CI
fe41adb0c7
Build pipeline: viash-hub.rnaseq.main-c7sdt
Source commit: 05d48ac2f8
Source message: Multiple fixes (#26)
* unset argument if not paired
* fix argument name
* add count_read_pairs argument
* output star log
* move biotypes header file into multiqc_custom_biotype component
* move deseq2 header files into deseq2_qc component
* update output defaults
* use biobox main
* add parameters to example
* update component
* update component
* ribo database processing moved to workflow
* clean code, remove unused arguments
1806 lines
83 KiB
Bash
Executable File
1806 lines
83 KiB
Bash
Executable File
#!/usr/bin/env bash
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# pre_processing main
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#
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# This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative
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# work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
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# Intuitive.
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#
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# The component may contain files which fall under a different license. The
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# authors of this component should specify the license in the header of such
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# files, or include a separate license file detailing the licenses of all included
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# files.
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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 $VIASH_META_RESOURCES_DIR`
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# define meta fields
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VIASH_META_NAME="pre_processing"
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VIASH_META_FUNCTIONALITY_NAME="pre_processing"
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VIASH_META_EXECUTABLE="$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 "pre_processing main"
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echo ""
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echo "A subworkflow for the pre-processing stage of the nf-core/rnaseq pipeline."
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echo ""
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echo "Inputs:"
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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 " --fastq_1"
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echo " type: file, required parameter, file must exist"
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echo " example: input.fastq.gz"
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echo " Path to the sample (or read 1 of paired end sample)."
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echo ""
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echo " --fastq_2"
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echo " type: file"
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echo " Path to read 2 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 " --bbsplit_index"
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echo " type: file, file must exist"
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echo " BBsplit index"
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echo ""
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echo " --bbsplit_fasta_list"
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echo " type: file, file must exist"
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echo " Path to comma-separated file containing a list of reference genomes to"
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echo " filter reads against with BBSplit. To use BBSplit, \"--skip_bbsplit\" must"
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echo " be explicitly set to \"false\". The file should contain 2 (comma"
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echo " separated) columns - short name and full path to reference genome(s)"
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echo ""
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echo " --ribo_database_manifest"
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echo " type: file, file must exist"
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echo " Text file containing paths to fasta files (one per line) that will be"
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echo " used to create the database for SortMeRNA."
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echo ""
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echo " --transcript_fasta"
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echo " type: file, file must exist"
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echo " Path to FASTA transcriptome file."
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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 " Path to GTF annotation file."
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echo ""
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echo " --salmon_index"
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echo " type: file, file must exist"
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echo " Path to directory containing the Salmon index"
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echo ""
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echo " --num_trimmed_reads"
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echo " type: integer"
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echo " Number of reads after trimming"
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echo ""
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echo "Extra pipeline options:"
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echo " --skip_qc"
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echo " type: boolean"
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echo " Skip QC steps of the workflow."
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echo ""
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echo "FastQC options:"
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echo " --skip_fastqc"
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echo " type: boolean"
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echo " default: false"
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echo " Skip FatQC step."
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echo ""
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echo "UMI-tools options:"
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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_umi_extract"
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echo " type: boolean"
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echo " default: false"
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echo " Skip umi_tools extract step."
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echo ""
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echo " --umitools_extract_method"
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echo " type: string"
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echo " default: string"
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echo " choices: [ string, regex ]"
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echo " UMI pattern to use."
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echo ""
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echo " --umitools_bc_pattern"
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echo " type: string"
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echo " default:"
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echo " The UMI barcode pattern to use e.g. 'NNNNNN' indicates that the first 6"
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echo " nucleotides of the read are from the UMI."
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echo ""
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echo " --umitools_bc_pattern2"
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echo " type: string"
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echo " default:"
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echo " The UMI barcode pattern to use if the UMI is located in read 2."
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echo ""
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echo " --umi_discard_read"
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echo " type: integer"
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echo " default: 0"
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echo " choices: [ 0, 1, 2 ]"
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echo " After UMI barcode extraction discard either R1 or R2 by setting this"
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echo " parameter to 1 or 2, respectively."
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echo ""
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echo " --umitools_umi_separator"
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echo " type: string"
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echo " default: _"
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echo " The character that separates the UMI in the read name. Most likely a"
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echo " colon if you skipped the extraction with UMI-tools and used other"
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echo " software."
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echo ""
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echo " --umitools_grouping_method"
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echo " type: string"
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echo " default: directional"
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echo " choices: [ unique, percentile, cluster, adjacency, directional ]"
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echo " Method to use to determine read groups by subsuming those with similar"
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echo " UMIs. All methods start by identifying the reads with the same mapping"
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echo " position, but treat similar yet nonidentical UMIs differently."
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echo ""
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echo " --save_umi_intermeds"
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echo " type: boolean"
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echo " default: false"
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echo " If this option is specified, intermediate FastQ and BAM files produced"
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echo " by UMI-tools are also saved in the results directory."
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echo ""
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echo "Read trimming options:"
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echo " --trimmer"
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echo " type: string"
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echo " default: trimgalore"
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echo " choices: [ trimgalore, fastp ]"
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echo " Specify the trimming tool to use."
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echo ""
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echo " --extra_trimgalore_args"
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echo " type: string"
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echo " Extra arguments to pass to Trim Galore! command in addition to defaults"
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echo " defined by the pipeline."
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echo ""
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echo " --min_trimmed_reads"
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echo " type: integer"
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echo " default: 10000"
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echo " Minimum number of trimmed reads below which samples are removed from"
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echo " further processing. Some downstream steps in the pipeline will fail if"
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echo " this threshold is too low."
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echo ""
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echo " --skip_trimming"
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echo " type: boolean"
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echo " default: false"
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echo " Skip the adapter trimming step."
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echo ""
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echo " --save_trimmed"
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echo " type: boolean"
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echo " default: false"
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echo " Save the trimmed FastQ files in the results directory."
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echo ""
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echo "Alignment options:"
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echo " --extra_salmon_quant_args"
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echo " type: string"
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echo " default:"
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echo " Extra arguments to pass to salmon quant command in addition to defaults"
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echo " defined by the pipeline."
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echo ""
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echo "Read filtering options:"
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echo " --skip_bbsplit"
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echo " type: boolean_true"
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echo " Skip BBSplit for removal of non-reference genome reads."
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echo ""
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echo " --remove_ribo_rna"
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echo " type: boolean_true"
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echo " Enable the removal of reads derived from ribosomal RNA using SortMeRNA."
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echo ""
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echo "Other options:"
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echo " --extra_fq_subsample_args"
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echo " type: string"
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echo " default: --record-count 1000000 --seed 1"
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echo " Extra arguments to pass to fq subsample command in addition to defaults"
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echo " defined by the pipeline."
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echo ""
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echo "Output:"
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echo " --qc_output1"
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echo " type: file, output"
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echo " default: \$id.read_1.fastq"
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echo " Path to output directory"
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echo ""
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echo " --qc_output2"
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echo " type: file, output"
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echo " default: \$id.read_2.fastq"
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echo " Path to output directory"
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echo ""
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echo " --fastqc_html_1"
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echo " type: file, output"
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echo " default: \$id.read_1.fastqc.html"
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echo " FastQC HTML report for read 1."
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echo ""
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echo " --fastqc_html_2"
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echo " type: file, output"
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echo " default: \$id.read_2.fastqc.html"
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echo " FastQC HTML report for read 2."
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echo ""
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echo " --fastqc_zip_1"
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echo " type: file, output"
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echo " default: \$id.read_1.fastqc.zip"
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echo " FastQC report archive for read 1."
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echo ""
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echo " --fastqc_zip_2"
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echo " type: file, output"
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echo " default: \$id.read_2.fastqc.zip"
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echo " FastQC report archive for read 2."
