CI
af89cea364
Build pipeline: viash-hub.biobox.main-69lmq
Source commit: 80aaf333dc
Source message: Add Kallisto index (#149)
1681 lines
68 KiB
Bash
Executable File
1681 lines
68 KiB
Bash
Executable File
#!/usr/bin/env bash
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# fastqc main
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#
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# This wrapper script is auto-generated by viash 0.9.0-RC7 and is thus a
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# derivative work thereof. This software comes with ABSOLUTELY NO WARRANTY from
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# Data 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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# * Theodoro Gasperin Terra Camargo (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 $VIASH_META_RESOURCES_DIR`
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# define meta fields
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VIASH_META_NAME="fastqc"
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VIASH_META_FUNCTIONALITY_NAME="fastqc"
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VIASH_META_EXECUTABLE="$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 "fastqc main"
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echo ""
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echo "FastQC - A high throughput sequence QC analysis tool."
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echo ""
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echo "Inputs:"
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echo " --input"
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echo " type: file, required parameter, multiple values allowed, file must exist"
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echo " example: input.fq"
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echo " FASTQ file(s) to be analyzed."
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echo ""
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echo "Outputs:"
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echo " At least one of the output options (--html, --zip, --summary, --data) must"
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echo " be used."
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echo ""
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echo " --html"
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echo " type: file, multiple values allowed, output, file must exist"
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echo " example: *.html"
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echo " Create the HTML report of the results."
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echo " '*' wild card must be provided in the output file name."
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echo " Wild card will be replaced by the input file basename."
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echo " e.g."
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echo " --input \"sample_1.fq\""
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echo " --html \"*.html\""
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echo " would create an output html file named sample_1.html"
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echo ""
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echo " --zip"
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echo " type: file, multiple values allowed, output, file must exist"
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echo " example: *.zip"
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echo " Create the zip file(s) containing: html report, data, images, icons,"
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echo " summary, etc."
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echo " '*' wild card must be provided in the output file name."
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echo " Wild card will be replaced by the input basename."
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echo " e.g."
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echo " --input \"sample_1.fq\""
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echo " --html \"*.zip\""
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echo " would create an output zip file named sample_1.zip"
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echo ""
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echo " --summary"
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echo " type: file, multiple values allowed, output, file must exist"
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echo " example: *_summary.txt"
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echo " Create the summary file(s)."
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echo " '*' wild card must be provided in the output file name."
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echo " Wild card will be replaced by the input basename."
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echo " e.g."
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echo " --input \"sample_1.fq\""
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echo " --summary \"*_summary.txt\""
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echo " would create an output summary.txt file named sample_1_summary.txt"
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echo ""
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echo " --data"
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echo " type: file, multiple values allowed, output, file must exist"
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echo " example: *_data.txt"
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echo " Create the data file(s)."
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echo " '*' wild card must be provided in the output file name."
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echo " Wild card will be replaced by the input basename."
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echo " e.g."
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echo " --input \"sample_1.fq\""
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echo " --summary \"*_data.txt\""
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echo " would create an output data.txt file named sample_1_data.txt"
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echo ""
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echo "Options:"
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echo " --casava"
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echo " type: boolean_true"
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echo " Files come from raw casava output. Files in the same sample"
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echo " group (differing only by the group number) will be analysed"
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echo " as a set rather than individually. Sequences with the filter"
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echo " flag set in the header will be excluded from the analysis."
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echo " Files must have the same names given to them by casava"
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echo " (including being gzipped and ending with .gz) otherwise they"
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echo " won't be grouped together correctly."
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echo ""
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echo " --nano"
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echo " type: boolean_true"
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echo " Files come from nanopore sequences and are in fast5 format. In"
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echo " this mode you can pass in directories to process and the program"
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echo " will take in all fast5 files within those directories and produce"
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echo " a single output file from the sequences found in all files."
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echo ""
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echo " --nofilter"
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echo " type: boolean_true"
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echo " If running with --casava then don't remove read flagged by"
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echo " casava as poor quality when performing the QC analysis."
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echo ""
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echo " --nogroup"
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echo " type: boolean_true"
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echo " Disable grouping of bases for reads >50bp."
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echo " All reports will show data for every base in the read."
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echo " WARNING: Using this option will cause fastqc to crash"
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echo " and burn if you use it on really long reads, and your"
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echo " plots may end up a ridiculous size. You have been warned!"
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echo ""
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echo " --min_length"
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echo " type: integer"
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echo " example: 0"
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echo " Sets an artificial lower limit on the length of the"
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echo " sequence to be shown in the report. As long as you"
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echo " set this to a value greater or equal to your longest"
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echo " read length then this will be the sequence length used"
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echo " to create your read groups. This can be useful for making"
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echo " directly comparable statistics from datasets with somewhat"
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echo " variable read lengths."
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echo ""
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echo " -f, --format"
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echo " type: string"
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echo " example: bam"
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echo " Bypasses the normal sequence file format detection and"
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echo " forces the program to use the specified format."
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echo " Valid formats are bam, sam, bam_mapped, sam_mapped, and fastq."
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echo ""
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echo " -c, --contaminants"
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echo " type: file, file must exist"
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echo " example: contaminants.txt"
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echo " Specifies a non-default file which contains the list"
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echo " of contaminants to screen overrepresented sequences against."
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echo " The file must contain sets of named contaminants in the form"
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echo " name[tab]sequence. Lines prefixed with a hash will be ignored."
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echo ""
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echo " -a, --adapters"
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echo " type: file, file must exist"
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echo " example: adapters.txt"
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echo " Specifies a non-default file which contains the list of"
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echo " adapter sequences which will be explicitly searched against"
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echo " the library. The file must contain sets of named adapters"
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echo " in the form name[tab]sequence. Lines prefixed with a hash will be"
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echo " ignored."
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echo ""
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echo " -l, --limits"
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echo " type: file, file must exist"
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echo " example: limits.txt"
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echo " Specifies a non-default file which contains"
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echo " a set of criteria which will be used to determine"
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echo " the warn/error limits for the various modules."
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echo " This file can also be used to selectively remove"
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echo " some modules from the output altogether. The format"
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echo " needs to mirror the default limits.txt file found in"
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echo " the Configuration folder."
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echo ""
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echo " -k, --kmers"
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echo " type: integer"
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echo " example: 7"
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echo " Specifies the length of Kmer to look for in the Kmer"
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echo " content module. Specified Kmer length must be between"
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echo " 2 and 10. Default length is 7 if not specified."
