CI
69e0b1ebaf
Build pipeline: viash-hub.rnaseq.v0.1-bs99g
Source commit: ed1f6955d0
Source message: Bump version to v0.1.0
1398 lines
65 KiB
Bash
Executable File
1398 lines
65 KiB
Bash
Executable File
#!/usr/bin/env bash
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# post_processing v0.1.0
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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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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 $VIASH_META_RESOURCES_DIR`
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# define meta fields
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VIASH_META_NAME="post_processing"
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VIASH_META_FUNCTIONALITY_NAME="post_processing"
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VIASH_META_EXECUTABLE="$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 "post_processing v0.1.0"
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echo ""
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echo "A viash sub-workflow for the post-processing stage of nf-core/rnaseq pipeline."
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echo ""
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echo "Input:"
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echo " --id"
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echo " type: string, required parameter"
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echo " example: foo"
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echo " ID of the sample."
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echo ""
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echo " --strandedness"
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echo " type: string"
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echo " default: auto"
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echo " Sample strand-specificity. Must be one of unstranded, forward, reverse"
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echo " or auto"
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echo ""
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echo " --paired"
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echo " type: boolean"
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echo " Paired fastq files or not?"
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echo ""
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echo " --fasta"
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echo " type: file, required parameter, file must exist"
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echo " Path to FASTA genome file."
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echo ""
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echo " --fai"
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echo " type: file, required parameter, file must exist"
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echo " Path to FASTA index"
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echo ""
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echo " --gtf"
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echo " type: file, file must exist"
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echo " GTF file"
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echo ""
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echo " --genome_bam"
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echo " type: file, file must exist"
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echo " Genome BAM file"
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echo ""
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echo " --chrom_sizes"
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echo " type: file, file must exist"
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echo " File containing chromosome lengths"
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echo ""
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echo " --star_multiqc"
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echo " type: file, file must exist"
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echo " STAR align log file."
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echo ""
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echo " --extra_picard_args"
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echo " type: string"
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echo " default:"
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echo " Extra arguments to pass to picard MarkDuplicates command in addition to"
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echo " defaults defined by the pipeline."
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echo ""
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echo " --extra_stringtie_args"
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echo " type: string"
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echo " default:"
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echo " Extra arguments to pass to stringtie command in addition to defaults"
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echo " defined by the pipeline."
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echo ""
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echo " --stringtie_ignore_gtf"
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echo " type: boolean"
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echo " Perform reference-guided de novo assembly of transcripts using"
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echo " StringTie, i.e. don't restrict to those in GTF file."
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echo ""
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echo " --extra_bedtools_args"
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echo " type: string"
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echo " default:"
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echo " Extra arguments to pass to bedtools genomecov command in addition to"
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echo " defaults defined by the pipeline."
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echo ""
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echo " --bam_csi_index"
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echo " type: boolean"
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echo " default: false"
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echo " Create a CSI index for BAM files instead of the traditional BAI index."
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echo " This will be required for genomes with larger chromosome sizes."
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echo ""
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echo " --min_mapped_reads"
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echo " type: integer"
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echo " Minimum percentage of uniquely mapped reads below which samples are"
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echo " removed from further processing."
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echo ""
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echo " --with_umi"
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echo " type: boolean"
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echo " default: false"
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echo " Enable UMI-based read deduplication."
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echo ""
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echo " --skip_qc"
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echo " type: boolean"
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echo ""
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echo " --skip_markduplicates"
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echo " type: boolean"
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echo ""
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echo " --skip_stringtie"
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echo " type: boolean"
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echo ""
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echo " --skip_bigwig"
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echo " type: boolean"
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echo ""
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echo "Output:"
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echo " --processed_genome_bam"
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echo " type: file, output, file must exist"
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echo " default: \$id.genome.bam"
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echo ""
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echo " --genome_bam_index"