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echo ""
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echo " --trim_log_1"
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echo " type: file, output"
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echo " default: \$id.read_1.trimming_report.txt"
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echo ""
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echo " --trim_log_2"
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echo " type: file, output"
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echo " default: \$id.read_2.trimming_report.txt"
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echo ""
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echo " --trim_html_1"
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echo " type: file, output"
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echo " default: \$id.read_1.trimmed_fastqc.html"
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echo ""
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echo " --trim_html_2"
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echo " type: file, output"
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echo " default: \$id.read_2.trimmed_fastqc.html"
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echo ""
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echo " --trim_zip_1"
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echo " type: file, output"
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echo " default: \$id.read_1.trimmed_fastqc.zip"
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echo ""
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echo " --trim_zip_2"
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echo " type: file, output"
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echo " default: \$id.read_2.trimmed_fastqc.zip"
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echo ""
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echo " --sortmerna_log"
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echo " type: file, output"
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echo " default: \$id.sortmerna.log"
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echo " Sortmerna log file."
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echo ""
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echo " --salmon_quant_output"
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echo " type: file, output, file must exist"
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echo " default: \$id.salmon_quant_output"
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echo " Results from Salmon quant"
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echo ""
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echo " --trim_json"
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echo " type: file, output, file must exist"
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echo " default: \$id.fastp_out.json"
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echo " The fastp json format report file name"
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echo ""
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echo " --trim_html"
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echo " type: file, output, file must exist"
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echo " default: \$id.fastp_out.html"
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echo " The fastp html format report file name"
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echo ""
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echo " --merged_out"
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echo " type: file, output, file must exist"
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echo " File name to store merged fastp output."
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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 "$1")"
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shift 1
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;;
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--version)
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|
echo "pre_processing main"
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exit
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;;
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--id)
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|
[ -n "$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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[ $# -lt 2 ] && ViashError Not enough arguments passed to --id. Use "--help" to get more information on the parameters. && exit 1
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shift 2
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;;
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|
--id=*)
|
|
[ -n "$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 "$1")
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shift 1
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;;
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|
--fastq_1)
|
|
[ -n "$VIASH_PAR_FASTQ_1" ] && ViashError Bad arguments for option \'--fastq_1\': \'$VIASH_PAR_FASTQ_1\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
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|
VIASH_PAR_FASTQ_1="$2"
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|
[ $# -lt 2 ] && ViashError Not enough arguments passed to --fastq_1. Use "--help" to get more information on the parameters. && exit 1
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|
shift 2
|
|
;;
|
|
--fastq_1=*)
|
|
[ -n "$VIASH_PAR_FASTQ_1" ] && ViashError Bad arguments for option \'--fastq_1=*\': \'$VIASH_PAR_FASTQ_1\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_FASTQ_1=$(ViashRemoveFlags "$1")
|
|
shift 1
|
|
;;
|
|
--fastq_2)
|
|
[ -n "$VIASH_PAR_FASTQ_2" ] && ViashError Bad arguments for option \'--fastq_2\': \'$VIASH_PAR_FASTQ_2\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_FASTQ_2="$2"
|
|
[ $# -lt 2 ] && ViashError Not enough arguments passed to --fastq_2. Use "--help" to get more information on the parameters. && exit 1
|
|
shift 2
|
|
;;
|
|
--fastq_2=*)
|
|