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echo ""
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echo " -q, --quiet"
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echo " type: boolean_true"
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echo " Suppress all progress messages on stdout and only report errors."
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}
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# initialise variables
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VIASH_MODE='run'
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VIASH_ENGINE_ID='docker'
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######## Helper functions for setting up Docker images for viash ########
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# expects: ViashDockerBuild
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# ViashDockerInstallationCheck: check whether Docker is installed correctly
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#
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# examples:
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# ViashDockerInstallationCheck
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function ViashDockerInstallationCheck {
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ViashDebug "Checking whether Docker is installed"
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if [ ! command -v docker &> /dev/null ]; then
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ViashCritical "Docker doesn't seem to be installed. See 'https://docs.docker.com/get-docker/' for instructions."
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exit 1
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fi
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ViashDebug "Checking whether the Docker daemon is running"
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local save=$-; set +e
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local docker_version=$(docker version --format '{{.Client.APIVersion}}' 2> /dev/null)
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local out=$?
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[[ $save =~ e ]] && set -e
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if [ $out -ne 0 ]; then
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ViashCritical "Docker daemon does not seem to be running. Try one of the following:"
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ViashCritical "- Try running 'dockerd' in the command line"
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ViashCritical "- See https://docs.docker.com/config/daemon/"
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exit 1
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fi
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}
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# ViashDockerRemoteTagCheck: check whether a Docker image is available
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# on a remote. Assumes `docker login` has been performed, if relevant.
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#
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# $1 : image identifier with format `[registry/]image[:tag]`
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# exit code $? : whether or not the image was found
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# examples:
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# ViashDockerRemoteTagCheck python:latest
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# echo $? # returns '0'
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# ViashDockerRemoteTagCheck sdaizudceahifu
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# echo $? # returns '1'
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function ViashDockerRemoteTagCheck {
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docker manifest inspect $1 > /dev/null 2> /dev/null
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}
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# ViashDockerLocalTagCheck: check whether a Docker image is available locally
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#
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# $1 : image identifier with format `[registry/]image[:tag]`
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# exit code $? : whether or not the image was found
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# examples:
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# docker pull python:latest
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# ViashDockerLocalTagCheck python:latest
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# echo $? # returns '0'
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# ViashDockerLocalTagCheck sdaizudceahifu
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# echo $? # returns '1'
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function ViashDockerLocalTagCheck {
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[ -n "$(docker images -q $1)" ]
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}
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# ViashDockerPull: pull a Docker image
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#
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# $1 : image identifier with format `[registry/]image[:tag]`
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# exit code $? : whether or not the image was found
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# examples:
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# ViashDockerPull python:latest
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# echo $? # returns '0'
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# ViashDockerPull sdaizudceahifu
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# echo $? # returns '1'
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function ViashDockerPull {
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ViashNotice "Checking if Docker image is available at '$1'"
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if [ $VIASH_VERBOSITY -ge $VIASH_LOGCODE_INFO ]; then
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docker pull $1 && return 0 || return 1
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else
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local save=$-; set +e
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docker pull $1 2> /dev/null > /dev/null
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local out=$?
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[[ $save =~ e ]] && set -e
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if [ $out -ne 0 ]; then
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ViashWarning "Could not pull from '$1'. Docker image doesn't exist or is not accessible."
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fi
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return $out
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fi
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}
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# ViashDockerPush: push a Docker image
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|
#
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# $1 : image identifier with format `[registry/]image[:tag]`
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# exit code $? : whether or not the image was found
|
|
# examples:
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# ViashDockerPush python:latest
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# echo $? # returns '0'
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# ViashDockerPush sdaizudceahifu
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# echo $? # returns '1'
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function ViashDockerPush {
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ViashNotice "Pushing image to '$1'"
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local save=$-; set +e
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local out
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if [ $VIASH_VERBOSITY -ge $VIASH_LOGCODE_INFO ]; then
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docker push $1
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out=$?
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else
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docker push $1 2> /dev/null > /dev/null
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out=$?
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fi
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[[ $save =~ e ]] && set -e
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if [ $out -eq 0 ]; then
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ViashNotice "Container '$1' push succeeded."
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else
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ViashError "Container '$1' push errored. You might not be logged in or have the necessary permissions."
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fi
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return $out
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}
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# ViashDockerPullElseBuild: pull a Docker image, else build it
|
|
#
|
|
# $1 : image identifier with format `[registry/]image[:tag]`
|
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# ViashDockerBuild : a Bash function which builds a docker image, takes image identifier as argument.
|
|
# examples:
|
|
# ViashDockerPullElseBuild mynewcomponent
|
|
function ViashDockerPullElseBuild {
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local save=$-; set +e
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ViashDockerPull $1
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local out=$?