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echo " type: file, output, file must exist"
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echo " default: \$id.genome.bam.bai"
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echo ""
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echo " --genome_bam_stats"
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echo " type: file, output, file must exist"
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echo " default: \$id.genome.stats"
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echo ""
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echo " --genome_bam_flagstat"
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echo " type: file, output, file must exist"
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echo " default: \$id.genome.flagstat"
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echo ""
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echo " --genome_bam_idxstats"
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echo " type: file, output, file must exist"
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echo " default: \$id.genome.idxstats"
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echo ""
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echo " --markduplicates_metrics"
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echo " type: file, output, file must exist"
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echo " default: \$id.MarkDuplicates.metrics.txt"
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echo ""
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echo " --stringtie_transcript_gtf"
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echo " type: file, output, file must exist"
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echo " default: \$id.stringtie.transcripts.gtf"
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echo ""
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echo " --stringtie_coverage_gtf"
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echo " type: file, output, file must exist"
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echo " default: \$id.stringtie.coverage.gtf"
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echo ""
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echo " --stringtie_abundance"
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echo " type: file, output, file must exist"
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echo " default: \$id.stringtie.gene_abundance.txt"
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echo ""
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echo " --stringtie_ballgown"
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echo " type: file, output, file must exist"
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echo " default: \$id.stringtie.ballgown"
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echo ""
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echo " --bedgraph_forward"
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echo " type: file, output, file must exist"
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echo " default: \$id.forward.bedgraph"
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echo ""
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echo " --bedgraph_reverse"
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echo " type: file, output, file must exist"
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echo " default: \$id.reverse.bedgraph"
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echo ""
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echo " --bigwig_forward"
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echo " type: file, output, file must exist"
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echo " default: \$id.forward.bigwig"
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echo ""
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echo " --bigwig_reverse"
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echo " type: file, output, file must exist"
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echo " default: \$id.reverse.bigwig"
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}
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# initialise variables
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VIASH_MODE='run'
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VIASH_ENGINE_ID='native'
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# initialise array
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VIASH_POSITIONAL_ARGS=''
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while [[ $# -gt 0 ]]; do
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case "$1" in
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-h|--help)
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ViashHelp
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exit
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;;
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---v|---verbose)
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let "VIASH_VERBOSITY=VIASH_VERBOSITY+1"
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shift 1
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;;
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---verbosity)
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VIASH_VERBOSITY="$2"
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shift 2
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;;
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---verbosity=*)
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VIASH_VERBOSITY="$(ViashRemoveFlags "$1")"
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shift 1
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;;
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--version)
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echo "post_processing v0.1.0"
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exit
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;;
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--id)
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[ -n "$VIASH_PAR_ID" ] && ViashError Bad arguments for option \'--id\': \'$VIASH_PAR_ID\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
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VIASH_PAR_ID="$2"
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[ $# -lt 2 ] && ViashError Not enough arguments passed to --id. Use "--help" to get more information on the parameters. && exit 1
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shift 2
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;;
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--id=*)
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[ -n "$VIASH_PAR_ID" ] && ViashError Bad arguments for option \'--id=*\': \'$VIASH_PAR_ID\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
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VIASH_PAR_ID=$(ViashRemoveFlags "$1")
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shift 1
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;;
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--strandedness)
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[ -n "$VIASH_PAR_STRANDEDNESS" ] && ViashError Bad arguments for option \'--strandedness\': \'$VIASH_PAR_STRANDEDNESS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
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VIASH_PAR_STRANDEDNESS="$2"
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[ $# -lt 2 ] && ViashError Not enough arguments passed to --strandedness. Use "--help" to get more information on the parameters. && exit 1
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shift 2
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;;
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--strandedness=*)
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[ -n "$VIASH_PAR_STRANDEDNESS" ] && ViashError Bad arguments for option \'--strandedness=*\': \'$VIASH_PAR_STRANDEDNESS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
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VIASH_PAR_STRANDEDNESS=$(ViashRemoveFlags "$1")
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shift 1
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;;
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--paired)
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[ -n "$VIASH_PAR_PAIRED" ] && ViashError Bad arguments for option \'--paired\': \'$VIASH_PAR_PAIRED\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
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VIASH_PAR_PAIRED="$2"
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[ $# -lt 2 ] && ViashError Not enough arguments passed to --paired. Use "--help" to get more information on the parameters. && exit 1
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shift 2
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;;
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--paired=*)