[ -n "$VIASH_PAR_FASTQ_2" ] && ViashError Bad arguments for option \'--fastq_2=*\': \'$VIASH_PAR_FASTQ_2\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_FASTQ_2=$(ViashRemoveFlags "$1")
|
|
shift 1
|
|
;;
|
|
--strandedness)
|
|
[ -n "$VIASH_PAR_STRANDEDNESS" ] && ViashError Bad arguments for option \'--strandedness\': \'$VIASH_PAR_STRANDEDNESS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_STRANDEDNESS="$2"
|
|
[ $# -lt 2 ] && ViashError Not enough arguments passed to --strandedness. Use "--help" to get more information on the parameters. && exit 1
|
|
shift 2
|
|
;;
|
|
--strandedness=*)
|
|
[ -n "$VIASH_PAR_STRANDEDNESS" ] && ViashError Bad arguments for option \'--strandedness=*\': \'$VIASH_PAR_STRANDEDNESS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_STRANDEDNESS=$(ViashRemoveFlags "$1")
|
|
shift 1
|
|
;;
|
|
--bbsplit_index)
|
|
[ -n "$VIASH_PAR_BBSPLIT_INDEX" ] && ViashError Bad arguments for option \'--bbsplit_index\': \'$VIASH_PAR_BBSPLIT_INDEX\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_BBSPLIT_INDEX="$2"
|
|
[ $# -lt 2 ] && ViashError Not enough arguments passed to --bbsplit_index. Use "--help" to get more information on the parameters. && exit 1
|
|
shift 2
|
|
;;
|
|
--bbsplit_index=*)
|
|
[ -n "$VIASH_PAR_BBSPLIT_INDEX" ] && ViashError Bad arguments for option \'--bbsplit_index=*\': \'$VIASH_PAR_BBSPLIT_INDEX\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_BBSPLIT_INDEX=$(ViashRemoveFlags "$1")
|
|
shift 1
|
|
;;
|
|
--bbsplit_fasta_list)
|
|
[ -n "$VIASH_PAR_BBSPLIT_FASTA_LIST" ] && ViashError Bad arguments for option \'--bbsplit_fasta_list\': \'$VIASH_PAR_BBSPLIT_FASTA_LIST\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_BBSPLIT_FASTA_LIST="$2"
|
|
[ $# -lt 2 ] && ViashError Not enough arguments passed to --bbsplit_fasta_list. Use "--help" to get more information on the parameters. && exit 1
|
|
shift 2
|
|
;;
|
|
--bbsplit_fasta_list=*)
|
|
[ -n "$VIASH_PAR_BBSPLIT_FASTA_LIST" ] && ViashError Bad arguments for option \'--bbsplit_fasta_list=*\': \'$VIASH_PAR_BBSPLIT_FASTA_LIST\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_BBSPLIT_FASTA_LIST=$(ViashRemoveFlags "$1")
|
|
shift 1
|
|
;;
|
|
--ribo_database_manifest)
|
|
[ -n "$VIASH_PAR_RIBO_DATABASE_MANIFEST" ] && ViashError Bad arguments for option \'--ribo_database_manifest\': \'$VIASH_PAR_RIBO_DATABASE_MANIFEST\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_RIBO_DATABASE_MANIFEST="$2"
|
|
[ $# -lt 2 ] && ViashError Not enough arguments passed to --ribo_database_manifest. Use "--help" to get more information on the parameters. && exit 1
|
|
shift 2
|
|
;;
|
|
--ribo_database_manifest=*)
|
|
[ -n "$VIASH_PAR_RIBO_DATABASE_MANIFEST" ] && ViashError Bad arguments for option \'--ribo_database_manifest=*\': \'$VIASH_PAR_RIBO_DATABASE_MANIFEST\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_RIBO_DATABASE_MANIFEST=$(ViashRemoveFlags "$1")
|
|
shift 1
|
|
;;
|
|
--transcript_fasta)
|
|
[ -n "$VIASH_PAR_TRANSCRIPT_FASTA" ] && ViashError Bad arguments for option \'--transcript_fasta\': \'$VIASH_PAR_TRANSCRIPT_FASTA\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_TRANSCRIPT_FASTA="$2"
|
|
[ $# -lt 2 ] && ViashError Not enough arguments passed to --transcript_fasta. Use "--help" to get more information on the parameters. && exit 1
|
|
shift 2
|
|
;;
|
|
--transcript_fasta=*)
|
|
[ -n "$VIASH_PAR_TRANSCRIPT_FASTA" ] && ViashError Bad arguments for option \'--transcript_fasta=*\': \'$VIASH_PAR_TRANSCRIPT_FASTA\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_TRANSCRIPT_FASTA=$(ViashRemoveFlags "$1")
|
|
shift 1
|
|
;;
|
|
--gtf)
|
|
[ -n "$VIASH_PAR_GTF" ] && ViashError Bad arguments for option \'--gtf\': \'$VIASH_PAR_GTF\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_GTF="$2"
|
|
[ $# -lt 2 ] && ViashError Not enough arguments passed to --gtf. Use "--help" to get more information on the parameters. && exit 1
|
|
shift 2
|
|
;;
|
|
--gtf=*)
|
|
[ -n "$VIASH_PAR_GTF" ] && ViashError Bad arguments for option \'--gtf=*\': \'$VIASH_PAR_GTF\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_GTF=$(ViashRemoveFlags "$1")
|
|
shift 1
|
|
;;
|
|
--salmon_index)
|
|
[ -n "$VIASH_PAR_SALMON_INDEX" ] && ViashError Bad arguments for option \'--salmon_index\': \'$VIASH_PAR_SALMON_INDEX\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_SALMON_INDEX="$2"
|
|
[ $# -lt 2 ] && ViashError Not enough arguments passed to --salmon_index. Use "--help" to get more information on the parameters. && exit 1
|
|
shift 2
|
|
;;
|
|
--salmon_index=*)
|
|
[ -n "$VIASH_PAR_SALMON_INDEX" ] && ViashError Bad arguments for option \'--salmon_index=*\': \'$VIASH_PAR_SALMON_INDEX\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_SALMON_INDEX=$(ViashRemoveFlags "$1")
|
|
shift 1
|
|
;;
|
|
--num_trimmed_reads)
|
|
[ -n "$VIASH_PAR_NUM_TRIMMED_READS" ] && ViashError Bad arguments for option \'--num_trimmed_reads\': \'$VIASH_PAR_NUM_TRIMMED_READS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_NUM_TRIMMED_READS="$2"
|
|
[ $# -lt 2 ] && ViashError Not enough arguments passed to --num_trimmed_reads. Use "--help" to get more information on the parameters. && exit 1
|
|
shift 2
|
|
;;
|
|
--num_trimmed_reads=*)
|
|
[ -n "$VIASH_PAR_NUM_TRIMMED_READS" ] && ViashError Bad arguments for option \'--num_trimmed_reads=*\': \'$VIASH_PAR_NUM_TRIMMED_READS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_NUM_TRIMMED_READS=$(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 "$1")
|
|
shift 1
|
|
;;
|
|
--skip_fastqc)
|
|
[ -n "$VIASH_PAR_SKIP_FASTQC" ] && ViashError Bad arguments for option \'--skip_fastqc\': \'$VIASH_PAR_SKIP_FASTQC\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_SKIP_FASTQC="$2"
|
|
[ $# -lt 2 ] && ViashError Not enough arguments passed to --skip_fastqc. Use "--help" to get more information on the parameters. && exit 1
|
|
shift 2
|
|
;;
|
|
--skip_fastqc=*)
|
|
[ -n "$VIASH_PAR_SKIP_FASTQC" ] && ViashError Bad arguments for option \'--skip_fastqc=*\': \'$VIASH_PAR_SKIP_FASTQC\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_SKIP_FASTQC=$(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 "$1")
|
|
shift 1
|
|
;;
|
|
--skip_umi_extract)
|
|
[ -n "$VIASH_PAR_SKIP_UMI_EXTRACT" ] && ViashError Bad arguments for option \'--skip_umi_extract\': \'$VIASH_PAR_SKIP_UMI_EXTRACT\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_SKIP_UMI_EXTRACT="$2"