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[[ $save =~ e ]] && set -e
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if [ $out -ne 0 ]; then
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ViashDockerBuild $@
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fi
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}
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# ViashDockerSetup: create a Docker image, according to specified docker setup strategy
|
|
#
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# $1 : image identifier with format `[registry/]image[:tag]`
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# $2 : docker setup strategy, see DockerSetupStrategy.scala
|
|
# examples:
|
|
# ViashDockerSetup mynewcomponent alwaysbuild
|
|
function ViashDockerSetup {
|
|
local image_id="$1"
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local setup_strategy="$2"
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if [ "$setup_strategy" == "alwaysbuild" -o "$setup_strategy" == "build" -o "$setup_strategy" == "b" ]; then
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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 biocontainers/fastqc:v0.11.9_cv8
|
|
ENTRYPOINT []
|
|
RUN echo "fastqc: $(fastqc --version | sed -n 's/^FastQC //p')" > /var/software_versions.txt
|
|
|
|
LABEL org.opencontainers.image.authors="Theodoro Gasperin Terra Camargo"
|
|
LABEL org.opencontainers.image.description="Companion container for running component fastqc"
|
|
LABEL org.opencontainers.image.created="2024-09-13T07:15:48Z"
|
|
LABEL org.opencontainers.image.source="https://github.com/s-andrews/FastQC"
|
|
LABEL org.opencontainers.image.revision="80aaf333dc1245b8bbec9aa7b628d85c5e413f4b"
|
|
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 "$1")"
|
|
shift 1
|
|
;;
|
|
--version)
|
|
echo "fastqc main"
|
|
exit
|
|
;;
|
|
--input)
|
|
if [ -z "$VIASH_PAR_INPUT" ]; then
|
|
VIASH_PAR_INPUT="$2"
|
|
else
|
|
VIASH_PAR_INPUT="$VIASH_PAR_INPUT;""$2"
|
|
fi
|
|
[ $# -lt 2 ] && ViashError Not enough arguments passed to --input. Use "--help" to get more information on the parameters. && exit 1
|
|
shift 2
|
|
;;
|
|
--input=*)
|
|
if [ -z "$VIASH_PAR_INPUT" ]; then
|
|
VIASH_PAR_INPUT=$(ViashRemoveFlags "$1")
|
|
else
|
|
VIASH_PAR_INPUT="$VIASH_PAR_INPUT;"$(ViashRemoveFlags "$1")
|
|
fi
|
|
shift 1
|
|
;;
|
|
--html)
|
|
[ -n "$VIASH_PAR_HTML" ] && ViashError Bad arguments for option \'--html\': \'$VIASH_PAR_HTML\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_HTML="$2"
|
|
[ $# -lt 2 ] && ViashError Not enough arguments passed to --html. Use "--help" to get more information on the parameters. && exit 1
|
|
shift 2
|
|
;;
|
|
--html=*)
|
|
[ -n "$VIASH_PAR_HTML" ] && ViashError Bad arguments for option \'--html=*\': \'$VIASH_PAR_HTML\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_HTML=$(ViashRemoveFlags "$1")
|
|
shift 1
|
|
;;
|
|
--zip)
|
|
[ -n "$VIASH_PAR_ZIP" ] && ViashError Bad arguments for option \'--zip\': \'$VIASH_PAR_ZIP\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_ZIP="$2"
|
|
[ $# -lt 2 ] && ViashError Not enough arguments passed to --zip. Use "--help" to get more information on the parameters. && exit 1
|
|
shift 2
|
|
;;
|
|
--zip=*)
|
|
[ -n "$VIASH_PAR_ZIP" ] && ViashError Bad arguments for option \'--zip=*\': \'$VIASH_PAR_ZIP\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_ZIP=$(ViashRemoveFlags "$1")
|
|
shift 1
|
|
;;
|
|
--summary)
|
|
[ -n "$VIASH_PAR_SUMMARY" ] && ViashError Bad arguments for option \'--summary\': \'$VIASH_PAR_SUMMARY\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_SUMMARY="$2"
|
|
[ $# -lt 2 ] && ViashError Not enough arguments passed to --summary. Use "--help" to get more information on the parameters. && exit 1
|
|
shift 2
|
|
;;
|
|
--summary=*)
|
|
[ -n "$VIASH_PAR_SUMMARY" ] && ViashError Bad arguments for option \'--summary=*\': \'$VIASH_PAR_SUMMARY\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_SUMMARY=$(ViashRemoveFlags "$1")
|
|
shift 1
|
|
;;
|
|
--data)
|
|
[ -n "$VIASH_PAR_DATA" ] && ViashError Bad arguments for option \'--data\': \'$VIASH_PAR_DATA\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_DATA="$2"
|
|
[ $# -lt 2 ] && ViashError Not enough arguments passed to --data. Use "--help" to get more information on the parameters. && exit 1
|
|
shift 2
|
|
;;
|
|
--data=*)
|
|
[ -n "$VIASH_PAR_DATA" ] && ViashError Bad arguments for option \'--data=*\': \'$VIASH_PAR_DATA\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_DATA=$(ViashRemoveFlags "$1")
|
|
shift 1
|
|
;;
|
|
--casava)
|
|
[ -n "$VIASH_PAR_CASAVA" ] && ViashError Bad arguments for option \'--casava\': \'$VIASH_PAR_CASAVA\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_CASAVA=true
|
|
shift 1
|
|
;;
|
|
--nano)
|
|
[ -n "$VIASH_PAR_NANO" ] && ViashError Bad arguments for option \'--nano\': \'$VIASH_PAR_NANO\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_NANO=true
|
|
shift 1
|
|
;;
|
|
--nofilter)
|
|
[ -n "$VIASH_PAR_NOFILTER" ] && ViashError Bad arguments for option \'--nofilter\': \'$VIASH_PAR_NOFILTER\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_NOFILTER=true
|
|
shift 1
|
|
;;
|
|
--nogroup)
|
|
[ -n "$VIASH_PAR_NOGROUP" ] && ViashError Bad arguments for option \'--nogroup\': \'$VIASH_PAR_NOGROUP\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_NOGROUP=true
|
|
shift 1
|
|
;;
|
|
--min_length)
|
|
[ -n "$VIASH_PAR_MIN_LENGTH" ] && ViashError Bad arguments for option \'--min_length\': \'$VIASH_PAR_MIN_LENGTH\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_MIN_LENGTH="$2"
|
|
[ $# -lt 2 ] && ViashError Not enough arguments passed to --min_length. Use "--help" to get more information on the parameters. && exit 1
|
|
shift 2
|
|
;;
|
|
--min_length=*)
|
|
[ -n "$VIASH_PAR_MIN_LENGTH" ] && ViashError Bad arguments for option \'--min_length=*\': \'$VIASH_PAR_MIN_LENGTH\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_MIN_LENGTH=$(ViashRemoveFlags "$1")