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[ -n "$VIASH_PAR_PAIRED" ] && ViashError Bad arguments for option \'--paired=*\': \'$VIASH_PAR_PAIRED\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
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VIASH_PAR_PAIRED=$(ViashRemoveFlags "$1")
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shift 1
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;;
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--fasta)
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[ -n "$VIASH_PAR_FASTA" ] && ViashError Bad arguments for option \'--fasta\': \'$VIASH_PAR_FASTA\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
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VIASH_PAR_FASTA="$2"
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[ $# -lt 2 ] && ViashError Not enough arguments passed to --fasta. Use "--help" to get more information on the parameters. && exit 1
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shift 2
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;;
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--fasta=*)
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[ -n "$VIASH_PAR_FASTA" ] && ViashError Bad arguments for option \'--fasta=*\': \'$VIASH_PAR_FASTA\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
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VIASH_PAR_FASTA=$(ViashRemoveFlags "$1")
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shift 1
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;;
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--fai)
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[ -n "$VIASH_PAR_FAI" ] && ViashError Bad arguments for option \'--fai\': \'$VIASH_PAR_FAI\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
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VIASH_PAR_FAI="$2"
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[ $# -lt 2 ] && ViashError Not enough arguments passed to --fai. Use "--help" to get more information on the parameters. && exit 1
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shift 2
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;;
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--fai=*)
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[ -n "$VIASH_PAR_FAI" ] && ViashError Bad arguments for option \'--fai=*\': \'$VIASH_PAR_FAI\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
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VIASH_PAR_FAI=$(ViashRemoveFlags "$1")
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shift 1
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;;
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--gtf)
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[ -n "$VIASH_PAR_GTF" ] && ViashError Bad arguments for option \'--gtf\': \'$VIASH_PAR_GTF\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
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VIASH_PAR_GTF="$2"
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[ $# -lt 2 ] && ViashError Not enough arguments passed to --gtf. Use "--help" to get more information on the parameters. && exit 1
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shift 2
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;;
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--gtf=*)
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[ -n "$VIASH_PAR_GTF" ] && ViashError Bad arguments for option \'--gtf=*\': \'$VIASH_PAR_GTF\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
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VIASH_PAR_GTF=$(ViashRemoveFlags "$1")
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shift 1
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;;
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--genome_bam)
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[ -n "$VIASH_PAR_GENOME_BAM" ] && ViashError Bad arguments for option \'--genome_bam\': \'$VIASH_PAR_GENOME_BAM\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
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VIASH_PAR_GENOME_BAM="$2"
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[ $# -lt 2 ] && ViashError Not enough arguments passed to --genome_bam. Use "--help" to get more information on the parameters. && exit 1
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shift 2
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;;
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--genome_bam=*)
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[ -n "$VIASH_PAR_GENOME_BAM" ] && ViashError Bad arguments for option \'--genome_bam=*\': \'$VIASH_PAR_GENOME_BAM\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
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VIASH_PAR_GENOME_BAM=$(ViashRemoveFlags "$1")
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shift 1
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;;
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--chrom_sizes)
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[ -n "$VIASH_PAR_CHROM_SIZES" ] && ViashError Bad arguments for option \'--chrom_sizes\': \'$VIASH_PAR_CHROM_SIZES\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
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VIASH_PAR_CHROM_SIZES="$2"
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[ $# -lt 2 ] && ViashError Not enough arguments passed to --chrom_sizes. Use "--help" to get more information on the parameters. && exit 1
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shift 2
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;;
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--chrom_sizes=*)
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[ -n "$VIASH_PAR_CHROM_SIZES" ] && ViashError Bad arguments for option \'--chrom_sizes=*\': \'$VIASH_PAR_CHROM_SIZES\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
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VIASH_PAR_CHROM_SIZES=$(ViashRemoveFlags "$1")
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shift 1
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;;
|
|
--star_multiqc)
|
|
[ -n "$VIASH_PAR_STAR_MULTIQC" ] && ViashError Bad arguments for option \'--star_multiqc\': \'$VIASH_PAR_STAR_MULTIQC\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_STAR_MULTIQC="$2"
|
|
[ $# -lt 2 ] && ViashError Not enough arguments passed to --star_multiqc. Use "--help" to get more information on the parameters. && exit 1
|
|
shift 2
|
|
;;
|
|
--star_multiqc=*)
|
|
[ -n "$VIASH_PAR_STAR_MULTIQC" ] && ViashError Bad arguments for option \'--star_multiqc=*\': \'$VIASH_PAR_STAR_MULTIQC\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_STAR_MULTIQC=$(ViashRemoveFlags "$1")
|
|
shift 1
|
|
;;
|
|
--extra_picard_args)
|
|
[ -n "$VIASH_PAR_EXTRA_PICARD_ARGS" ] && ViashError Bad arguments for option \'--extra_picard_args\': \'$VIASH_PAR_EXTRA_PICARD_ARGS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_EXTRA_PICARD_ARGS="$2"
|
|
[ $# -lt 2 ] && ViashError Not enough arguments passed to --extra_picard_args. Use "--help" to get more information on the parameters. && exit 1
|
|
shift 2
|
|
;;
|
|
--extra_picard_args=*)
|
|
[ -n "$VIASH_PAR_EXTRA_PICARD_ARGS" ] && ViashError Bad arguments for option \'--extra_picard_args=*\': \'$VIASH_PAR_EXTRA_PICARD_ARGS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_EXTRA_PICARD_ARGS=$(ViashRemoveFlags "$1")
|
|
shift 1
|
|
;;
|
|
--extra_stringtie_args)
|
|
[ -n "$VIASH_PAR_EXTRA_STRINGTIE_ARGS" ] && ViashError Bad arguments for option \'--extra_stringtie_args\': \'$VIASH_PAR_EXTRA_STRINGTIE_ARGS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_EXTRA_STRINGTIE_ARGS="$2"
|
|
[ $# -lt 2 ] && ViashError Not enough arguments passed to --extra_stringtie_args. Use "--help" to get more information on the parameters. && exit 1
|
|
shift 2
|
|
;;
|
|
--extra_stringtie_args=*)
|
|
[ -n "$VIASH_PAR_EXTRA_STRINGTIE_ARGS" ] && ViashError Bad arguments for option \'--extra_stringtie_args=*\': \'$VIASH_PAR_EXTRA_STRINGTIE_ARGS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_EXTRA_STRINGTIE_ARGS=$(ViashRemoveFlags "$1")
|
|
shift 1
|
|
;;
|
|
--stringtie_ignore_gtf)
|
|
[ -n "$VIASH_PAR_STRINGTIE_IGNORE_GTF" ] && ViashError Bad arguments for option \'--stringtie_ignore_gtf\': \'$VIASH_PAR_STRINGTIE_IGNORE_GTF\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_STRINGTIE_IGNORE_GTF="$2"
|
|
[ $# -lt 2 ] && ViashError Not enough arguments passed to --stringtie_ignore_gtf. Use "--help" to get more information on the parameters. && exit 1
|
|
shift 2
|
|
;;
|
|
--stringtie_ignore_gtf=*)
|
|
[ -n "$VIASH_PAR_STRINGTIE_IGNORE_GTF" ] && ViashError Bad arguments for option \'--stringtie_ignore_gtf=*\': \'$VIASH_PAR_STRINGTIE_IGNORE_GTF\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_STRINGTIE_IGNORE_GTF=$(ViashRemoveFlags "$1")
|
|
shift 1
|
|
;;
|
|
--extra_bedtools_args)
|
|
