorizationBins "\${par_range_factorization_bins}"} \\
|
|
\${par_num_Gibbs_samples:+--numGibbsSamples "\${par_num_Gibbs_samples}"} \\
|
|
\${par_no_Gamma_draw:+--noGammaDraw} \\
|
|
\${par_num_bootstraps:+--numBootstraps "\${par_num_bootstraps}"} \\
|
|
\${par_bootstrap_reproject:+--bootstrapReproject} \\
|
|
\${par_thinning_factor:+--thinningFactor "\${par_thinning_factor}"} \\
|
|
\${par_quiet:+--quiet} \\
|
|
\${par_per_transcript_prior:+--perTranscriptPrior} \\
|
|
\${par_per_nucleotide_prior:+--perNucleotidePrior} \\
|
|
\${par_sig_digits:+--sigDigits "\${par_sig_digits}"} \\
|
|
\${par_vb_prior:+--vbPrior "\${par_vb_prior}"} \\
|
|
\${par_write_orphan_links:+--writeOrphanLinks} \\
|
|
\${par_write_unmapped_names:+--writeUnmappedNames} \\
|
|
\${par_no_error_model:+--noErrorModel} \\
|
|
\${par_num_error_bins:+--numErrorBins "\${par_num_error_bins}"} \\
|
|
\${par_sample_out:+--sampleOut} \\
|
|
\${par_sample_unaligned:+--sampleUnaligned} \\
|
|
\${par_gencode:+--gencode} \\
|
|
\${par_mapping_cache_memory_limit:+--mappingCacheMemoryLimit "\${par_mapping_cache_memory_limit}"}
|
|
|
|
if [ -f "\$par_output/quant.sf" ]; then
|
|
mv \$par_output/quant.sf \$par_quant_results
|
|
else
|
|
echo "Quantification file not generated!"
|
|
fi
|
|
VIASHMAIN
|
|
bash "\$tempscript" &
|
|
wait "\$!"
|
|
|
|
VIASHEOF
|
|
|
|
|
|
if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then
|
|
# strip viash automount from file paths
|
|
|
|
if [ ! -z "$VIASH_PAR_INDEX" ]; then
|
|
VIASH_PAR_INDEX=$(ViashDockerStripAutomount "$VIASH_PAR_INDEX")
|
|
fi
|
|
if [ ! -z "$VIASH_PAR_UNMATED_READS" ]; then
|
|
unset VIASH_TEST_UNMATED_READS
|
|
IFS=';'
|
|
for var in $VIASH_PAR_UNMATED_READS; do
|
|
unset IFS
|
|
if [ -z "$VIASH_TEST_UNMATED_READS" ]; then
|
|
VIASH_TEST_UNMATED_READS="$(ViashDockerStripAutomount "$var")"
|
|
else
|
|
VIASH_TEST_UNMATED_READS="$VIASH_TEST_UNMATED_READS;""$(ViashDockerStripAutomount "$var")"
|
|
fi
|
|
done
|
|
VIASH_PAR_UNMATED_READS="$VIASH_TEST_UNMATED_READS"
|
|
fi
|
|
if [ ! -z "$VIASH_PAR_MATES1" ]; then
|
|
unset VIASH_TEST_MATES1
|
|
IFS=';'
|
|
for var in $VIASH_PAR_MATES1; do
|
|
unset IFS
|
|
if [ -z "$VIASH_TEST_MATES1" ]; then
|
|
VIASH_TEST_MATES1="$(ViashDockerStripAutomount "$var")"
|
|
else
|
|
VIASH_TEST_MATES1="$VIASH_TEST_MATES1;""$(ViashDockerStripAutomount "$var")"
|
|
fi
|
|
done
|
|
VIASH_PAR_MATES1="$VIASH_TEST_MATES1"
|
|
fi
|
|
if [ ! -z "$VIASH_PAR_MATES2" ]; then
|
|
unset VIASH_TEST_MATES2
|
|
IFS=';'
|
|
for var in $VIASH_PAR_MATES2; do
|
|
unset IFS
|
|
if [ -z "$VIASH_TEST_MATES2" ]; then
|
|
VIASH_TEST_MATES2="$(ViashDockerStripAutomount "$var")"
|
|
else
|
|
VIASH_TEST_MATES2="$VIASH_TEST_MATES2;""$(ViashDockerStripAutomount "$var")"
|
|
fi
|
|
done
|
|