|
|
[ $# -lt 2 ] && ViashError Not enough arguments passed to --skip_umi_extract. Use "--help" to get more information on the parameters. && exit 1
|
|
shift 2
|
|
;;
|
|
--skip_umi_extract=*)
|
|
[ -n "$VIASH_PAR_SKIP_UMI_EXTRACT" ] && ViashError Bad arguments for option \'--skip_umi_extract=*\': \'$VIASH_PAR_SKIP_UMI_EXTRACT\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_SKIP_UMI_EXTRACT=$(ViashRemoveFlags "$1")
|
|
shift 1
|
|
;;
|
|
--umitools_extract_method)
|
|
[ -n "$VIASH_PAR_UMITOOLS_EXTRACT_METHOD" ] && ViashError Bad arguments for option \'--umitools_extract_method\': \'$VIASH_PAR_UMITOOLS_EXTRACT_METHOD\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_UMITOOLS_EXTRACT_METHOD="$2"
|
|
[ $# -lt 2 ] && ViashError Not enough arguments passed to --umitools_extract_method. Use "--help" to get more information on the parameters. && exit 1
|
|
shift 2
|
|
;;
|
|
--umitools_extract_method=*)
|
|
[ -n "$VIASH_PAR_UMITOOLS_EXTRACT_METHOD" ] && ViashError Bad arguments for option \'--umitools_extract_method=*\': \'$VIASH_PAR_UMITOOLS_EXTRACT_METHOD\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_UMITOOLS_EXTRACT_METHOD=$(ViashRemoveFlags "$1")
|
|
shift 1
|
|
;;
|
|
--umitools_bc_pattern)
|
|
[ -n "$VIASH_PAR_UMITOOLS_BC_PATTERN" ] && ViashError Bad arguments for option \'--umitools_bc_pattern\': \'$VIASH_PAR_UMITOOLS_BC_PATTERN\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_UMITOOLS_BC_PATTERN="$2"
|
|
[ $# -lt 2 ] && ViashError Not enough arguments passed to --umitools_bc_pattern. Use "--help" to get more information on the parameters. && exit 1
|
|
shift 2
|
|
;;
|
|
--umitools_bc_pattern=*)
|
|
[ -n "$VIASH_PAR_UMITOOLS_BC_PATTERN" ] && ViashError Bad arguments for option \'--umitools_bc_pattern=*\': \'$VIASH_PAR_UMITOOLS_BC_PATTERN\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_UMITOOLS_BC_PATTERN=$(ViashRemoveFlags "$1")
|
|
shift 1
|
|
;;
|
|
--umitools_bc_pattern2)
|
|
[ -n "$VIASH_PAR_UMITOOLS_BC_PATTERN2" ] && ViashError Bad arguments for option \'--umitools_bc_pattern2\': \'$VIASH_PAR_UMITOOLS_BC_PATTERN2\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_UMITOOLS_BC_PATTERN2="$2"
|
|
[ $# -lt 2 ] && ViashError Not enough arguments passed to --umitools_bc_pattern2. Use "--help" to get more information on the parameters. && exit 1
|
|
shift 2
|
|
;;
|
|
--umitools_bc_pattern2=*)
|
|
[ -n "$VIASH_PAR_UMITOOLS_BC_PATTERN2" ] && ViashError Bad arguments for option \'--umitools_bc_pattern2=*\': \'$VIASH_PAR_UMITOOLS_BC_PATTERN2\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_UMITOOLS_BC_PATTERN2=$(ViashRemoveFlags "$1")
|
|
shift 1
|
|
;;
|
|
--umi_discard_read)
|
|
[ -n "$VIASH_PAR_UMI_DISCARD_READ" ] && ViashError Bad arguments for option \'--umi_discard_read\': \'$VIASH_PAR_UMI_DISCARD_READ\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_UMI_DISCARD_READ="$2"
|
|
[ $# -lt 2 ] && ViashError Not enough arguments passed to --umi_discard_read. Use "--help" to get more information on the parameters. && exit 1
|
|
shift 2
|
|
;;
|
|
--umi_discard_read=*)
|
|
[ -n "$VIASH_PAR_UMI_DISCARD_READ" ] && ViashError Bad arguments for option \'--umi_discard_read=*\': \'$VIASH_PAR_UMI_DISCARD_READ\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_UMI_DISCARD_READ=$(ViashRemoveFlags "$1")
|
|
shift 1
|
|
;;
|
|
--umitools_umi_separator)
|
|
[ -n "$VIASH_PAR_UMITOOLS_UMI_SEPARATOR" ] && ViashError Bad arguments for option \'--umitools_umi_separator\': \'$VIASH_PAR_UMITOOLS_UMI_SEPARATOR\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_UMITOOLS_UMI_SEPARATOR="$2"
|
|
[ $# -lt 2 ] && ViashError Not enough arguments passed to --umitools_umi_separator. Use "--help" to get more information on the parameters. && exit 1
|
|
shift 2
|
|
;;
|
|
--umitools_umi_separator=*)
|
|
[ -n "$VIASH_PAR_UMITOOLS_UMI_SEPARATOR" ] && ViashError Bad arguments for option \'--umitools_umi_separator=*\': \'$VIASH_PAR_UMITOOLS_UMI_SEPARATOR\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_UMITOOLS_UMI_SEPARATOR=$(ViashRemoveFlags "$1")
|
|
shift 1
|
|
;;
|
|
--umitools_grouping_method)
|
|
[ -n "$VIASH_PAR_UMITOOLS_GROUPING_METHOD" ] && ViashError Bad arguments for option \'--umitools_grouping_method\': \'$VIASH_PAR_UMITOOLS_GROUPING_METHOD\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_UMITOOLS_GROUPING_METHOD="$2"
|
|
[ $# -lt 2 ] && ViashError Not enough arguments passed to --umitools_grouping_method. Use "--help" to get more information on the parameters. && exit 1
|
|
shift 2
|
|
;;
|
|
--umitools_grouping_method=*)
|
|
[ -n "$VIASH_PAR_UMITOOLS_GROUPING_METHOD" ] && ViashError Bad arguments for option \'--umitools_grouping_method=*\': \'$VIASH_PAR_UMITOOLS_GROUPING_METHOD\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_UMITOOLS_GROUPING_METHOD=$(ViashRemoveFlags "$1")
|
|
shift 1
|
|
;;
|
|
--save_umi_intermeds)
|
|
[ -n "$VIASH_PAR_SAVE_UMI_INTERMEDS" ] && ViashError Bad arguments for option \'--save_umi_intermeds\': \'$VIASH_PAR_SAVE_UMI_INTERMEDS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_SAVE_UMI_INTERMEDS="$2"
|
|
[ $# -lt 2 ] && ViashError Not enough arguments passed to --save_umi_intermeds. Use "--help" to get more information on the parameters. && exit 1
|
|
shift 2
|
|
;;
|
|
--save_umi_intermeds=*)
|
|
[ -n "$VIASH_PAR_SAVE_UMI_INTERMEDS" ] && ViashError Bad arguments for option \'--save_umi_intermeds=*\': \'$VIASH_PAR_SAVE_UMI_INTERMEDS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_SAVE_UMI_INTERMEDS=$(ViashRemoveFlags "$1")
|
|
shift 1
|
|
;;
|
|
--trimmer)
|
|
[ -n "$VIASH_PAR_TRIMMER" ] && ViashError Bad arguments for option \'--trimmer\': \'$VIASH_PAR_TRIMMER\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_TRIMMER="$2"
|
|
[ $# -lt 2 ] && ViashError Not enough arguments passed to --trimmer. Use "--help" to get more information on the parameters. && exit 1
|
|
shift 2
|
|
;;
|
|
--trimmer=*)
|
|
[ -n "$VIASH_PAR_TRIMMER" ] && ViashError Bad arguments for option \'--trimmer=*\': \'$VIASH_PAR_TRIMMER\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_TRIMMER=$(ViashRemoveFlags "$1")
|
|
shift 1
|
|
;;
|
|
--extra_trimgalore_args)
|
|
[ -n "$VIASH_PAR_EXTRA_TRIMGALORE_ARGS" ] && ViashError Bad arguments for option \'--extra_trimgalore_args\': \'$VIASH_PAR_EXTRA_TRIMGALORE_ARGS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_EXTRA_TRIMGALORE_ARGS="$2"