|
|
shift 1
|
|
;;
|
|
--format)
|
|
[ -n "$VIASH_PAR_FORMAT" ] && ViashError Bad arguments for option \'--format\': \'$VIASH_PAR_FORMAT\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_FORMAT="$2"
|
|
[ $# -lt 2 ] && ViashError Not enough arguments passed to --format. Use "--help" to get more information on the parameters. && exit 1
|
|
shift 2
|
|
;;
|
|
--format=*)
|
|
[ -n "$VIASH_PAR_FORMAT" ] && ViashError Bad arguments for option \'--format=*\': \'$VIASH_PAR_FORMAT\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_FORMAT=$(ViashRemoveFlags "$1")
|
|
shift 1
|
|
;;
|
|
-f)
|
|
[ -n "$VIASH_PAR_FORMAT" ] && ViashError Bad arguments for option \'-f\': \'$VIASH_PAR_FORMAT\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_FORMAT="$2"
|
|
[ $# -lt 2 ] && ViashError Not enough arguments passed to -f. Use "--help" to get more information on the parameters. && exit 1
|
|
shift 2
|
|
;;
|
|
--contaminants)
|
|
[ -n "$VIASH_PAR_CONTAMINANTS" ] && ViashError Bad arguments for option \'--contaminants\': \'$VIASH_PAR_CONTAMINANTS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_CONTAMINANTS="$2"
|
|
[ $# -lt 2 ] && ViashError Not enough arguments passed to --contaminants. Use "--help" to get more information on the parameters. && exit 1
|
|
shift 2
|
|
;;
|
|
--contaminants=*)
|
|
[ -n "$VIASH_PAR_CONTAMINANTS" ] && ViashError Bad arguments for option \'--contaminants=*\': \'$VIASH_PAR_CONTAMINANTS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_CONTAMINANTS=$(ViashRemoveFlags "$1")
|
|
shift 1
|
|
;;
|
|
-c)
|
|
[ -n "$VIASH_PAR_CONTAMINANTS" ] && ViashError Bad arguments for option \'-c\': \'$VIASH_PAR_CONTAMINANTS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_CONTAMINANTS="$2"
|
|
[ $# -lt 2 ] && ViashError Not enough arguments passed to -c. Use "--help" to get more information on the parameters. && exit 1
|
|
shift 2
|
|
;;
|
|
--adapters)
|
|
[ -n "$VIASH_PAR_ADAPTERS" ] && ViashError Bad arguments for option \'--adapters\': \'$VIASH_PAR_ADAPTERS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_ADAPTERS="$2"
|
|
[ $# -lt 2 ] && ViashError Not enough arguments passed to --adapters. Use "--help" to get more information on the parameters. && exit 1
|
|
shift 2
|
|
;;
|
|
--adapters=*)
|
|
[ -n "$VIASH_PAR_ADAPTERS" ] && ViashError Bad arguments for option \'--adapters=*\': \'$VIASH_PAR_ADAPTERS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_ADAPTERS=$(ViashRemoveFlags "$1")
|
|
shift 1
|
|
;;
|
|
-a)
|
|
[ -n "$VIASH_PAR_ADAPTERS" ] && ViashError Bad arguments for option \'-a\': \'$VIASH_PAR_ADAPTERS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_ADAPTERS="$2"
|
|
[ $# -lt 2 ] && ViashError Not enough arguments passed to -a. Use "--help" to get more information on the parameters. && exit 1
|
|
shift 2
|
|
;;
|
|
--limits)
|
|
[ -n "$VIASH_PAR_LIMITS" ] && ViashError Bad arguments for option \'--limits\': \'$VIASH_PAR_LIMITS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_LIMITS="$2"
|
|
[ $# -lt 2 ] && ViashError Not enough arguments passed to --limits. Use "--help" to get more information on the parameters. && exit 1
|
|
shift 2
|
|
;;
|
|
--limits=*)
|
|
[ -n "$VIASH_PAR_LIMITS" ] && ViashError Bad arguments for option \'--limits=*\': \'$VIASH_PAR_LIMITS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_LIMITS=$(ViashRemoveFlags "$1")
|
|
shift 1
|
|
;;
|
|
-l)
|
|
[ -n "$VIASH_PAR_LIMITS" ] && ViashError Bad arguments for option \'-l\': \'$VIASH_PAR_LIMITS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_LIMITS="$2"
|
|
[ $# -lt 2 ] && ViashError Not enough arguments passed to -l. Use "--help" to get more information on the parameters. && exit 1
|
|
shift 2
|
|
;;
|
|
--kmers)
|
|
[ -n "$VIASH_PAR_KMERS" ] && ViashError Bad arguments for option \'--kmers\': \'$VIASH_PAR_KMERS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_KMERS="$2"
|
|
[ $# -lt 2 ] && ViashError Not enough arguments passed to --kmers. Use "--help" to get more information on the parameters. && exit 1
|
|
shift 2
|
|
;;
|
|
--kmers=*)
|
|
[ -n "$VIASH_PAR_KMERS" ] && ViashError Bad arguments for option \'--kmers=*\': \'$VIASH_PAR_KMERS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_KMERS=$(ViashRemoveFlags "$1")
|
|
shift 1
|
|
;;
|
|
-k)
|
|
[ -n "$VIASH_PAR_KMERS" ] && ViashError Bad arguments for option \'-k\': \'$VIASH_PAR_KMERS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_KMERS="$2"
|
|
[ $# -lt 2 ] && ViashError Not enough arguments passed to -k. Use "--help" to get more information on the parameters. && exit 1
|
|
shift 2
|
|
;;
|
|
--quiet)
|
|
[ -n "$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
|
|
;;
|
|
---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/fastqc: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_INPUT+x} ]; then
|
|
ViashError '--input' 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_CASAVA+x} ]; then
|
|
VIASH_PAR_CASAVA="false"
|
|
fi
|
|
if [ -z ${VIASH_PAR_NANO+x} ]; then
|
|
VIASH_PAR_NANO="false"
|
|
fi
|
|
if [ -z ${VIASH_PAR_NOFILTER+x} ]; then
|
|
VIASH_PAR_NOFILTER="false"
|
|
fi
|
|
if [ -z ${VIASH_PAR_NOGROUP+x} ]; then
|
|
VIASH_PAR_NOGROUP="false"
|
|
fi
|
|
if [ -z ${VIASH_PAR_QUIET+x} ]; then
|
|
VIASH_PAR_QUIET="false"
|
|
fi
|
|
|
|
# check whether required files exist
|
|
if [ ! -z "$VIASH_PAR_INPUT" ]; then
|
|
IFS=';'
|
|
set -f
|
|
for file in $VIASH_PAR_INPUT; do
|
|
unset IFS
|
|
if [ ! -e "$file" ]; then
|
|
ViashError "Input file '$file' does not exist."
|
|
exit 1
|
|
fi
|
|
done
|
|
set +f
|
|
fi
|
|
if [ ! -z "$VIASH_PAR_CONTAMINANTS" ] && [ ! -e "$VIASH_PAR_CONTAMINANTS" ]; then
|
|
ViashError "Input file '$VIASH_PAR_CONTAMINANTS' does not exist."
|
|
exit 1
|
|
fi
|
|
if [ ! -z "$VIASH_PAR_ADAPTERS" ] && [ ! -e "$VIASH_PAR_ADAPTERS" ]; then
|
|
ViashError "Input file '$VIASH_PAR_ADAPTERS' does not exist."
|
|
exit 1
|
|
fi
|
|
if [ ! -z "$VIASH_PAR_LIMITS" ] && [ ! -e "$VIASH_PAR_LIMITS" ]; then
|
|
ViashError "Input file '$VIASH_PAR_LIMITS' does not exist."