VIASH_PAR_MATES2="$VIASH_TEST_MATES2"
|
|
fi
|
|
if [ ! -z "$VIASH_PAR_ALIGNMENTS" ]; then
|
|
unset VIASH_TEST_ALIGNMENTS
|
|
IFS=';'
|
|
for var in $VIASH_PAR_ALIGNMENTS; do
|
|
unset IFS
|
|
if [ -z "$VIASH_TEST_ALIGNMENTS" ]; then
|
|
VIASH_TEST_ALIGNMENTS="$(ViashDockerStripAutomount "$var")"
|
|
else
|
|
VIASH_TEST_ALIGNMENTS="$VIASH_TEST_ALIGNMENTS;""$(ViashDockerStripAutomount "$var")"
|
|
fi
|
|
done
|
|
VIASH_PAR_ALIGNMENTS="$VIASH_TEST_ALIGNMENTS"
|
|
fi
|
|
if [ ! -z "$VIASH_PAR_EQCLASSES" ]; then
|
|
VIASH_PAR_EQCLASSES=$(ViashDockerStripAutomount "$VIASH_PAR_EQCLASSES")
|
|
fi
|
|
if [ ! -z "$VIASH_PAR_TARGETS" ]; then
|
|
VIASH_PAR_TARGETS=$(ViashDockerStripAutomount "$VIASH_PAR_TARGETS")
|
|
fi
|
|
if [ ! -z "$VIASH_PAR_OUTPUT" ]; then
|
|
VIASH_PAR_OUTPUT=$(ViashDockerStripAutomount "$VIASH_PAR_OUTPUT")
|
|
fi
|
|
if [ ! -z "$VIASH_PAR_QUANT_RESULTS" ]; then
|
|
VIASH_PAR_QUANT_RESULTS=$(ViashDockerStripAutomount "$VIASH_PAR_QUANT_RESULTS")
|
|
fi
|
|
if [ ! -z "$VIASH_PAR_GENE_MAP" ]; then
|
|
VIASH_PAR_GENE_MAP=$(ViashDockerStripAutomount "$VIASH_PAR_GENE_MAP")
|
|
fi
|
|
if [ ! -z "$VIASH_PAR_AUX_TARGET_FILE" ]; then
|
|
VIASH_PAR_AUX_TARGET_FILE=$(ViashDockerStripAutomount "$VIASH_PAR_AUX_TARGET_FILE")
|
|
fi
|
|
if [ ! -z "$VIASH_PAR_MAPPING_SAM" ]; then
|
|
VIASH_PAR_MAPPING_SAM=$(ViashDockerStripAutomount "$VIASH_PAR_MAPPING_SAM")
|
|
fi
|
|
if [ ! -z "$VIASH_PAR_AUX_DIR" ]; then
|
|
VIASH_PAR_AUX_DIR=$(ViashDockerStripAutomount "$VIASH_PAR_AUX_DIR")
|
|
fi
|
|
if [ ! -z "$VIASH_META_RESOURCES_DIR" ]; then
|
|
VIASH_META_RESOURCES_DIR=$(ViashDockerStripAutomount "$VIASH_META_RESOURCES_DIR")
|
|
fi
|
|
if [ ! -z "$VIASH_META_EXECUTABLE" ]; then
|
|
VIASH_META_EXECUTABLE=$(ViashDockerStripAutomount "$VIASH_META_EXECUTABLE")
|
|
fi
|
|
if [ ! -z "$VIASH_META_CONFIG" ]; then
|
|
VIASH_META_CONFIG=$(ViashDockerStripAutomount "$VIASH_META_CONFIG")
|
|
fi
|
|
if [ ! -z "$VIASH_META_TEMP_DIR" ]; then
|
|
VIASH_META_TEMP_DIR=$(ViashDockerStripAutomount "$VIASH_META_TEMP_DIR")
|
|
fi
|
|
fi
|
|
|
|
|
|
# check whether required files exist
|
|
if [ ! -z "$VIASH_PAR_OUTPUT" ] && [ ! -e "$VIASH_PAR_OUTPUT" ]; then
|
|
ViashError "Output file '$VIASH_PAR_OUTPUT' does not exist."
|
|
exit 1
|
|
fi
|
|
if [ ! -z "$VIASH_PAR_QUANT_RESULTS" ] && [ ! -e "$VIASH_PAR_QUANT_RESULTS" ]; then
|
|
ViashError "Output file '$VIASH_PAR_QUANT_RESULTS' does not exist."
|
|
exit 1
|
|
fi
|
|
if [ ! -z "$VIASH_PAR_MAPPING_SAM" ] && [ ! -e "$VIASH_PAR_MAPPING_SAM" ]; then
|
|
ViashError "Output file '$VIASH_PAR_MAPPING_SAM' does not exist."
|
|
exit 1
|
|
fi
|
|
if [ ! -z "$VIASH_PAR_AUX_DIR" ] && [ ! -e "$VIASH_PAR_AUX_DIR" ]; then
|
|
ViashError "Output file '$VIASH_PAR_AUX_DIR' does not exist."
|
|
exit 1
|
|
fi
|
|
|
|
|
|
exit 0
|