|
|
[ $# -lt 2 ] && ViashError Not enough arguments passed to --extra_trimgalore_args. Use "--help" to get more information on the parameters. && exit 1
|
|
shift 2
|
|
;;
|
|
--extra_trimgalore_args=*)
|
|
[ -n "$VIASH_PAR_EXTRA_TRIMGALORE_ARGS" ] && ViashError Bad arguments for option \'--extra_trimgalore_args=*\': \'$VIASH_PAR_EXTRA_TRIMGALORE_ARGS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_EXTRA_TRIMGALORE_ARGS=$(ViashRemoveFlags "$1")
|
|
shift 1
|
|
;;
|
|
--min_trimmed_reads)
|
|
[ -n "$VIASH_PAR_MIN_TRIMMED_READS" ] && ViashError Bad arguments for option \'--min_trimmed_reads\': \'$VIASH_PAR_MIN_TRIMMED_READS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_MIN_TRIMMED_READS="$2"
|
|
[ $# -lt 2 ] && ViashError Not enough arguments passed to --min_trimmed_reads. Use "--help" to get more information on the parameters. && exit 1
|
|
shift 2
|
|
;;
|
|
--min_trimmed_reads=*)
|
|
[ -n "$VIASH_PAR_MIN_TRIMMED_READS" ] && ViashError Bad arguments for option \'--min_trimmed_reads=*\': \'$VIASH_PAR_MIN_TRIMMED_READS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_MIN_TRIMMED_READS=$(ViashRemoveFlags "$1")
|
|
shift 1
|
|
;;
|
|
--skip_trimming)
|
|
[ -n "$VIASH_PAR_SKIP_TRIMMING" ] && ViashError Bad arguments for option \'--skip_trimming\': \'$VIASH_PAR_SKIP_TRIMMING\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_SKIP_TRIMMING="$2"
|
|
[ $# -lt 2 ] && ViashError Not enough arguments passed to --skip_trimming. Use "--help" to get more information on the parameters. && exit 1
|
|
shift 2
|
|
;;
|
|
--skip_trimming=*)
|
|
[ -n "$VIASH_PAR_SKIP_TRIMMING" ] && ViashError Bad arguments for option \'--skip_trimming=*\': \'$VIASH_PAR_SKIP_TRIMMING\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_SKIP_TRIMMING=$(ViashRemoveFlags "$1")
|
|
shift 1
|
|
;;
|
|
--save_trimmed)
|
|
[ -n "$VIASH_PAR_SAVE_TRIMMED" ] && ViashError Bad arguments for option \'--save_trimmed\': \'$VIASH_PAR_SAVE_TRIMMED\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_SAVE_TRIMMED="$2"
|
|
[ $# -lt 2 ] && ViashError Not enough arguments passed to --save_trimmed. Use "--help" to get more information on the parameters. && exit 1
|
|
shift 2
|
|
;;
|
|
--save_trimmed=*)
|
|
[ -n "$VIASH_PAR_SAVE_TRIMMED" ] && ViashError Bad arguments for option \'--save_trimmed=*\': \'$VIASH_PAR_SAVE_TRIMMED\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_SAVE_TRIMMED=$(ViashRemoveFlags "$1")
|
|
shift 1
|
|
;;
|
|
--extra_salmon_quant_args)
|
|
[ -n "$VIASH_PAR_EXTRA_SALMON_QUANT_ARGS" ] && ViashError Bad arguments for option \'--extra_salmon_quant_args\': \'$VIASH_PAR_EXTRA_SALMON_QUANT_ARGS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_EXTRA_SALMON_QUANT_ARGS="$2"
|
|
[ $# -lt 2 ] && ViashError Not enough arguments passed to --extra_salmon_quant_args. Use "--help" to get more information on the parameters. && exit 1
|
|
shift 2
|
|
;;
|
|
--extra_salmon_quant_args=*)
|
|
[ -n "$VIASH_PAR_EXTRA_SALMON_QUANT_ARGS" ] && ViashError Bad arguments for option \'--extra_salmon_quant_args=*\': \'$VIASH_PAR_EXTRA_SALMON_QUANT_ARGS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_EXTRA_SALMON_QUANT_ARGS=$(ViashRemoveFlags "$1")
|
|
shift 1
|
|
;;
|
|
--skip_bbsplit)
|
|
[ -n "$VIASH_PAR_SKIP_BBSPLIT" ] && ViashError Bad arguments for option \'--skip_bbsplit\': \'$VIASH_PAR_SKIP_BBSPLIT\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_SKIP_BBSPLIT=true
|
|
shift 1
|
|
;;
|
|
--remove_ribo_rna)
|
|
[ -n "$VIASH_PAR_REMOVE_RIBO_RNA" ] && ViashError Bad arguments for option \'--remove_ribo_rna\': \'$VIASH_PAR_REMOVE_RIBO_RNA\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_REMOVE_RIBO_RNA=true
|
|
shift 1
|
|
;;
|
|
--extra_fq_subsample_args)
|
|
[ -n "$VIASH_PAR_EXTRA_FQ_SUBSAMPLE_ARGS" ] && ViashError Bad arguments for option \'--extra_fq_subsample_args\': \'$VIASH_PAR_EXTRA_FQ_SUBSAMPLE_ARGS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_EXTRA_FQ_SUBSAMPLE_ARGS="$2"
|
|
[ $# -lt 2 ] && ViashError Not enough arguments passed to --extra_fq_subsample_args. Use "--help" to get more information on the parameters. && exit 1
|
|
shift 2
|
|
;;
|
|
--extra_fq_subsample_args=*)
|
|
[ -n "$VIASH_PAR_EXTRA_FQ_SUBSAMPLE_ARGS" ] && ViashError Bad arguments for option \'--extra_fq_subsample_args=*\': \'$VIASH_PAR_EXTRA_FQ_SUBSAMPLE_ARGS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_EXTRA_FQ_SUBSAMPLE_ARGS=$(ViashRemoveFlags "$1")
|
|
shift 1
|
|
;;
|
|
--qc_output1)
|
|
[ -n "$VIASH_PAR_QC_OUTPUT1" ] && ViashError Bad arguments for option \'--qc_output1\': \'$VIASH_PAR_QC_OUTPUT1\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_QC_OUTPUT1="$2"
|
|
[ $# -lt 2 ] && ViashError Not enough arguments passed to --qc_output1. Use "--help" to get more information on the parameters. && exit 1
|
|
shift 2
|
|
;;
|
|
--qc_output1=*)
|
|
[ -n "$VIASH_PAR_QC_OUTPUT1" ] && ViashError Bad arguments for option \'--qc_output1=*\': \'$VIASH_PAR_QC_OUTPUT1\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_QC_OUTPUT1=$(ViashRemoveFlags "$1")
|
|
shift 1
|
|
;;
|
|
--qc_output2)
|
|
[ -n "$VIASH_PAR_QC_OUTPUT2" ] && ViashError Bad arguments for option \'--qc_output2\': \'$VIASH_PAR_QC_OUTPUT2\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_QC_OUTPUT2="$2"
|
|
[ $# -lt 2 ] && ViashError Not enough arguments passed to --qc_output2. Use "--help" to get more information on the parameters. && exit 1
|
|
shift 2
|
|
;;
|
|
--qc_output2=*)
|
|
[ -n "$VIASH_PAR_QC_OUTPUT2" ] && ViashError Bad arguments for option \'--qc_output2=*\': \'$VIASH_PAR_QC_OUTPUT2\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_QC_OUTPUT2=$(ViashRemoveFlags "$1")
|
|
shift 1
|
|
;;
|
|
--fastqc_html_1)
|
|
[ -n "$VIASH_PAR_FASTQC_HTML_1" ] && ViashError Bad arguments for option \'--fastqc_html_1\': \'$VIASH_PAR_FASTQC_HTML_1\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_FASTQC_HTML_1="$2"
|
|
[ $# -lt 2 ] && ViashError Not enough arguments passed to --fastqc_html_1. Use "--help" to get more information on the parameters. && exit 1
|
|
shift 2
|
|
;;
|
|
--fastqc_html_1=*)
|
|
[ -n "$VIASH_PAR_FASTQC_HTML_1" ] && ViashError Bad arguments for option \'--fastqc_html_1=*\': \'$VIASH_PAR_FASTQC_HTML_1\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_FASTQC_HTML_1=$(ViashRemoveFlags "$1")