|
|
exit 1
|
|
fi
|
|
|
|
# check whether parameters values are of the right type
|
|
if [[ -n "$VIASH_PAR_HTML" ]]; then
|
|
if ! [[ "$VIASH_PAR_HTML" =~ \* ]]; then
|
|
ViashError '--html' has to be a path containing a wildcard, e.g. 'output_*.txt'. Use "--help" to get more information on the parameters.
|
|
exit 1
|
|
fi
|
|
fi
|
|
if [[ -n "$VIASH_PAR_ZIP" ]]; then
|
|
if ! [[ "$VIASH_PAR_ZIP" =~ \* ]]; then
|
|
ViashError '--zip' has to be a path containing a wildcard, e.g. 'output_*.txt'. Use "--help" to get more information on the parameters.
|
|
exit 1
|
|
fi
|
|
fi
|
|
if [[ -n "$VIASH_PAR_SUMMARY" ]]; then
|
|
if ! [[ "$VIASH_PAR_SUMMARY" =~ \* ]]; then
|
|
ViashError '--summary' has to be a path containing a wildcard, e.g. 'output_*.txt'. Use "--help" to get more information on the parameters.
|
|
exit 1
|
|
fi
|
|
fi
|
|
if [[ -n "$VIASH_PAR_DATA" ]]; then
|
|
if ! [[ "$VIASH_PAR_DATA" =~ \* ]]; then
|
|
ViashError '--data' has to be a path containing a wildcard, e.g. 'output_*.txt'. Use "--help" to get more information on the parameters.
|
|
exit 1
|
|
fi
|
|
fi
|
|
if [[ -n "$VIASH_PAR_CASAVA" ]]; then
|
|
if ! [[ "$VIASH_PAR_CASAVA" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then
|
|
ViashError '--casava' has to be a boolean_true. Use "--help" to get more information on the parameters.
|
|
exit 1
|
|
fi
|
|
fi
|
|
if [[ -n "$VIASH_PAR_NANO" ]]; then
|
|
if ! [[ "$VIASH_PAR_NANO" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then
|
|
ViashError '--nano' has to be a boolean_true. Use "--help" to get more information on the parameters.
|
|
exit 1
|
|
fi
|
|
fi
|
|
if [[ -n "$VIASH_PAR_NOFILTER" ]]; then
|
|
if ! [[ "$VIASH_PAR_NOFILTER" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then
|
|
ViashError '--nofilter' has to be a boolean_true. Use "--help" to get more information on the parameters.
|
|
exit 1
|
|
fi
|
|
fi
|
|
if [[ -n "$VIASH_PAR_NOGROUP" ]]; then
|
|
if ! [[ "$VIASH_PAR_NOGROUP" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then
|
|
ViashError '--nogroup' has to be a boolean_true. Use "--help" to get more information on the parameters.
|
|
exit 1
|
|
fi
|
|
fi
|
|
if [[ -n "$VIASH_PAR_MIN_LENGTH" ]]; then
|
|
if ! [[ "$VIASH_PAR_MIN_LENGTH" =~ ^[-+]?[0-9]+$ ]]; then
|
|
ViashError '--min_length' has to be an integer. Use "--help" to get more information on the parameters.
|
|
exit 1
|
|
fi
|
|
fi
|
|
if [[ -n "$VIASH_PAR_KMERS" ]]; then
|
|
if ! [[ "$VIASH_PAR_KMERS" =~ ^[-+]?[0-9]+$ ]]; then
|
|
ViashError '--kmers' 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 "$VIASH_META_CPUS" ]]; then
|
|
if ! [[ "$VIASH_META_CPUS" =~ ^[-+]?[0-9]+$ ]]; then
|
|
ViashError 'cpus' has to be an integer. Use "--help" to get more information on the parameters.
|
|
exit 1
|
|
fi
|
|
fi
|
|
if [[ -n "$VIASH_META_MEMORY_B" ]]; then
|
|
if ! [[ "$VIASH_META_MEMORY_B" =~ ^[-+]?[0-9]+$ ]]; then
|
|
ViashError 'memory_b' has to be a long. Use "--help" to get more information on the parameters.
|
|
exit 1
|
|
fi
|
|
fi
|
|
if [[ -n "$VIASH_META_MEMORY_KB" ]]; then
|
|
if ! [[ "$VIASH_META_MEMORY_KB" =~ ^[-+]?[0-9]+$ ]]; then
|
|
ViashError 'memory_kb' has to be a long. Use "--help" to get more information on the parameters.
|
|
exit 1
|
|
fi
|
|
fi
|
|
if [[ -n "$VIASH_META_MEMORY_MB" ]]; then
|
|
if ! [[ "$VIASH_META_MEMORY_MB" =~ ^[-+]?[0-9]+$ ]]; then
|
|
ViashError 'memory_mb' has to be a long. Use "--help" to get more information on the parameters.
|
|
exit 1
|
|
fi
|
|
fi
|
|
if [[ -n "$VIASH_META_MEMORY_GB" ]]; then
|
|
if ! [[ "$VIASH_META_MEMORY_GB" =~ ^[-+]?[0-9]+$ ]]; then
|
|
ViashError 'memory_gb' has to be a long. Use "--help" to get more information on the parameters.
|
|
exit 1
|
|
fi
|
|
fi
|
|
if [[ -n "$VIASH_META_MEMORY_TB" ]]; then
|
|
if ! [[ "$VIASH_META_MEMORY_TB" =~ ^[-+]?[0-9]+$ ]]; then
|
|
ViashError 'memory_tb' has to be a long. Use "--help" to get more information on the parameters.
|
|
exit 1
|
|
fi
|
|
fi
|
|
if [[ -n "$VIASH_META_MEMORY_PB" ]]; then
|
|
if ! [[ "$VIASH_META_MEMORY_PB" =~ ^[-+]?[0-9]+$ ]]; then
|
|
ViashError 'memory_pb' has to be a long. Use "--help" to get more information on the parameters.
|
|
exit 1
|
|
fi
|
|
fi
|
|
if [[ -n "$VIASH_META_MEMORY_KIB" ]]; then
|
|
if ! [[ "$VIASH_META_MEMORY_KIB" =~ ^[-+]?[0-9]+$ ]]; then
|
|
ViashError 'memory_kib' has to be a long. Use "--help" to get more information on the parameters.