[ -n "$VIASH_PAR_EXTRA_BEDTOOLS_ARGS" ] && ViashError Bad arguments for option \'--extra_bedtools_args\': \'$VIASH_PAR_EXTRA_BEDTOOLS_ARGS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_EXTRA_BEDTOOLS_ARGS="$2"
|
|
[ $# -lt 2 ] && ViashError Not enough arguments passed to --extra_bedtools_args. Use "--help" to get more information on the parameters. && exit 1
|
|
shift 2
|
|
;;
|
|
--extra_bedtools_args=*)
|
|
[ -n "$VIASH_PAR_EXTRA_BEDTOOLS_ARGS" ] && ViashError Bad arguments for option \'--extra_bedtools_args=*\': \'$VIASH_PAR_EXTRA_BEDTOOLS_ARGS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_EXTRA_BEDTOOLS_ARGS=$(ViashRemoveFlags "$1")
|
|
shift 1
|
|
;;
|
|
--bam_csi_index)
|
|
[ -n "$VIASH_PAR_BAM_CSI_INDEX" ] && ViashError Bad arguments for option \'--bam_csi_index\': \'$VIASH_PAR_BAM_CSI_INDEX\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_BAM_CSI_INDEX="$2"
|
|
[ $# -lt 2 ] && ViashError Not enough arguments passed to --bam_csi_index. Use "--help" to get more information on the parameters. && exit 1
|
|
shift 2
|
|
;;
|
|
--bam_csi_index=*)
|
|
[ -n "$VIASH_PAR_BAM_CSI_INDEX" ] && ViashError Bad arguments for option \'--bam_csi_index=*\': \'$VIASH_PAR_BAM_CSI_INDEX\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_BAM_CSI_INDEX=$(ViashRemoveFlags "$1")
|
|
shift 1
|
|
;;
|
|
--min_mapped_reads)
|
|
[ -n "$VIASH_PAR_MIN_MAPPED_READS" ] && ViashError Bad arguments for option \'--min_mapped_reads\': \'$VIASH_PAR_MIN_MAPPED_READS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_MIN_MAPPED_READS="$2"
|
|
[ $# -lt 2 ] && ViashError Not enough arguments passed to --min_mapped_reads. Use "--help" to get more information on the parameters. && exit 1
|
|
shift 2
|
|
;;
|
|
--min_mapped_reads=*)
|
|
[ -n "$VIASH_PAR_MIN_MAPPED_READS" ] && ViashError Bad arguments for option \'--min_mapped_reads=*\': \'$VIASH_PAR_MIN_MAPPED_READS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_MIN_MAPPED_READS=$(ViashRemoveFlags "$1")
|
|
shift 1
|
|
;;
|
|
--with_umi)
|
|
[ -n "$VIASH_PAR_WITH_UMI" ] && ViashError Bad arguments for option \'--with_umi\': \'$VIASH_PAR_WITH_UMI\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_WITH_UMI="$2"
|
|
[ $# -lt 2 ] && ViashError Not enough arguments passed to --with_umi. Use "--help" to get more information on the parameters. && exit 1
|
|
shift 2
|
|
;;
|
|
--with_umi=*)
|
|
[ -n "$VIASH_PAR_WITH_UMI" ] && ViashError Bad arguments for option \'--with_umi=*\': \'$VIASH_PAR_WITH_UMI\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_WITH_UMI=$(ViashRemoveFlags "$1")
|
|
shift 1
|
|
;;
|
|
--skip_qc)
|
|
[ -n "$VIASH_PAR_SKIP_QC" ] && ViashError Bad arguments for option \'--skip_qc\': \'$VIASH_PAR_SKIP_QC\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_SKIP_QC="$2"
|
|
[ $# -lt 2 ] && ViashError Not enough arguments passed to --skip_qc. Use "--help" to get more information on the parameters. && exit 1
|
|
shift 2
|
|
;;
|
|
--skip_qc=*)
|
|
[ -n "$VIASH_PAR_SKIP_QC" ] && ViashError Bad arguments for option \'--skip_qc=*\': \'$VIASH_PAR_SKIP_QC\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_SKIP_QC=$(ViashRemoveFlags "$1")
|
|
shift 1
|
|
;;
|
|
--skip_markduplicates)
|
|
[ -n "$VIASH_PAR_SKIP_MARKDUPLICATES" ] && ViashError Bad arguments for option \'--skip_markduplicates\': \'$VIASH_PAR_SKIP_MARKDUPLICATES\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_SKIP_MARKDUPLICATES="$2"
|
|
[ $# -lt 2 ] && ViashError Not enough arguments passed to --skip_markduplicates. Use "--help" to get more information on the parameters. && exit 1
|
|
shift 2
|
|
;;
|
|
--skip_markduplicates=*)
|
|
[ -n "$VIASH_PAR_SKIP_MARKDUPLICATES" ] && ViashError Bad arguments for option \'--skip_markduplicates=*\': \'$VIASH_PAR_SKIP_MARKDUPLICATES\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_SKIP_MARKDUPLICATES=$(ViashRemoveFlags "$1")
|
|
shift 1
|
|
;;
|
|
--skip_stringtie)
|
|
[ -n "$VIASH_PAR_SKIP_STRINGTIE" ] && ViashError Bad arguments for option \'--skip_stringtie\': \'$VIASH_PAR_SKIP_STRINGTIE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_SKIP_STRINGTIE="$2"
|
|
[ $# -lt 2 ] && ViashError Not enough arguments passed to --skip_stringtie. Use "--help" to get more information on the parameters. && exit 1
|
|
shift 2
|
|
;;
|
|
--skip_stringtie=*)
|
|
[ -n "$VIASH_PAR_SKIP_STRINGTIE" ] && ViashError Bad arguments for option \'--skip_stringtie=*\': \'$VIASH_PAR_SKIP_STRINGTIE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_SKIP_STRINGTIE=$(ViashRemoveFlags "$1")
|
|
shift 1
|
|
;;
|
|
--skip_bigwig)
|
|
[ -n "$VIASH_PAR_SKIP_BIGWIG" ] && ViashError Bad arguments for option \'--skip_bigwig\': \'$VIASH_PAR_SKIP_BIGWIG\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_SKIP_BIGWIG="$2"
|
|
[ $# -lt 2 ] && ViashError Not enough arguments passed to --skip_bigwig. Use "--help" to get more information on the parameters. && exit 1
|
|
shift 2
|
|
;;
|
|
--skip_bigwig=*)
|
|
[ -n "$VIASH_PAR_SKIP_BIGWIG" ] && ViashError Bad arguments for option \'--skip_bigwig=*\': \'$VIASH_PAR_SKIP_BIGWIG\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_SKIP_BIGWIG=$(ViashRemoveFlags "$1")
|
|
shift 1
|
|
;;
|
|
--processed_genome_bam)
|
|
[ -n "$VIASH_PAR_PROCESSED_GENOME_BAM" ] && ViashError Bad arguments for option \'--processed_genome_bam\': \'$VIASH_PAR_PROCESSED_GENOME_BAM\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_PROCESSED_GENOME_BAM="$2"
|
|
[ $# -lt 2 ] && ViashError Not enough arguments passed to --processed_genome_bam. Use "--help" to get more information on the parameters. && exit 1
|
|
shift 2
|
|
;;
|
|
--processed_genome_bam=*)
|
|
[ -n "$VIASH_PAR_PROCESSED_GENOME_BAM" ] && ViashError Bad arguments for option \'--processed_genome_bam=*\': \'$VIASH_PAR_PROCESSED_GENOME_BAM\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_PROCESSED_GENOME_BAM=$(ViashRemoveFlags "$1")
|
|
shift 1
|
|
;;
|
|
--genome_bam_index)
|
|
[ -n "$VIASH_PAR_GENOME_BAM_INDEX" ] && ViashError Bad arguments for option \'--genome_bam_index\': \'$VIASH_PAR_GENOME_BAM_INDEX\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_GENOME_BAM_INDEX="$2"
|
|
[ $# -lt 2 ] && ViashError Not enough arguments passed to --genome_bam_index. Use "--help" to get more information on the parameters. && exit 1
|
|
shift 2
|
|
;;
|
|
--genome_bam_index=*)
|
|
[ -n "$VIASH_PAR_GENOME_BAM_INDEX" ] && ViashError Bad arguments for option \'--genome_bam_index=*\': \'$VIASH_PAR_GENOME_BAM_INDEX\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_GENOME_BAM_INDEX=$(ViashRemoveFlags "$1")
|
|
shift 1
|
|
;;
|
|
--genome_bam_stats)
|
|
[ -n "$VIASH_PAR_GENOME_BAM_STATS" ] && ViashError Bad arguments for option \'--genome_bam_stats\': \'$VIASH_PAR_GENOME_BAM_STATS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_GENOME_BAM_STATS="$2"
|
|
[ $# -lt 2 ] && ViashError Not enough arguments passed to --genome_bam_stats. Use "--help" to get more information on the parameters. && exit 1
|
|
shift 2
|
|
;;
|
|
--genome_bam_stats=*)
|
|
[ -n "$VIASH_PAR_GENOME_BAM_STATS" ] && ViashError Bad arguments for option \'--genome_bam_stats=*\': \'$VIASH_PAR_GENOME_BAM_STATS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_GENOME_BAM_STATS=$(ViashRemoveFlags "$1")
|
|
shift 1
|
|
;;
|
|
--genome_bam_flagstat)
|
|
[ -n "$VIASH_PAR_GENOME_BAM_FLAGSTAT" ] && ViashError Bad arguments for option \'--genome_bam_flagstat\': \'$VIASH_PAR_GENOME_BAM_FLAGSTAT\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_GENOME_BAM_FLAGSTAT="$2"
|
|
[ $# -lt 2 ] && ViashError Not enough arguments passed to --genome_bam_flagstat. Use "--help" to get more information on the parameters. && exit 1
|
|
shift 2
|
|
;;
|
|
--genome_bam_flagstat=*)
|
|
[ -n "$VIASH_PAR_GENOME_BAM_FLAGSTAT" ] && ViashError Bad arguments for option \'--genome_bam_flagstat=*\': \'$VIASH_PAR_GENOME_BAM_FLAGSTAT\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_GENOME_BAM_FLAGSTAT=$(ViashRemoveFlags "$1")
|
|
shift 1
|
|
;;
|
|
--genome_bam_idxstats)
|
|
[ -n "$VIASH_PAR_GENOME_BAM_IDXSTATS" ] && ViashError Bad arguments for option \'--genome_bam_idxstats\': \'$VIASH_PAR_GENOME_BAM_IDXSTATS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_GENOME_BAM_IDXSTATS="$2"
|
|
[ $# -lt 2 ] && ViashError Not enough arguments passed to --genome_bam_idxstats. Use "--help" to get more information on the parameters. && exit 1
|
|
shift 2
|
|
;;
|
|
--genome_bam_idxstats=*)
|
|
[ -n "$VIASH_PAR_GENOME_BAM_IDXSTATS" ] && ViashError Bad arguments for option \'--genome_bam_idxstats=*\': \'$VIASH_PAR_GENOME_BAM_IDXSTATS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_GENOME_BAM_IDXSTATS=$(ViashRemoveFlags "$1")
|
|
shift 1
|
|
;;
|
|
--markduplicates_metrics)
|
|
[ -n "$VIASH_PAR_MARKDUPLICATES_METRICS" ] && ViashError Bad arguments for option \'--markduplicates_metrics\': \'$VIASH_PAR_MARKDUPLICATES_METRICS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_MARKDUPLICATES_METRICS="$2"
|
|
[ $# -lt 2 ] && ViashError Not enough arguments passed to --markduplicates_metrics. Use "--help" to get more information on the parameters. && exit 1
|
|
shift 2
|
|
;;
|
|
--markduplicates_metrics=*)
|
|