|
|
shift 1
|
|
;;
|
|
--fastqc_html_2)
|
|
[ -n "$VIASH_PAR_FASTQC_HTML_2" ] && ViashError Bad arguments for option \'--fastqc_html_2\': \'$VIASH_PAR_FASTQC_HTML_2\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_FASTQC_HTML_2="$2"
|
|
[ $# -lt 2 ] && ViashError Not enough arguments passed to --fastqc_html_2. Use "--help" to get more information on the parameters. && exit 1
|
|
shift 2
|
|
;;
|
|
--fastqc_html_2=*)
|
|
[ -n "$VIASH_PAR_FASTQC_HTML_2" ] && ViashError Bad arguments for option \'--fastqc_html_2=*\': \'$VIASH_PAR_FASTQC_HTML_2\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_FASTQC_HTML_2=$(ViashRemoveFlags "$1")
|
|
shift 1
|
|
;;
|
|
--fastqc_zip_1)
|
|
[ -n "$VIASH_PAR_FASTQC_ZIP_1" ] && ViashError Bad arguments for option \'--fastqc_zip_1\': \'$VIASH_PAR_FASTQC_ZIP_1\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_FASTQC_ZIP_1="$2"
|
|
[ $# -lt 2 ] && ViashError Not enough arguments passed to --fastqc_zip_1. Use "--help" to get more information on the parameters. && exit 1
|
|
shift 2
|
|
;;
|
|
--fastqc_zip_1=*)
|
|
[ -n "$VIASH_PAR_FASTQC_ZIP_1" ] && ViashError Bad arguments for option \'--fastqc_zip_1=*\': \'$VIASH_PAR_FASTQC_ZIP_1\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_FASTQC_ZIP_1=$(ViashRemoveFlags "$1")
|
|
shift 1
|
|
;;
|
|
--fastqc_zip_2)
|
|
[ -n "$VIASH_PAR_FASTQC_ZIP_2" ] && ViashError Bad arguments for option \'--fastqc_zip_2\': \'$VIASH_PAR_FASTQC_ZIP_2\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_FASTQC_ZIP_2="$2"
|
|
[ $# -lt 2 ] && ViashError Not enough arguments passed to --fastqc_zip_2. Use "--help" to get more information on the parameters. && exit 1
|
|
shift 2
|
|
;;
|
|
--fastqc_zip_2=*)
|
|
[ -n "$VIASH_PAR_FASTQC_ZIP_2" ] && ViashError Bad arguments for option \'--fastqc_zip_2=*\': \'$VIASH_PAR_FASTQC_ZIP_2\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_FASTQC_ZIP_2=$(ViashRemoveFlags "$1")
|
|
shift 1
|
|
;;
|
|
--trim_log_1)
|
|
[ -n "$VIASH_PAR_TRIM_LOG_1" ] && ViashError Bad arguments for option \'--trim_log_1\': \'$VIASH_PAR_TRIM_LOG_1\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_TRIM_LOG_1="$2"
|
|
[ $# -lt 2 ] && ViashError Not enough arguments passed to --trim_log_1. Use "--help" to get more information on the parameters. && exit 1
|
|
shift 2
|
|
;;
|
|
--trim_log_1=*)
|
|
[ -n "$VIASH_PAR_TRIM_LOG_1" ] && ViashError Bad arguments for option \'--trim_log_1=*\': \'$VIASH_PAR_TRIM_LOG_1\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_TRIM_LOG_1=$(ViashRemoveFlags "$1")
|
|
shift 1
|
|
;;
|
|
--trim_log_2)
|
|
[ -n "$VIASH_PAR_TRIM_LOG_2" ] && ViashError Bad arguments for option \'--trim_log_2\': \'$VIASH_PAR_TRIM_LOG_2\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_TRIM_LOG_2="$2"
|
|
[ $# -lt 2 ] && ViashError Not enough arguments passed to --trim_log_2. Use "--help" to get more information on the parameters. && exit 1
|
|
shift 2
|
|
;;
|
|
--trim_log_2=*)
|
|
[ -n "$VIASH_PAR_TRIM_LOG_2" ] && ViashError Bad arguments for option \'--trim_log_2=*\': \'$VIASH_PAR_TRIM_LOG_2\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_TRIM_LOG_2=$(ViashRemoveFlags "$1")
|
|
shift 1
|
|
;;
|
|
--trim_html_1)
|
|
[ -n "$VIASH_PAR_TRIM_HTML_1" ] && ViashError Bad arguments for option \'--trim_html_1\': \'$VIASH_PAR_TRIM_HTML_1\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_TRIM_HTML_1="$2"
|
|
[ $# -lt 2 ] && ViashError Not enough arguments passed to --trim_html_1. Use "--help" to get more information on the parameters. && exit 1
|
|
shift 2
|
|
;;
|
|
--trim_html_1=*)
|
|
[ -n "$VIASH_PAR_TRIM_HTML_1" ] && ViashError Bad arguments for option \'--trim_html_1=*\': \'$VIASH_PAR_TRIM_HTML_1\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_TRIM_HTML_1=$(ViashRemoveFlags "$1")
|
|
shift 1
|
|
;;
|
|
--trim_html_2)
|
|
[ -n "$VIASH_PAR_TRIM_HTML_2" ] && ViashError Bad arguments for option \'--trim_html_2\': \'$VIASH_PAR_TRIM_HTML_2\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_TRIM_HTML_2="$2"
|
|
[ $# -lt 2 ] && ViashError Not enough arguments passed to --trim_html_2. Use "--help" to get more information on the parameters. && exit 1
|
|
shift 2
|
|
;;
|
|
--trim_html_2=*)
|
|
[ -n "$VIASH_PAR_TRIM_HTML_2" ] && ViashError Bad arguments for option \'--trim_html_2=*\': \'$VIASH_PAR_TRIM_HTML_2\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_TRIM_HTML_2=$(ViashRemoveFlags "$1")
|
|
shift 1
|
|
;;
|
|
--trim_zip_1)
|
|
[ -n "$VIASH_PAR_TRIM_ZIP_1" ] && ViashError Bad arguments for option \'--trim_zip_1\': \'$VIASH_PAR_TRIM_ZIP_1\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_TRIM_ZIP_1="$2"
|
|
[ $# -lt 2 ] && ViashError Not enough arguments passed to --trim_zip_1. Use "--help" to get more information on the parameters. && exit 1
|
|
shift 2
|
|
;;
|
|
--trim_zip_1=*)
|
|
[ -n "$VIASH_PAR_TRIM_ZIP_1" ] && ViashError Bad arguments for option \'--trim_zip_1=*\': \'$VIASH_PAR_TRIM_ZIP_1\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_TRIM_ZIP_1=$(ViashRemoveFlags "$1")
|
|
shift 1
|
|
;;
|
|
--trim_zip_2)
|
|
[ -n "$VIASH_PAR_TRIM_ZIP_2" ] && ViashError Bad arguments for option \'--trim_zip_2\': \'$VIASH_PAR_TRIM_ZIP_2\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_TRIM_ZIP_2="$2"
|
|
[ $# -lt 2 ] && ViashError Not enough arguments passed to --trim_zip_2. Use "--help" to get more information on the parameters. && exit 1
|
|
shift 2
|
|
;;
|
|
--trim_zip_2=*)
|
|
[ -n "$VIASH_PAR_TRIM_ZIP_2" ] && ViashError Bad arguments for option \'--trim_zip_2=*\': \'$VIASH_PAR_TRIM_ZIP_2\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_TRIM_ZIP_2=$(ViashRemoveFlags "$1")
|
|
shift 1
|
|
;;
|
|
--sortmerna_log)
|
|
[ -n "$VIASH_PAR_SORTMERNA_LOG" ] && ViashError Bad arguments for option \'--sortmerna_log\': \'$VIASH_PAR_SORTMERNA_LOG\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_SORTMERNA_LOG="$2"
|
|
[ $# -lt 2 ] && ViashError Not enough arguments passed to --sortmerna_log. Use "--help" to get more information on the parameters. && exit 1
|
|
shift 2
|
|
;;
|
|
--sortmerna_log=*)
|
|
[ -n "$VIASH_PAR_SORTMERNA_LOG" ] && ViashError Bad arguments for option \'--sortmerna_log=*\': \'$VIASH_PAR_SORTMERNA_LOG\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_SORTMERNA_LOG=$(ViashRemoveFlags "$1")
|
|
shift 1
|
|
;;
|
|