|
|
exit 1
|
|
fi
|
|
fi
|
|
if [[ -n "$VIASH_META_MEMORY_MIB" ]]; then
|
|
if ! [[ "$VIASH_META_MEMORY_MIB" =~ ^[-+]?[0-9]+$ ]]; then
|
|
ViashError 'memory_mib' has to be a long. Use "--help" to get more information on the parameters.
|
|
exit 1
|
|
fi
|
|
fi
|
|
if [[ -n "$VIASH_META_MEMORY_GIB" ]]; then
|
|
if ! [[ "$VIASH_META_MEMORY_GIB" =~ ^[-+]?[0-9]+$ ]]; then
|
|
ViashError 'memory_gib' has to be a long. Use "--help" to get more information on the parameters.
|
|
exit 1
|
|
fi
|
|
fi
|
|
if [[ -n "$VIASH_META_MEMORY_TIB" ]]; then
|
|
if ! [[ "$VIASH_META_MEMORY_TIB" =~ ^[-+]?[0-9]+$ ]]; then
|
|
ViashError 'memory_tib' has to be a long. Use "--help" to get more information on the parameters.
|
|
exit 1
|
|
fi
|
|
fi
|
|
if [[ -n "$VIASH_META_MEMORY_PIB" ]]; then
|
|
if ! [[ "$VIASH_META_MEMORY_PIB" =~ ^[-+]?[0-9]+$ ]]; then
|
|
ViashError 'memory_pib' has to be a long. Use "--help" to get more information on the parameters.
|
|
exit 1
|
|
fi
|
|
fi
|
|
|
|
# create parent directories of output files, if so desired
|
|
if [ ! -z "$VIASH_PAR_HTML" ] && [ ! -d "$(dirname "$VIASH_PAR_HTML")" ]; then
|
|
mkdir -p "$(dirname "$VIASH_PAR_HTML")"
|
|
fi
|
|
if [ ! -z "$VIASH_PAR_ZIP" ] && [ ! -d "$(dirname "$VIASH_PAR_ZIP")" ]; then
|
|
mkdir -p "$(dirname "$VIASH_PAR_ZIP")"
|
|
fi
|
|
if [ ! -z "$VIASH_PAR_SUMMARY" ] && [ ! -d "$(dirname "$VIASH_PAR_SUMMARY")" ]; then
|
|
mkdir -p "$(dirname "$VIASH_PAR_SUMMARY")"
|
|
fi
|
|
if [ ! -z "$VIASH_PAR_DATA" ] && [ ! -d "$(dirname "$VIASH_PAR_DATA")" ]; then
|
|
mkdir -p "$(dirname "$VIASH_PAR_DATA")"
|
|
fi
|
|
|
|
if [ "$VIASH_ENGINE_ID" == "native" ] ; then
|
|
if [ "$VIASH_MODE" == "run" ]; then
|
|
VIASH_CMD="bash"
|
|
else
|
|
ViashError "Engine '$VIASH_ENGINE_ID' does not support mode '$VIASH_MODE'."
|
|
exit 1
|
|
fi
|
|
fi
|
|
|
|
if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then
|
|
# detect volumes from file arguments
|
|
VIASH_CHOWN_VARS=()
|
|
if [ ! -z "$VIASH_PAR_INPUT" ]; then
|
|
VIASH_TEST_INPUT=()
|
|
IFS=';'
|
|
for var in $VIASH_PAR_INPUT; do
|
|
unset IFS
|
|
VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$var")" )
|
|
var=$(ViashDockerAutodetectMount "$var")
|
|
VIASH_TEST_INPUT+=( "$var" )
|
|
done
|
|
VIASH_PAR_INPUT=$(IFS=';' ; echo "${VIASH_TEST_INPUT[*]}")
|
|
fi
|
|
if [ ! -z "$VIASH_PAR_HTML" ]; then
|
|
VIASH_TEST_HTML=()
|
|
IFS=';'
|
|
for var in $VIASH_PAR_HTML; do
|
|
unset IFS
|
|
VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$var")" )
|
|
var=$(ViashDockerAutodetectMount "$var")
|
|
VIASH_TEST_HTML+=( "$var" )
|
|
VIASH_CHOWN_VARS+=( "$var" )
|
|
done
|
|
VIASH_PAR_HTML=$(IFS=';' ; echo "${VIASH_TEST_HTML[*]}")
|
|
fi
|
|
if [ ! -z "$VIASH_PAR_ZIP" ]; then
|
|
VIASH_TEST_ZIP=()
|
|
IFS=';'
|
|
for var in $VIASH_PAR_ZIP; do
|
|
unset IFS
|
|
VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$var")" )
|
|
var=$(ViashDockerAutodetectMount "$var")
|
|
VIASH_TEST_ZIP+=( "$var" )
|
|
VIASH_CHOWN_VARS+=( "$var" )
|
|
done
|
|
VIASH_PAR_ZIP=$(IFS=';' ; echo "${VIASH_TEST_ZIP[*]}")
|
|
fi
|
|
if [ ! -z "$VIASH_PAR_SUMMARY" ]; then
|
|
VIASH_TEST_SUMMARY=()
|
|
IFS=';'
|
|
for var in $VIASH_PAR_SUMMARY; do
|
|
unset IFS
|
|
VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$var")" )
|
|
var=$(ViashDockerAutodetectMount "$var")
|
|
VIASH_TEST_SUMMARY+=( "$var" )
|
|
VIASH_CHOWN_VARS+=( "$var" )
|
|
done
|
|
VIASH_PAR_SUMMARY=$(IFS=';' ; echo "${VIASH_TEST_SUMMARY[*]}")
|
|
fi
|
|
if [ ! -z "$VIASH_PAR_DATA" ]; then
|
|
VIASH_TEST_DATA=()
|
|
IFS=';'
|
|
for var in $VIASH_PAR_DATA; do
|
|
unset IFS
|
|
VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$var")" )
|
|
var=$(ViashDockerAutodetectMount "$var")
|
|
VIASH_TEST_DATA+=( "$var" )
|
|
VIASH_CHOWN_VARS+=( "$var" )
|
|
done
|
|
VIASH_PAR_DATA=$(IFS=';' ; echo "${VIASH_TEST_DATA[*]}")
|
|
fi
|
|
if [ ! -z "$VIASH_PAR_CONTAMINANTS" ]; then
|
|
VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$VIASH_PAR_CONTAMINANTS")" )
|
|
VIASH_PAR_CONTAMINANTS=$(ViashDockerAutodetectMount "$VIASH_PAR_CONTAMINANTS")
|
|
fi
|
|
if [ ! -z "$VIASH_PAR_ADAPTERS" ]; then
|
|
VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$VIASH_PAR_ADAPTERS")" )
|
|
VIASH_PAR_ADAPTERS=$(ViashDockerAutodetectMount "$VIASH_PAR_ADAPTERS")
|
|
fi
|
|
if [ ! -z "$VIASH_PAR_LIMITS" ]; then
|
|
VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$VIASH_PAR_LIMITS")" )
|
|
VIASH_PAR_LIMITS=$(ViashDockerAutodetectMount "$VIASH_PAR_LIMITS")
|
|
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-fastqc-XXXXXX").sh
|
|
function clean_up {
|
|
rm "\$tempscript"
|
|
}
|
|
function interrupt {
|
|
echo -e "\nCTRL-C Pressed..."