[ -n "$VIASH_PAR_MARKDUPLICATES_METRICS" ] && ViashError Bad arguments for option \'--markduplicates_metrics=*\': \'$VIASH_PAR_MARKDUPLICATES_METRICS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_MARKDUPLICATES_METRICS=$(ViashRemoveFlags "$1")
|
|
shift 1
|
|
;;
|
|
--stringtie_transcript_gtf)
|
|
[ -n "$VIASH_PAR_STRINGTIE_TRANSCRIPT_GTF" ] && ViashError Bad arguments for option \'--stringtie_transcript_gtf\': \'$VIASH_PAR_STRINGTIE_TRANSCRIPT_GTF\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_STRINGTIE_TRANSCRIPT_GTF="$2"
|
|
[ $# -lt 2 ] && ViashError Not enough arguments passed to --stringtie_transcript_gtf. Use "--help" to get more information on the parameters. && exit 1
|
|
shift 2
|
|
;;
|
|
--stringtie_transcript_gtf=*)
|
|
[ -n "$VIASH_PAR_STRINGTIE_TRANSCRIPT_GTF" ] && ViashError Bad arguments for option \'--stringtie_transcript_gtf=*\': \'$VIASH_PAR_STRINGTIE_TRANSCRIPT_GTF\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_STRINGTIE_TRANSCRIPT_GTF=$(ViashRemoveFlags "$1")
|
|
shift 1
|
|
;;
|
|
--stringtie_coverage_gtf)
|
|
[ -n "$VIASH_PAR_STRINGTIE_COVERAGE_GTF" ] && ViashError Bad arguments for option \'--stringtie_coverage_gtf\': \'$VIASH_PAR_STRINGTIE_COVERAGE_GTF\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_STRINGTIE_COVERAGE_GTF="$2"
|
|
[ $# -lt 2 ] && ViashError Not enough arguments passed to --stringtie_coverage_gtf. Use "--help" to get more information on the parameters. && exit 1
|
|
shift 2
|
|
;;
|
|
--stringtie_coverage_gtf=*)
|
|
[ -n "$VIASH_PAR_STRINGTIE_COVERAGE_GTF" ] && ViashError Bad arguments for option \'--stringtie_coverage_gtf=*\': \'$VIASH_PAR_STRINGTIE_COVERAGE_GTF\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_STRINGTIE_COVERAGE_GTF=$(ViashRemoveFlags "$1")
|
|
shift 1
|
|
;;
|
|
--stringtie_abundance)
|
|
[ -n "$VIASH_PAR_STRINGTIE_ABUNDANCE" ] && ViashError Bad arguments for option \'--stringtie_abundance\': \'$VIASH_PAR_STRINGTIE_ABUNDANCE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_STRINGTIE_ABUNDANCE="$2"
|
|
[ $# -lt 2 ] && ViashError Not enough arguments passed to --stringtie_abundance. Use "--help" to get more information on the parameters. && exit 1
|
|
shift 2
|
|
;;
|
|
--stringtie_abundance=*)
|
|
[ -n "$VIASH_PAR_STRINGTIE_ABUNDANCE" ] && ViashError Bad arguments for option \'--stringtie_abundance=*\': \'$VIASH_PAR_STRINGTIE_ABUNDANCE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_STRINGTIE_ABUNDANCE=$(ViashRemoveFlags "$1")
|
|
shift 1
|
|
;;
|
|
--stringtie_ballgown)
|
|
[ -n "$VIASH_PAR_STRINGTIE_BALLGOWN" ] && ViashError Bad arguments for option \'--stringtie_ballgown\': \'$VIASH_PAR_STRINGTIE_BALLGOWN\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_STRINGTIE_BALLGOWN="$2"
|
|
[ $# -lt 2 ] && ViashError Not enough arguments passed to --stringtie_ballgown. Use "--help" to get more information on the parameters. && exit 1
|
|
shift 2
|
|
;;
|
|
--stringtie_ballgown=*)
|
|
[ -n "$VIASH_PAR_STRINGTIE_BALLGOWN" ] && ViashError Bad arguments for option \'--stringtie_ballgown=*\': \'$VIASH_PAR_STRINGTIE_BALLGOWN\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_STRINGTIE_BALLGOWN=$(ViashRemoveFlags "$1")
|
|
shift 1
|
|
;;
|
|
--bedgraph_forward)
|
|
[ -n "$VIASH_PAR_BEDGRAPH_FORWARD" ] && ViashError Bad arguments for option \'--bedgraph_forward\': \'$VIASH_PAR_BEDGRAPH_FORWARD\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_BEDGRAPH_FORWARD="$2"
|
|
[ $# -lt 2 ] && ViashError Not enough arguments passed to --bedgraph_forward. Use "--help" to get more information on the parameters. && exit 1
|
|
shift 2
|
|
;;
|
|
--bedgraph_forward=*)
|
|
[ -n "$VIASH_PAR_BEDGRAPH_FORWARD" ] && ViashError Bad arguments for option \'--bedgraph_forward=*\': \'$VIASH_PAR_BEDGRAPH_FORWARD\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_BEDGRAPH_FORWARD=$(ViashRemoveFlags "$1")
|
|
shift 1
|
|
;;
|
|
--bedgraph_reverse)
|
|
[ -n "$VIASH_PAR_BEDGRAPH_REVERSE" ] && ViashError Bad arguments for option \'--bedgraph_reverse\': \'$VIASH_PAR_BEDGRAPH_REVERSE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_BEDGRAPH_REVERSE="$2"
|
|
[ $# -lt 2 ] && ViashError Not enough arguments passed to --bedgraph_reverse. Use "--help" to get more information on the parameters. && exit 1
|
|
shift 2
|
|
;;
|
|
--bedgraph_reverse=*)
|
|
[ -n "$VIASH_PAR_BEDGRAPH_REVERSE" ] && ViashError Bad arguments for option \'--bedgraph_reverse=*\': \'$VIASH_PAR_BEDGRAPH_REVERSE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_BEDGRAPH_REVERSE=$(ViashRemoveFlags "$1")
|
|
shift 1
|
|
;;
|
|
--bigwig_forward)
|
|
[ -n "$VIASH_PAR_BIGWIG_FORWARD" ] && ViashError Bad arguments for option \'--bigwig_forward\': \'$VIASH_PAR_BIGWIG_FORWARD\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_BIGWIG_FORWARD="$2"
|
|
[ $# -lt 2 ] && ViashError Not enough arguments passed to --bigwig_forward. Use "--help" to get more information on the parameters. && exit 1
|
|
shift 2
|
|
;;
|
|
--bigwig_forward=*)
|
|
[ -n "$VIASH_PAR_BIGWIG_FORWARD" ] && ViashError Bad arguments for option \'--bigwig_forward=*\': \'$VIASH_PAR_BIGWIG_FORWARD\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_BIGWIG_FORWARD=$(ViashRemoveFlags "$1")
|
|
shift 1
|
|
;;
|
|
--bigwig_reverse)
|
|
[ -n "$VIASH_PAR_BIGWIG_REVERSE" ] && ViashError Bad arguments for option \'--bigwig_reverse\': \'$VIASH_PAR_BIGWIG_REVERSE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_BIGWIG_REVERSE="$2"
|
|
[ $# -lt 2 ] && ViashError Not enough arguments passed to --bigwig_reverse. Use "--help" to get more information on the parameters. && exit 1
|
|
shift 2
|
|
;;
|
|
--bigwig_reverse=*)
|
|
[ -n "$VIASH_PAR_BIGWIG_REVERSE" ] && ViashError Bad arguments for option \'--bigwig_reverse=*\': \'$VIASH_PAR_BIGWIG_REVERSE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_BIGWIG_REVERSE=$(ViashRemoveFlags "$1")
|
|
shift 1
|
|
;;
|
|
---engine)
|
|
VIASH_ENGINE_ID="$2"
|
|
shift 2
|
|
;;
|
|
---engine=*)
|
|
VIASH_ENGINE_ID="$(ViashRemoveFlags "$1")"
|
|
shift 1
|
|
;;
|
|
---cpus)
|
|
[ -n "$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'
|
|
else
|
|
ViashError "Engine '$VIASH_ENGINE_ID' is not recognized. Options are: native."
|
|
exit 1
|
|
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_ID+x} ]; then
|
|
ViashError '--id' is a required argument. Use "--help" to get more information on the parameters.
|
|
exit 1
|
|
fi
|
|
if [ -z ${VIASH_PAR_FASTA+x} ]; then
|
|
ViashError '--fasta' is a required argument. Use "--help" to get more information on the parameters.
|
|
exit 1
|
|
fi
|
|
if [ -z ${VIASH_PAR_FAI+x} ]; then
|
|
ViashError '--fai' 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_STRANDEDNESS+x} ]; then
|
|
VIASH_PAR_STRANDEDNESS="auto"
|
|
fi
|
|
if [ -z ${VIASH_PAR_EXTRA_PICARD_ARGS+x} ]; then
|
|
VIASH_PAR_EXTRA_PICARD_ARGS=""
|
|
fi
|
|
if [ -z ${VIASH_PAR_EXTRA_STRINGTIE_ARGS+x} ]; then
|
|
VIASH_PAR_EXTRA_STRINGTIE_ARGS=""
|
|
fi
|
|
if [ -z ${VIASH_PAR_EXTRA_BEDTOOLS_ARGS+x} ]; then
|
|
VIASH_PAR_EXTRA_BEDTOOLS_ARGS=""
|
|
fi
|
|
if [ -z ${VIASH_PAR_BAM_CSI_INDEX+x} ]; then
|
|
VIASH_PAR_BAM_CSI_INDEX="false"
|
|
fi
|
|
if [ -z ${VIASH_PAR_WITH_UMI+x} ]; then
|
|
VIASH_PAR_WITH_UMI="false"
|
|
fi
|
|
if [ -z ${VIASH_PAR_PROCESSED_GENOME_BAM+x} ]; then
|
|
VIASH_PAR_PROCESSED_GENOME_BAM="\$id.genome.bam"
|
|
fi
|
|
if [ -z ${VIASH_PAR_GENOME_BAM_INDEX+x} ]; then
|
|
VIASH_PAR_GENOME_BAM_INDEX="\$id.genome.bam.bai"
|
|
fi
|
|
if [ -z ${VIASH_PAR_GENOME_BAM_STATS+x} ]; then
|
|
VIASH_PAR_GENOME_BAM_STATS="\$id.genome.stats"
|
|
fi
|
|
if [ -z ${VIASH_PAR_GENOME_BAM_FLAGSTAT+x} ]; then
|
|
VIASH_PAR_GENOME_BAM_FLAGSTAT="\$id.genome.flagstat"
|
|
fi
|
|
if [ -z ${VIASH_PAR_GENOME_BAM_IDXSTATS+x} ]; then
|
|
VIASH_PAR_GENOME_BAM_IDXSTATS="\$id.genome.idxstats"
|
|
fi
|
|
if [ -z ${VIASH_PAR_MARKDUPLICATES_METRICS+x} ]; then
|
|
VIASH_PAR_MARKDUPLICATES_METRICS="\$id.MarkDuplicates.metrics.txt"
|
|
fi
|
|
if [ -z ${VIASH_PAR_STRINGTIE_TRANSCRIPT_GTF+x} ]; then
|
|
VIASH_PAR_STRINGTIE_TRANSCRIPT_GTF="\$id.stringtie.transcripts.gtf"
|
|
fi
|
|
if [ -z ${VIASH_PAR_STRINGTIE_COVERAGE_GTF+x} ]; then
|
|
VIASH_PAR_STRINGTIE_COVERAGE_GTF="\$id.stringtie.coverage.gtf"
|
|
fi
|
|
if [ -z ${VIASH_PAR_STRINGTIE_ABUNDANCE+x} ]; then
|
|
VIASH_PAR_STRINGTIE_ABUNDANCE="\$id.stringtie.gene_abundance.txt"
|
|
fi
|
|
if [ -z ${VIASH_PAR_STRINGTIE_BALLGOWN+x} ]; then
|
|
VIASH_PAR_STRINGTIE_BALLGOWN="\$id.stringtie.ballgown"
|
|
fi
|
|
if [ -z ${VIASH_PAR_BEDGRAPH_FORWARD+x} ]; then
|
|
VIASH_PAR_BEDGRAPH_FORWARD="\$id.forward.bedgraph"
|
|
fi
|
|
if [ -z ${VIASH_PAR_BEDGRAPH_REVERSE+x} ]; then
|
|
VIASH_PAR_BEDGRAPH_REVERSE="\$id.reverse.bedgraph"
|
|
fi
|
|
if [ -z ${VIASH_PAR_BIGWIG_FORWARD+x} ]; then
|
|
VIASH_PAR_BIGWIG_FORWARD="\$id.forward.bigwig"
|
|
fi
|
|
if [ -z ${VIASH_PAR_BIGWIG_REVERSE+x} ]; then
|
|
VIASH_PAR_BIGWIG_REVERSE="\$id.reverse.bigwig"
|
|
fi
|
|
|
|
# check whether required files exist
|
|
if [ ! -z "$VIASH_PAR_FASTA" ] && [ ! -e "$VIASH_PAR_FASTA" ]; then
|
|
ViashError "Input file '$VIASH_PAR_FASTA' does not exist."