--salmon_quant_output)
|
|
[ -n "$VIASH_PAR_SALMON_QUANT_OUTPUT" ] && ViashError Bad arguments for option \'--salmon_quant_output\': \'$VIASH_PAR_SALMON_QUANT_OUTPUT\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_SALMON_QUANT_OUTPUT="$2"
|
|
[ $# -lt 2 ] && ViashError Not enough arguments passed to --salmon_quant_output. Use "--help" to get more information on the parameters. && exit 1
|
|
shift 2
|
|
;;
|
|
--salmon_quant_output=*)
|
|
[ -n "$VIASH_PAR_SALMON_QUANT_OUTPUT" ] && ViashError Bad arguments for option \'--salmon_quant_output=*\': \'$VIASH_PAR_SALMON_QUANT_OUTPUT\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_SALMON_QUANT_OUTPUT=$(ViashRemoveFlags "$1")
|
|
shift 1
|
|
;;
|
|
--trim_json)
|
|
[ -n "$VIASH_PAR_TRIM_JSON" ] && ViashError Bad arguments for option \'--trim_json\': \'$VIASH_PAR_TRIM_JSON\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_TRIM_JSON="$2"
|
|
[ $# -lt 2 ] && ViashError Not enough arguments passed to --trim_json. Use "--help" to get more information on the parameters. && exit 1
|
|
shift 2
|
|
;;
|
|
--trim_json=*)
|
|
[ -n "$VIASH_PAR_TRIM_JSON" ] && ViashError Bad arguments for option \'--trim_json=*\': \'$VIASH_PAR_TRIM_JSON\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_TRIM_JSON=$(ViashRemoveFlags "$1")
|
|
shift 1
|
|
;;
|
|
--trim_html)
|
|
[ -n "$VIASH_PAR_TRIM_HTML" ] && ViashError Bad arguments for option \'--trim_html\': \'$VIASH_PAR_TRIM_HTML\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_TRIM_HTML="$2"
|
|
[ $# -lt 2 ] && ViashError Not enough arguments passed to --trim_html. Use "--help" to get more information on the parameters. && exit 1
|
|
shift 2
|
|
;;
|
|
--trim_html=*)
|
|
[ -n "$VIASH_PAR_TRIM_HTML" ] && ViashError Bad arguments for option \'--trim_html=*\': \'$VIASH_PAR_TRIM_HTML\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_TRIM_HTML=$(ViashRemoveFlags "$1")
|
|
shift 1
|
|
;;
|
|
--merged_out)
|
|
[ -n "$VIASH_PAR_MERGED_OUT" ] && ViashError Bad arguments for option \'--merged_out\': \'$VIASH_PAR_MERGED_OUT\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_MERGED_OUT="$2"
|
|
[ $# -lt 2 ] && ViashError Not enough arguments passed to --merged_out. Use "--help" to get more information on the parameters. && exit 1
|
|
shift 2
|
|
;;
|
|
--merged_out=*)
|
|
[ -n "$VIASH_PAR_MERGED_OUT" ] && ViashError Bad arguments for option \'--merged_out=*\': \'$VIASH_PAR_MERGED_OUT\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_MERGED_OUT=$(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_FASTQ_1+x} ]; then
|
|
ViashError '--fastq_1' 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_SKIP_FASTQC+x} ]; then
|
|
VIASH_PAR_SKIP_FASTQC="false"
|
|
fi
|
|
if [ -z ${VIASH_PAR_WITH_UMI+x} ]; then
|
|
VIASH_PAR_WITH_UMI="false"
|
|
fi
|
|
if [ -z ${VIASH_PAR_SKIP_UMI_EXTRACT+x} ]; then
|
|
VIASH_PAR_SKIP_UMI_EXTRACT="false"
|
|
fi
|
|
if [ -z ${VIASH_PAR_UMITOOLS_EXTRACT_METHOD+x} ]; then
|
|
VIASH_PAR_UMITOOLS_EXTRACT_METHOD="string"
|
|
fi
|
|
if [ -z ${VIASH_PAR_UMITOOLS_BC_PATTERN+x} ]; then
|
|
VIASH_PAR_UMITOOLS_BC_PATTERN=""
|
|
fi
|
|
if [ -z ${VIASH_PAR_UMITOOLS_BC_PATTERN2+x} ]; then
|
|
VIASH_PAR_UMITOOLS_BC_PATTERN2=""
|
|
fi
|
|
if [ -z ${VIASH_PAR_UMI_DISCARD_READ+x} ]; then
|
|
VIASH_PAR_UMI_DISCARD_READ="0"
|
|
fi
|
|
if [ -z ${VIASH_PAR_UMITOOLS_UMI_SEPARATOR+x} ]; then
|
|
VIASH_PAR_UMITOOLS_UMI_SEPARATOR="_"
|
|
fi
|
|
if [ -z ${VIASH_PAR_UMITOOLS_GROUPING_METHOD+x} ]; then
|
|
VIASH_PAR_UMITOOLS_GROUPING_METHOD="directional"
|
|
fi
|
|
if [ -z ${VIASH_PAR_SAVE_UMI_INTERMEDS+x} ]; then
|
|
VIASH_PAR_SAVE_UMI_INTERMEDS="false"
|
|
fi
|
|
if [ -z ${VIASH_PAR_TRIMMER+x} ]; then
|
|
VIASH_PAR_TRIMMER="trimgalore"
|
|
fi
|
|
if [ -z ${VIASH_PAR_MIN_TRIMMED_READS+x} ]; then
|
|
VIASH_PAR_MIN_TRIMMED_READS="10000"
|
|
fi
|
|
if [ -z ${VIASH_PAR_SKIP_TRIMMING+x} ]; then
|
|
VIASH_PAR_SKIP_TRIMMING="false"
|
|
fi
|
|
if [ -z ${VIASH_PAR_SAVE_TRIMMED+x} ]; then
|
|
VIASH_PAR_SAVE_TRIMMED="false"
|
|
fi
|
|
if [ -z ${VIASH_PAR_EXTRA_SALMON_QUANT_ARGS+x} ]; then
|
|
VIASH_PAR_EXTRA_SALMON_QUANT_ARGS=""
|
|
fi
|
|
if [ -z ${VIASH_PAR_SKIP_BBSPLIT+x} ]; then
|
|
VIASH_PAR_SKIP_BBSPLIT="false"
|
|
fi
|
|
if [ -z ${VIASH_PAR_REMOVE_RIBO_RNA+x} ]; then
|
|
VIASH_PAR_REMOVE_RIBO_RNA="false"
|
|
fi
|
|
if [ -z ${VIASH_PAR_EXTRA_FQ_SUBSAMPLE_ARGS+x} ]; then
|
|
VIASH_PAR_EXTRA_FQ_SUBSAMPLE_ARGS="--record-count 1000000 --seed 1"
|
|
fi
|
|
if [ -z ${VIASH_PAR_QC_OUTPUT1+x} ]; then
|
|
VIASH_PAR_QC_OUTPUT1="\$id.read_1.fastq"
|
|
fi
|
|
if [ -z ${VIASH_PAR_QC_OUTPUT2+x} ]; then
|
|
VIASH_PAR_QC_OUTPUT2="\$id.read_2.fastq"
|
|
fi
|
|
if [ -z ${VIASH_PAR_FASTQC_HTML_1+x} ]; then
|
|
VIASH_PAR_FASTQC_HTML_1="\$id.read_1.fastqc.html"
|
|
fi
|
|
if [ -z ${VIASH_PAR_FASTQC_HTML_2+x} ]; then
|
|
VIASH_PAR_FASTQC_HTML_2="\$id.read_2.fastqc.html"
|
|
fi
|
|
if [ -z ${VIASH_PAR_FASTQC_ZIP_1+x} ]; then
|
|
VIASH_PAR_FASTQC_ZIP_1="\$id.read_1.fastqc.zip"
|
|
fi
|
|
if [ -z ${VIASH_PAR_FASTQC_ZIP_2+x} ]; then
|
|
VIASH_PAR_FASTQC_ZIP_2="\$id.read_2.fastqc.zip"
|
|
fi
|
|
if [ -z ${VIASH_PAR_TRIM_LOG_1+x} ]; then
|
|
VIASH_PAR_TRIM_LOG_1="\$id.read_1.trimming_report.txt"
|
|
fi
|
|
if [ -z ${VIASH_PAR_TRIM_LOG_2+x} ]; then
|
|
VIASH_PAR_TRIM_LOG_2="\$id.read_2.trimming_report.txt"
|
|
fi
|
|
if [ -z ${VIASH_PAR_TRIM_HTML_1+x} ]; then
|
|
VIASH_PAR_TRIM_HTML_1="\$id.read_1.trimmed_fastqc.html"
|
|
fi
|
|
if [ -z ${VIASH_PAR_TRIM_HTML_2+x} ]; then
|
|
VIASH_PAR_TRIM_HTML_2="\$id.read_2.trimmed_fastqc.html"
|
|
fi
|
|
if [ -z ${VIASH_PAR_TRIM_ZIP_1+x} ]; then
|
|
VIASH_PAR_TRIM_ZIP_1="\$id.read_1.trimmed_fastqc.zip"
|
|
fi
|
|
if [ -z ${VIASH_PAR_TRIM_ZIP_2+x} ]; then
|
|
VIASH_PAR_TRIM_ZIP_2="\$id.read_2.trimmed_fastqc.zip"
|
|
fi
|
|
if [ -z ${VIASH_PAR_SORTMERNA_LOG+x} ]; then
|
|
VIASH_PAR_SORTMERNA_LOG="\$id.sortmerna.log"
|
|
fi
|
|
if [ -z ${VIASH_PAR_SALMON_QUANT_OUTPUT+x} ]; then
|
|
VIASH_PAR_SALMON_QUANT_OUTPUT="\$id.salmon_quant_output"
|
|
fi
|
|
if [ -z ${VIASH_PAR_TRIM_JSON+x} ]; then
|
|
VIASH_PAR_TRIM_JSON="\$id.fastp_out.json"
|
|
fi
|
|
if [ -z ${VIASH_PAR_TRIM_HTML+x} ]; then
|
|
VIASH_PAR_TRIM_HTML="\$id.fastp_out.html"
|
|
fi
|
|
|
|
# check whether required files exist
|
|
if [ ! -z "$VIASH_PAR_FASTQ_1" ] && [ ! -e "$VIASH_PAR_FASTQ_1" ]; then
|
|
ViashError "Input file '$VIASH_PAR_FASTQ_1' does not exist."