|
|
exit 1
|
|
}
|
|
trap clean_up EXIT
|
|
trap interrupt INT SIGINT
|
|
cat > "\$tempscript" << 'VIASHMAIN'
|
|
#!/bin/bash
|
|
|
|
## VIASH START
|
|
# The following code has been auto-generated by Viash.
|
|
$( if [ ! -z ${VIASH_PAR_INPUT+x} ]; then echo "${VIASH_PAR_INPUT}" | sed "s#'#'\"'\"'#g;s#.*#par_input='&'#" ; else echo "# par_input="; fi )
|
|
$( if [ ! -z ${VIASH_PAR_HTML+x} ]; then echo "${VIASH_PAR_HTML}" | sed "s#'#'\"'\"'#g;s#.*#par_html='&'#" ; else echo "# par_html="; fi )
|
|
$( if [ ! -z ${VIASH_PAR_ZIP+x} ]; then echo "${VIASH_PAR_ZIP}" | sed "s#'#'\"'\"'#g;s#.*#par_zip='&'#" ; else echo "# par_zip="; fi )
|
|
$( if [ ! -z ${VIASH_PAR_SUMMARY+x} ]; then echo "${VIASH_PAR_SUMMARY}" | sed "s#'#'\"'\"'#g;s#.*#par_summary='&'#" ; else echo "# par_summary="; fi )
|
|
$( if [ ! -z ${VIASH_PAR_DATA+x} ]; then echo "${VIASH_PAR_DATA}" | sed "s#'#'\"'\"'#g;s#.*#par_data='&'#" ; else echo "# par_data="; fi )
|
|
$( if [ ! -z ${VIASH_PAR_CASAVA+x} ]; then echo "${VIASH_PAR_CASAVA}" | sed "s#'#'\"'\"'#g;s#.*#par_casava='&'#" ; else echo "# par_casava="; fi )
|
|
$( if [ ! -z ${VIASH_PAR_NANO+x} ]; then echo "${VIASH_PAR_NANO}" | sed "s#'#'\"'\"'#g;s#.*#par_nano='&'#" ; else echo "# par_nano="; fi )
|
|
$( if [ ! -z ${VIASH_PAR_NOFILTER+x} ]; then echo "${VIASH_PAR_NOFILTER}" | sed "s#'#'\"'\"'#g;s#.*#par_nofilter='&'#" ; else echo "# par_nofilter="; fi )
|
|
$( if [ ! -z ${VIASH_PAR_NOGROUP+x} ]; then echo "${VIASH_PAR_NOGROUP}" | sed "s#'#'\"'\"'#g;s#.*#par_nogroup='&'#" ; else echo "# par_nogroup="; fi )
|
|
$( if [ ! -z ${VIASH_PAR_MIN_LENGTH+x} ]; then echo "${VIASH_PAR_MIN_LENGTH}" | sed "s#'#'\"'\"'#g;s#.*#par_min_length='&'#" ; else echo "# par_min_length="; fi )
|
|
$( if [ ! -z ${VIASH_PAR_FORMAT+x} ]; then echo "${VIASH_PAR_FORMAT}" | sed "s#'#'\"'\"'#g;s#.*#par_format='&'#" ; else echo "# par_format="; fi )
|
|
$( if [ ! -z ${VIASH_PAR_CONTAMINANTS+x} ]; then echo "${VIASH_PAR_CONTAMINANTS}" | sed "s#'#'\"'\"'#g;s#.*#par_contaminants='&'#" ; else echo "# par_contaminants="; fi )
|
|
$( if [ ! -z ${VIASH_PAR_ADAPTERS+x} ]; then echo "${VIASH_PAR_ADAPTERS}" | sed "s#'#'\"'\"'#g;s#.*#par_adapters='&'#" ; else echo "# par_adapters="; fi )
|
|
$( if [ ! -z ${VIASH_PAR_LIMITS+x} ]; then echo "${VIASH_PAR_LIMITS}" | sed "s#'#'\"'\"'#g;s#.*#par_limits='&'#" ; else echo "# par_limits="; fi )
|
|
$( if [ ! -z ${VIASH_PAR_KMERS+x} ]; then echo "${VIASH_PAR_KMERS}" | sed "s#'#'\"'\"'#g;s#.*#par_kmers='&'#" ; else echo "# par_kmers="; 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 ${VIASH_META_NAME+x} ]; then echo "${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
|
|
|
|
# exit on error
|
|
set -eo pipefail
|
|
|
|
# Check if both outputs are empty, at least one must be passed.
|
|
if [[ -z "\$par_html" ]] && [[ -z "\$par_zip" ]] && [[ -z "\$par_summary" ]] && [[ -z "\$par_data" ]]; then
|
|
echo "Error: At least one of the output arguments (--html, --zip, --summary, and --data) must be passed."