|
|
exit 1
|
|
fi
|
|
if [ ! -z "$VIASH_PAR_FAI" ] && [ ! -e "$VIASH_PAR_FAI" ]; then
|
|
ViashError "Input file '$VIASH_PAR_FAI' does not exist."
|
|
exit 1
|
|
fi
|
|
if [ ! -z "$VIASH_PAR_GTF" ] && [ ! -e "$VIASH_PAR_GTF" ]; then
|
|
ViashError "Input file '$VIASH_PAR_GTF' does not exist."
|
|
exit 1
|
|
fi
|
|
if [ ! -z "$VIASH_PAR_GENOME_BAM" ] && [ ! -e "$VIASH_PAR_GENOME_BAM" ]; then
|
|
ViashError "Input file '$VIASH_PAR_GENOME_BAM' does not exist."
|
|
exit 1
|
|
fi
|
|
if [ ! -z "$VIASH_PAR_CHROM_SIZES" ] && [ ! -e "$VIASH_PAR_CHROM_SIZES" ]; then
|
|
ViashError "Input file '$VIASH_PAR_CHROM_SIZES' does not exist."
|
|
exit 1
|
|
fi
|
|
if [ ! -z "$VIASH_PAR_STAR_MULTIQC" ] && [ ! -e "$VIASH_PAR_STAR_MULTIQC" ]; then
|
|
ViashError "Input file '$VIASH_PAR_STAR_MULTIQC' does not exist."
|
|
exit 1
|
|
fi
|
|
|
|
# check whether parameters values are of the right type
|
|
if [[ -n "$VIASH_PAR_PAIRED" ]]; then
|
|
if ! [[ "$VIASH_PAR_PAIRED" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then
|
|
ViashError '--paired' has to be a boolean. Use "--help" to get more information on the parameters.
|
|
exit 1
|
|
fi
|
|
fi
|
|
if [[ -n "$VIASH_PAR_STRINGTIE_IGNORE_GTF" ]]; then
|
|
if ! [[ "$VIASH_PAR_STRINGTIE_IGNORE_GTF" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then
|
|
ViashError '--stringtie_ignore_gtf' has to be a boolean. Use "--help" to get more information on the parameters.
|
|
exit 1
|
|
fi
|
|
fi
|
|
if [[ -n "$VIASH_PAR_BAM_CSI_INDEX" ]]; then
|
|
if ! [[ "$VIASH_PAR_BAM_CSI_INDEX" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then
|
|
ViashError '--bam_csi_index' has to be a boolean. Use "--help" to get more information on the parameters.
|
|
exit 1
|
|
fi
|
|
fi
|
|
if [[ -n "$VIASH_PAR_MIN_MAPPED_READS" ]]; then
|
|
if ! [[ "$VIASH_PAR_MIN_MAPPED_READS" =~ ^[-+]?[0-9]+$ ]]; then
|
|
ViashError '--min_mapped_reads' has to be an integer. Use "--help" to get more information on the parameters.
|
|
exit 1
|
|
fi
|
|
fi
|
|
if [[ -n "$VIASH_PAR_WITH_UMI" ]]; then
|
|
if ! [[ "$VIASH_PAR_WITH_UMI" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then
|
|
ViashError '--with_umi' has to be a boolean. Use "--help" to get more information on the parameters.
|
|
exit 1
|
|
fi
|
|
fi
|
|
if [[ -n "$VIASH_PAR_SKIP_QC" ]]; then
|
|
if ! [[ "$VIASH_PAR_SKIP_QC" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then
|
|
ViashError '--skip_qc' has to be a boolean. Use "--help" to get more information on the parameters.
|
|
exit 1
|
|
fi
|
|
fi
|
|
if [[ -n "$VIASH_PAR_SKIP_MARKDUPLICATES" ]]; then
|
|
if ! [[ "$VIASH_PAR_SKIP_MARKDUPLICATES" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then
|
|
ViashError '--skip_markduplicates' has to be a boolean. Use "--help" to get more information on the parameters.
|
|
exit 1
|
|
fi
|
|
fi
|
|
if [[ -n "$VIASH_PAR_SKIP_STRINGTIE" ]]; then
|
|
if ! [[ "$VIASH_PAR_SKIP_STRINGTIE" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then
|
|
ViashError '--skip_stringtie' has to be a boolean. Use "--help" to get more information on the parameters.
|
|
exit 1
|
|
fi
|
|
fi
|
|
if [[ -n "$VIASH_PAR_SKIP_BIGWIG" ]]; then
|
|
if ! [[ "$VIASH_PAR_SKIP_BIGWIG" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then
|
|
ViashError '--skip_bigwig' has to be a boolean. 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 "$VIASH_PAR_PROCESSED_GENOME_BAM" ] && [ ! -d "$(dirname "$VIASH_PAR_PROCESSED_GENOME_BAM")" ]; then
|
|
mkdir -p "$(dirname "$VIASH_PAR_PROCESSED_GENOME_BAM")"
|
|
fi
|
|
if [ ! -z "$VIASH_PAR_GENOME_BAM_INDEX" ] && [ ! -d "$(dirname "$VIASH_PAR_GENOME_BAM_INDEX")" ]; then
|
|
mkdir -p "$(dirname "$VIASH_PAR_GENOME_BAM_INDEX")"
|
|
fi
|
|
if [ ! -z "$VIASH_PAR_GENOME_BAM_STATS" ] && [ ! -d "$(dirname "$VIASH_PAR_GENOME_BAM_STATS")" ]; then
|
|
mkdir -p "$(dirname "$VIASH_PAR_GENOME_BAM_STATS")"
|
|
fi
|
|
if [ ! -z "$VIASH_PAR_GENOME_BAM_FLAGSTAT" ] && [ ! -d "$(dirname "$VIASH_PAR_GENOME_BAM_FLAGSTAT")" ]; then
|
|
mkdir -p "$(dirname "$VIASH_PAR_GENOME_BAM_FLAGSTAT")"
|
|
fi
|
|
if [ ! -z "$VIASH_PAR_GENOME_BAM_IDXSTATS" ] && [ ! -d "$(dirname "$VIASH_PAR_GENOME_BAM_IDXSTATS")" ]; then
|
|
mkdir -p "$(dirname "$VIASH_PAR_GENOME_BAM_IDXSTATS")"
|
|
fi
|
|
if [ ! -z "$VIASH_PAR_MARKDUPLICATES_METRICS" ] && [ ! -d "$(dirname "$VIASH_PAR_MARKDUPLICATES_METRICS")" ]; then
|
|
mkdir -p "$(dirname "$VIASH_PAR_MARKDUPLICATES_METRICS")"
|
|
fi
|
|
if [ ! -z "$VIASH_PAR_STRINGTIE_TRANSCRIPT_GTF" ] && [ ! -d "$(dirname "$VIASH_PAR_STRINGTIE_TRANSCRIPT_GTF")" ]; then
|
|
mkdir -p "$(dirname "$VIASH_PAR_STRINGTIE_TRANSCRIPT_GTF")"
|
|
fi
|
|
if [ ! -z "$VIASH_PAR_STRINGTIE_COVERAGE_GTF" ] && [ ! -d "$(dirname "$VIASH_PAR_STRINGTIE_COVERAGE_GTF")" ]; then
|
|
mkdir -p "$(dirname "$VIASH_PAR_STRINGTIE_COVERAGE_GTF")"
|
|
fi
|
|
if [ ! -z "$VIASH_PAR_STRINGTIE_ABUNDANCE" ] && [ ! -d "$(dirname "$VIASH_PAR_STRINGTIE_ABUNDANCE")" ]; then
|
|
mkdir -p "$(dirname "$VIASH_PAR_STRINGTIE_ABUNDANCE")"
|
|
fi
|
|
if [ ! -z "$VIASH_PAR_STRINGTIE_BALLGOWN" ] && [ ! -d "$(dirname "$VIASH_PAR_STRINGTIE_BALLGOWN")" ]; then
|
|
mkdir -p "$(dirname "$VIASH_PAR_STRINGTIE_BALLGOWN")"
|
|
fi
|
|
if [ ! -z "$VIASH_PAR_BEDGRAPH_FORWARD" ] && [ ! -d "$(dirname "$VIASH_PAR_BEDGRAPH_FORWARD")" ]; then
|
|
mkdir -p "$(dirname "$VIASH_PAR_BEDGRAPH_FORWARD")"
|
|
fi
|
|
if [ ! -z "$VIASH_PAR_BEDGRAPH_REVERSE" ] && [ ! -d "$(dirname "$VIASH_PAR_BEDGRAPH_REVERSE")" ]; then
|
|
mkdir -p "$(dirname "$VIASH_PAR_BEDGRAPH_REVERSE")"
|
|
fi
|
|
if [ ! -z "$VIASH_PAR_BIGWIG_FORWARD" ] && [ ! -d "$(dirname "$VIASH_PAR_BIGWIG_FORWARD")" ]; then
|
|
mkdir -p "$(dirname "$VIASH_PAR_BIGWIG_FORWARD")"
|
|
fi
|
|
if [ ! -z "$VIASH_PAR_BIGWIG_REVERSE" ] && [ ! -d "$(dirname "$VIASH_PAR_BIGWIG_REVERSE")" ]; then
|
|
mkdir -p "$(dirname "$VIASH_PAR_BIGWIG_REVERSE")"
|
|
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
|
|
|
|
|
|
# set dependency paths
|
|
VIASH_DEP_PICARD_MARKDUPLICATES="$VIASH_META_RESOURCES_DIR/../../../nextflow/picard_markduplicates/main.nf"
|
|
VIASH_DEP_STRINGTIE="$VIASH_META_RESOURCES_DIR/../../../nextflow/stringtie/main.nf"
|
|
VIASH_DEP_BEDTOOLS_GENOMECOV="$VIASH_META_RESOURCES_DIR/../../../nextflow/bedtools_genomecov/main.nf"
|
|
VIASH_DEP_UCSC_BEDCLIP="$VIASH_META_RESOURCES_DIR/../../../nextflow/ucsc/bedclip/main.nf"
|
|
VIASH_DEP_UCSC_BEDGRAPHTOBIGWIG="$VIASH_META_RESOURCES_DIR/../../../nextflow/ucsc/bedgraphtobigwig/main.nf"
|
|
VIASH_DEP_SAMTOOLS_SAMTOOLS_SORT="$VIASH_TARGET_DIR/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/samtools/samtools_sort/main.nf"
|
|
VIASH_DEP_SAMTOOLS_SAMTOOLS_INDEX="$VIASH_TARGET_DIR/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/samtools/samtools_index/main.nf"
|
|
VIASH_DEP_SAMTOOLS_SAMTOOLS_STATS="$VIASH_TARGET_DIR/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/samtools/samtools_stats/main.nf"
|
|
VIASH_DEP_SAMTOOLS_SAMTOOLS_FLAGSTAT="$VIASH_TARGET_DIR/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/samtools/samtools_flagstat/main.nf"
|
|
VIASH_DEP_SAMTOOLS_SAMTOOLS_IDXSTATS="$VIASH_TARGET_DIR/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/samtools/samtools_idxstats/main.nf"
|
|
|
|
ViashDebug "Running command: $(echo $VIASH_CMD)"
|
|
cat << VIASHEOF | eval $VIASH_CMD
|
|
set -e
|
|
tempscript=\$(mktemp "$VIASH_META_TEMP_DIR/viash-run-post_processing-XXXXXX").nf
|
|
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'
|
|
//// VIASH START
|
|
// The following code has been auto-generated by Viash.
|
|
|
|
//// VIASH END
|
|
// Note: some helper functionality is added at the end of this file
|
|
|
|
workflow run_wf {
|
|
take:
|
|
input_ch
|
|
|
|
main:
|
|
output_ch = input_ch
|
|
|
|
| picard_markduplicates.run (
|
|
runIf: { id, state -> !state.skip_markduplicates && !state.with_umi },
|
|
fromState: [
|
|
"bam": "genome_bam",
|
|
"fasta": "fasta",
|
|
"fai": "fai",
|
|
"extra_picard_args": "extra_picard_args"
|
|
],
|
|
toState: [
|
|
"processed_genome_bam": "output_bam",
|
|
"markduplicates_metrics": "metrics"
|
|
]
|
|
)
|
|
| samtools_sort.run (
|
|
runIf: { id, state -> !state.skip_markduplicates && !state.with_umi },
|
|
fromState: [ "input": "processed_genome_bam" ],
|
|
toState: [ "processed_genome_bam": "output" ],
|
|
key: "genome_sorted_MarkDuplicates"
|
|
)
|
|
| samtools_index.run (
|
|
runIf: { id, state -> !state.skip_markduplicates && !state.with_umi },
|
|
fromState: [
|
|
"input": "processed_genome_bam",
|
|
"csi": "bam_csi_index"
|
|
],
|
|
toState: [ "genome_bam_index": "output" ],
|
|
key: "genome_sorted_MarkDuplicates",
|
|
)
|
|
| samtools_stats.run (
|
|
runIf: { id, state -> !state.skip_markduplicates && !state.with_umi },
|
|
fromState: [
|
|
"input": "processed_genome_bam",
|
|
"bai": "genome_bam_index"
|
|
],
|
|
toState: [ "genome_bam_stats": "output" ],
|
|
key: "MarkDuplicates_stats"
|
|
)
|
|
| samtools_flagstat.run (
|
|
runIf: { id, state -> !state.skip_markduplicates && !state.with_umi },
|
|
fromState: [
|
|
"bam": "processed_genome_bam",
|
|
"bai": "genome_bam_index"
|
|
],
|
|
toState: [ "genome_bam_flagstat": "output" ],
|
|
key: "MarkDuplicates_flagstat"
|
|
)
|
|
| samtools_idxstats.run(
|
|
runIf: { id, state -> !state.skip_markduplicates && !state.with_umi },
|
|
fromState: [
|
|
"bam": "processed_genome_bam",
|
|
"bai": "genome_bam_index"
|
|
],
|
|
toState: [ "genome_bam_idxstats": "output" ],
|
|
key: "MarkDuplicates_idxstats"
|
|
)
|
|
|
|
| stringtie.run (
|
|
runIf: { id, state -> !state.skip_stringtie },
|
|
fromState: [
|
|
"strandedness": "strandedness",
|
|
"bam": "processed_genome_bam",
|
|
"annotation_gtf": "gtf",
|
|
"extra_stringtie_args": "extra_stringtie_args"
|
|
],
|
|
toState: [
|
|
"stringtie_transcript_gtf": "transcript_gtf",
|
|
"stringtie_coverage_gtf": "coverage_gtf",
|
|
"stringtie_abundance": "abundance",
|
|
"stringtie_ballgown": "ballgown"
|
|
]
|
|
)
|
|
|
|
// Genome-wide coverage with BEDTools
|
|
|
|
| bedtools_genomecov.run (
|
|
runIf: { id, state -> !state.skip_bigwig },
|
|
fromState: [
|
|
"strandedness": "strandedness",