|
|
exit 1
|
|
fi
|
|
|
|
# unset flags
|
|
unset_if_false=(
|
|
par_casava
|
|
par_nano
|
|
par_nofilter
|
|
par_extract
|
|
par_noextract
|
|
par_nogroup
|
|
par_quiet
|
|
)
|
|
|
|
for par in \${unset_if_false[@]}; do
|
|
test_val="\${!par}"
|
|
[[ "\$test_val" == "false" ]] && unset \$par
|
|
done
|
|
|
|
tmpdir=\$(mktemp -d "\${meta_temp_dir}/\${meta_name}-XXXXXXXX")
|
|
function clean_up {
|
|
rm -rf "\$tmpdir"
|
|
}
|
|
trap clean_up EXIT
|
|
|
|
# Create input array
|
|
IFS=";" read -ra input <<< \$par_input
|
|
|
|
# Run fastqc
|
|
fastqc \\
|
|
--extract \\
|
|
\${par_casava:+--casava} \\
|
|
\${par_nano:+--nano} \\
|
|
\${par_nofilter:+--nofilter} \\
|
|
\${par_nogroup:+--nogroup} \\
|
|
\${par_min_length:+--min_length "\$par_min_length"} \\
|
|
\${par_format:+--format "\$par_format"} \\
|
|
\${par_contaminants:+--contaminants "\$par_contaminants"} \\
|
|
\${par_adapters:+--adapters "\$par_adapters"} \\
|
|
\${par_limits:+--limits "\$par_limits"} \\
|
|
\${par_kmers:+--kmers "\$par_kmers"} \\
|
|
\${par_quiet:+--quiet} \\
|
|
\${meta_cpus:+--threads "\$meta_cpus"} \\
|
|
\${meta_temp_dir:+--dir "\$meta_temp_dir"} \\
|
|
--outdir "\${tmpdir}" \\
|
|
"\${input[@]}"
|
|
|
|
# Move output files
|
|
for file in "\${input[@]}"; do
|
|
# Removes everthing after the first dot of the basename
|
|
sample_name=\$(basename "\${file}" | sed 's/\\..*\$//')
|
|
if [[ -n "\$par_html" ]]; then
|
|
input_html="\${tmpdir}/\${sample_name}_fastqc.html"
|
|
html_file="\${par_html//\\*/\$sample_name}"
|
|
mv "\$input_html" "\$html_file"
|
|
fi
|
|
if [[ -n "\$par_zip" ]]; then
|
|
input_zip="\${tmpdir}/\${sample_name}_fastqc.zip"
|
|
zip_file="\${par_zip//\\*/\$sample_name}"
|
|
mv "\$input_zip" "\$zip_file"
|
|
fi
|
|
if [[ -n "\$par_summary" ]]; then
|
|
summary_file="\${tmpdir}/\${sample_name}_fastqc/summary.txt"
|
|
new_summary="\${par_summary//\\*/\$sample_name}"
|
|
mv "\$summary_file" "\$new_summary"
|
|
fi
|
|
if [[ -n "\$par_data" ]]; then
|
|
data_file="\${tmpdir}/\${sample_name}_fastqc/fastqc_data.txt"
|
|
new_data="\${par_data//\\*/\$sample_name}"
|
|
mv "\$data_file" "\$new_data"
|
|
fi
|
|
# Remove the extracted directory
|
|
rm -r "\${tmpdir}/\${sample_name}_fastqc"
|
|
done
|
|
VIASHMAIN
|
|
bash "\$tempscript" &
|
|
wait "\$!"
|
|
|
|
VIASHEOF
|
|
|
|
|
|
if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then
|
|
# strip viash automount from file paths
|
|
|
|
if [ ! -z "$VIASH_PAR_INPUT" ]; then
|
|
unset VIASH_TEST_INPUT
|
|
IFS=';'
|
|
for var in $VIASH_PAR_INPUT; do
|
|
unset IFS
|
|
if [ -z "$VIASH_TEST_INPUT" ]; then
|
|
VIASH_TEST_INPUT="$(ViashDockerStripAutomount "$var")"
|
|
else
|
|
VIASH_TEST_INPUT="$VIASH_TEST_INPUT;""$(ViashDockerStripAutomount "$var")"
|
|
fi
|
|
done
|
|
VIASH_PAR_INPUT="$VIASH_TEST_INPUT"
|
|
fi
|
|
if [ ! -z "$VIASH_PAR_HTML" ]; then
|
|
VIASH_PAR_HTML=$(ViashDockerStripAutomount "$VIASH_PAR_HTML")
|
|
fi
|
|
if [ ! -z "$VIASH_PAR_ZIP" ]; then
|
|
VIASH_PAR_ZIP=$(ViashDockerStripAutomount "$VIASH_PAR_ZIP")
|
|
fi
|
|
if [ ! -z "$VIASH_PAR_SUMMARY" ]; then
|
|
VIASH_PAR_SUMMARY=$(ViashDockerStripAutomount "$VIASH_PAR_SUMMARY")
|
|
fi
|
|
if [ ! -z "$VIASH_PAR_DATA" ]; then
|
|
VIASH_PAR_DATA=$(ViashDockerStripAutomount "$VIASH_PAR_DATA")
|
|
fi
|
|
if [ ! -z "$VIASH_PAR_CONTAMINANTS" ]; then
|
|
VIASH_PAR_CONTAMINANTS=$(ViashDockerStripAutomount "$VIASH_PAR_CONTAMINANTS")
|
|
fi
|
|
if [ ! -z "$VIASH_PAR_ADAPTERS" ]; then
|
|
VIASH_PAR_ADAPTERS=$(ViashDockerStripAutomount "$VIASH_PAR_ADAPTERS")
|
|
fi
|
|
if [ ! -z "$VIASH_PAR_LIMITS" ]; then
|
|
VIASH_PAR_LIMITS=$(ViashDockerStripAutomount "$VIASH_PAR_LIMITS")
|
|
fi
|
|
if [ ! -z "$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_HTML" ] && ! compgen -G "$VIASH_PAR_HTML" > /dev/null; then
|
|
ViashError "Output file '$VIASH_PAR_HTML' does not exist."
|
|
exit 1
|
|
fi
|
|
if [ ! -z "$VIASH_PAR_ZIP" ] && ! compgen -G "$VIASH_PAR_ZIP" > /dev/null; then
|
|
ViashError "Output file '$VIASH_PAR_ZIP' does not exist."
|
|
exit 1
|
|
fi
|
|
if [ ! -z "$VIASH_PAR_SUMMARY" ] && ! compgen -G "$VIASH_PAR_SUMMARY" > /dev/null; then
|
|
ViashError "Output file '$VIASH_PAR_SUMMARY' does not exist."
|
|
exit 1
|
|
fi
|
|
if [ ! -z "$VIASH_PAR_DATA" ] && ! compgen -G "$VIASH_PAR_DATA" > /dev/null; then
|
|
ViashError "Output file '$VIASH_PAR_DATA' does not exist."
|
|
exit 1
|
|
fi
|
|
|
|
|
|
exit 0
|