|
|
"bam": "processed_genome_bam",
|
|
"extra_bedtools_args": "extra_bedtools_args"
|
|
],
|
|
toState: [
|
|
"bedgraph_forward": "bedgraph_forward",
|
|
"bedgraph_reverse": "bedgraph_reverse"
|
|
]
|
|
)
|
|
|
|
| bedclip.run (
|
|
runIf: { id, state -> !state.skip_bigwig },
|
|
fromState: [
|
|
"input_bedgraph": "bedgraph_forward",
|
|
"sizes": "chrom_sizes"
|
|
],
|
|
toState: [ "bedgraph_forward": "output_bedgraph" ],
|
|
key: "bedclip_forward"
|
|
)
|
|
|
|
| bedgraphtobigwig.run (
|
|
runIf: { id, state -> !state.skip_bigwig },
|
|
fromState: [
|
|
"bedgraph": "bedgraph_forward",
|
|
"sizes": "chrom_sizes"
|
|
],
|
|
toState: [ "bigwig_forward": "bigwig" ],
|
|
key: "bedgraphtobigwig_forward"
|
|
)
|
|
|
|
| bedclip.run (
|
|
runIf: { id, state -> !state.skip_bigwig },
|
|
fromState: [
|
|
"input_bedgraph": "bedgraph_reverse",
|
|
"sizes": "chrom_sizes",
|
|
],
|
|
toState: [ "bedgraph_reverse": "output_bedgraph" ],
|
|
key: "bedclip_reverse"
|
|
)
|
|
|
|
| bedgraphtobigwig.run (
|
|
runIf: { id, state -> !state.skip_bigwig },
|
|
fromState: [
|
|
"bedgraph": "bedgraph_reverse",
|
|
"sizes": "chrom_sizes"
|
|
],
|
|
toState: [ "bigwig_reverse": "bigwig" ],
|
|
key: "bedgraphtobigwig_reverse"
|
|
)
|
|
|
|
| map { id, state ->
|
|
def mod_state = state.findAll { key, value -> value instanceof java.nio.file.Path && value.exists() }
|
|
[ id, mod_state ]
|
|
}
|
|
|
|
| setState (
|
|
"processed_genome_bam": "processed_genome_bam",
|
|
"genome_bam_index": "genome_bam_index",
|
|
"genome_bam_stats": "genome_bam_stats",
|
|
"genome_bam_flagstat": "genome_bam_flagstat",
|
|
"genome_bam_idxstats": "genome_bam_idxstats",
|
|
"markduplicates_metrics": "markduplicates_metrics",
|
|
"stringtie_transcript_gtf": "stringtie_transcript_gtf",
|
|
"stringtie_coverage_gtf": "stringtie_coverage_gtf",
|
|
"stringtie_abundance": "stringtie_abundance",
|
|
"stringtie_ballgown": "stringtie_ballgown",
|
|
"bedgraph_forward": "bedgraph_forward",
|
|
"bedgraph_reverse": "bedgraph_reverse",
|
|
"bigwig_forward": "bigwig_forward",
|
|
"bigwig_reverse": "bigwig_reverse"
|
|
)
|
|
|
|
emit:
|
|
output_ch
|
|
}
|
|
VIASHMAIN
|
|
nextflow run . -main-script "\$tempscript" &
|
|
wait "\$!"
|
|
|
|
VIASHEOF
|
|
|
|
|
|
# check whether required files exist
|
|
if [ ! -z "$VIASH_PAR_PROCESSED_GENOME_BAM" ] && [ ! -e "$VIASH_PAR_PROCESSED_GENOME_BAM" ]; then
|
|
ViashError "Output file '$VIASH_PAR_PROCESSED_GENOME_BAM' does not exist."
|
|
exit 1
|
|
fi
|
|
if [ ! -z "$VIASH_PAR_GENOME_BAM_INDEX" ] && [ ! -e "$VIASH_PAR_GENOME_BAM_INDEX" ]; then
|
|
ViashError "Output file '$VIASH_PAR_GENOME_BAM_INDEX' does not exist."
|
|
exit 1
|
|
fi
|
|
if [ ! -z "$VIASH_PAR_GENOME_BAM_STATS" ] && [ ! -e "$VIASH_PAR_GENOME_BAM_STATS" ]; then
|
|
ViashError "Output file '$VIASH_PAR_GENOME_BAM_STATS' does not exist."
|
|
exit 1
|
|
fi
|
|
if [ ! -z "$VIASH_PAR_GENOME_BAM_FLAGSTAT" ] && [ ! -e "$VIASH_PAR_GENOME_BAM_FLAGSTAT" ]; then
|
|
ViashError "Output file '$VIASH_PAR_GENOME_BAM_FLAGSTAT' does not exist."
|
|
exit 1
|
|
fi
|
|
if [ ! -z "$VIASH_PAR_GENOME_BAM_IDXSTATS" ] && [ ! -e "$VIASH_PAR_GENOME_BAM_IDXSTATS" ]; then
|
|
ViashError "Output file '$VIASH_PAR_GENOME_BAM_IDXSTATS' does not exist."
|
|
exit 1
|
|
fi
|
|
if [ ! -z "$VIASH_PAR_MARKDUPLICATES_METRICS" ] && [ ! -e "$VIASH_PAR_MARKDUPLICATES_METRICS" ]; then
|
|
ViashError "Output file '$VIASH_PAR_MARKDUPLICATES_METRICS' does not exist."
|
|
exit 1
|
|
fi
|
|
if [ ! -z "$VIASH_PAR_STRINGTIE_TRANSCRIPT_GTF" ] && [ ! -e "$VIASH_PAR_STRINGTIE_TRANSCRIPT_GTF" ]; then
|
|
ViashError "Output file '$VIASH_PAR_STRINGTIE_TRANSCRIPT_GTF' does not exist."
|
|
exit 1
|
|
fi
|
|
if [ ! -z "$VIASH_PAR_STRINGTIE_COVERAGE_GTF" ] && [ ! -e "$VIASH_PAR_STRINGTIE_COVERAGE_GTF" ]; then
|
|
ViashError "Output file '$VIASH_PAR_STRINGTIE_COVERAGE_GTF' does not exist."
|
|
exit 1
|
|
fi
|
|
if [ ! -z "$VIASH_PAR_STRINGTIE_ABUNDANCE" ] && [ ! -e "$VIASH_PAR_STRINGTIE_ABUNDANCE" ]; then
|
|
ViashError "Output file '$VIASH_PAR_STRINGTIE_ABUNDANCE' does not exist."
|
|
exit 1
|
|
fi
|
|
if [ ! -z "$VIASH_PAR_STRINGTIE_BALLGOWN" ] && [ ! -e "$VIASH_PAR_STRINGTIE_BALLGOWN" ]; then
|
|
ViashError "Output file '$VIASH_PAR_STRINGTIE_BALLGOWN' does not exist."
|
|
exit 1
|
|
fi
|
|
if [ ! -z "$VIASH_PAR_BEDGRAPH_FORWARD" ] && [ ! -e "$VIASH_PAR_BEDGRAPH_FORWARD" ]; then
|
|
ViashError "Output file '$VIASH_PAR_BEDGRAPH_FORWARD' does not exist."
|
|
exit 1
|
|
fi
|
|
if [ ! -z "$VIASH_PAR_BEDGRAPH_REVERSE" ] && [ ! -e "$VIASH_PAR_BEDGRAPH_REVERSE" ]; then
|
|
ViashError "Output file '$VIASH_PAR_BEDGRAPH_REVERSE' does not exist."
|
|
exit 1
|
|
fi
|
|
if [ ! -z "$VIASH_PAR_BIGWIG_FORWARD" ] && [ ! -e "$VIASH_PAR_BIGWIG_FORWARD" ]; then
|
|
ViashError "Output file '$VIASH_PAR_BIGWIG_FORWARD' does not exist."
|
|
exit 1
|
|
fi
|
|
if [ ! -z "$VIASH_PAR_BIGWIG_REVERSE" ] && [ ! -e "$VIASH_PAR_BIGWIG_REVERSE" ]; then
|
|
ViashError "Output file '$VIASH_PAR_BIGWIG_REVERSE' does not exist."
|
|
exit 1
|
|
fi
|
|
|
|
|
|
exit 0
|