|
|
exit 1
|
|
fi
|
|
if [ ! -z "$VIASH_PAR_BBSPLIT_INDEX" ] && [ ! -e "$VIASH_PAR_BBSPLIT_INDEX" ]; then
|
|
ViashError "Input file '$VIASH_PAR_BBSPLIT_INDEX' does not exist."
|
|
exit 1
|
|
fi
|
|
if [ ! -z "$VIASH_PAR_BBSPLIT_FASTA_LIST" ] && [ ! -e "$VIASH_PAR_BBSPLIT_FASTA_LIST" ]; then
|
|
ViashError "Input file '$VIASH_PAR_BBSPLIT_FASTA_LIST' does not exist."
|
|
exit 1
|
|
fi
|
|
if [ ! -z "$VIASH_PAR_RIBO_DATABASE_MANIFEST" ] && [ ! -e "$VIASH_PAR_RIBO_DATABASE_MANIFEST" ]; then
|
|
ViashError "Input file '$VIASH_PAR_RIBO_DATABASE_MANIFEST' does not exist."
|
|
exit 1
|
|
fi
|
|
if [ ! -z "$VIASH_PAR_TRANSCRIPT_FASTA" ] && [ ! -e "$VIASH_PAR_TRANSCRIPT_FASTA" ]; then
|
|
ViashError "Input file '$VIASH_PAR_TRANSCRIPT_FASTA' 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_SALMON_INDEX" ] && [ ! -e "$VIASH_PAR_SALMON_INDEX" ]; then
|
|
ViashError "Input file '$VIASH_PAR_SALMON_INDEX' does not exist."
|
|
exit 1
|
|
fi
|
|
|
|
# check whether parameters values are of the right type
|
|
if [[ -n "$VIASH_PAR_NUM_TRIMMED_READS" ]]; then
|
|
if ! [[ "$VIASH_PAR_NUM_TRIMMED_READS" =~ ^[-+]?[0-9]+$ ]]; then
|
|
ViashError '--num_trimmed_reads' has to be an integer. 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 "$VIASH_PAR_SKIP_FASTQC" ]]; then
|
|
if ! [[ "$VIASH_PAR_SKIP_FASTQC" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then
|
|
ViashError '--skip_fastqc' has to be a boolean. 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 "$VIASH_PAR_SKIP_UMI_EXTRACT" ]]; then
|
|
if ! [[ "$VIASH_PAR_SKIP_UMI_EXTRACT" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then
|
|
ViashError '--skip_umi_extract' has to be a boolean. Use "--help" to get more information on the parameters.
|
|
exit 1
|
|
fi
|
|
fi
|
|
if [[ -n "$VIASH_PAR_UMI_DISCARD_READ" ]]; then
|
|
if ! [[ "$VIASH_PAR_UMI_DISCARD_READ" =~ ^[-+]?[0-9]+$ ]]; then
|
|
ViashError '--umi_discard_read' has to be an integer. Use "--help" to get more information on the parameters.
|
|
exit 1
|
|
fi
|
|
fi
|
|
if [[ -n "$VIASH_PAR_SAVE_UMI_INTERMEDS" ]]; then
|
|
if ! [[ "$VIASH_PAR_SAVE_UMI_INTERMEDS" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then
|
|
ViashError '--save_umi_intermeds' has to be a boolean. Use "--help" to get more information on the parameters.
|
|
exit 1
|
|
fi
|
|
fi
|
|
if [[ -n "$VIASH_PAR_MIN_TRIMMED_READS" ]]; then
|
|
if ! [[ "$VIASH_PAR_MIN_TRIMMED_READS" =~ ^[-+]?[0-9]+$ ]]; then
|
|
ViashError '--min_trimmed_reads' has to be an integer. Use "--help" to get more information on the parameters.
|
|
exit 1
|
|
fi
|
|
fi
|
|
if [[ -n "$VIASH_PAR_SKIP_TRIMMING" ]]; then
|
|
if ! [[ "$VIASH_PAR_SKIP_TRIMMING" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then
|
|
ViashError '--skip_trimming' has to be a boolean. Use "--help" to get more information on the parameters.
|
|
exit 1
|
|
fi
|
|
fi
|
|
if [[ -n "$VIASH_PAR_SAVE_TRIMMED" ]]; then
|
|
if ! [[ "$VIASH_PAR_SAVE_TRIMMED" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then
|
|
ViashError '--save_trimmed' has to be a boolean. Use "--help" to get more information on the parameters.
|
|
exit 1
|
|
fi
|
|
fi
|
|
if [[ -n "$VIASH_PAR_SKIP_BBSPLIT" ]]; then
|
|
if ! [[ "$VIASH_PAR_SKIP_BBSPLIT" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then
|
|
ViashError '--skip_bbsplit' has to be a boolean_true. Use "--help" to get more information on the parameters.
|
|
exit 1
|
|
fi
|
|
fi
|
|
if [[ -n "$VIASH_PAR_REMOVE_RIBO_RNA" ]]; then
|
|
if ! [[ "$VIASH_PAR_REMOVE_RIBO_RNA" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then
|
|
ViashError '--remove_ribo_rna' has to be a boolean_true. Use "--help" to get more information on the parameters.
|
|
exit 1
|
|
fi
|
|
fi
|
|
if [[ -n "$VIASH_META_CPUS" ]]; then
|
|
if ! [[ "$VIASH_META_CPUS" =~ ^[-+]?[0-9]+$ ]]; then
|
|
ViashError 'cpus' has to be an integer. Use "--help" to get more information on the parameters.
|
|
exit 1
|
|
fi
|
|
fi
|
|
if [[ -n "$VIASH_META_MEMORY_B" ]]; then
|
|
if ! [[ "$VIASH_META_MEMORY_B" =~ ^[-+]?[0-9]+$ ]]; then
|
|
ViashError 'memory_b' has to be a long. Use "--help" to get more information on the parameters.
|
|
exit 1
|
|
fi
|
|
fi
|
|
if [[ -n "$VIASH_META_MEMORY_KB" ]]; then
|
|
if ! [[ "$VIASH_META_MEMORY_KB" =~ ^[-+]?[0-9]+$ ]]; then
|
|
ViashError 'memory_kb' has to be a long. Use "--help" to get more information on the parameters.
|
|
exit 1
|
|
fi
|
|
fi
|
|
if [[ -n "$VIASH_META_MEMORY_MB" ]]; then
|
|
if ! [[ "$VIASH_META_MEMORY_MB" =~ ^[-+]?[0-9]+$ ]]; then
|
|
ViashError 'memory_mb' has to be a long. Use "--help" to get more information on the parameters.
|
|
exit 1
|
|
fi
|
|
fi
|
|
if [[ -n "$VIASH_META_MEMORY_GB" ]]; then
|
|
if ! [[ "$VIASH_META_MEMORY_GB" =~ ^[-+]?[0-9]+$ ]]; then
|
|
ViashError 'memory_gb' has to be a long. Use "--help" to get more information on the parameters.
|
|
exit 1
|
|
fi
|
|
fi
|
|
if [[ -n "$VIASH_META_MEMORY_TB" ]]; then
|
|
if ! [[ "$VIASH_META_MEMORY_TB" =~ ^[-+]?[0-9]+$ ]]; then
|
|
ViashError 'memory_tb' has to be a long. Use "--help" to get more information on the parameters.
|
|
exit 1
|
|
fi
|
|
fi
|
|
if [[ -n "$VIASH_META_MEMORY_PB" ]]; then
|
|
if ! [[ "$VIASH_META_MEMORY_PB" =~ ^[-+]?[0-9]+$ ]]; then
|
|
ViashError 'memory_pb' has to be a long. Use "--help" to get more information on the parameters.
|
|
exit 1
|
|
fi
|
|
fi
|
|
if [[ -n "$VIASH_META_MEMORY_KIB" ]]; then
|
|
if ! [[ "$VIASH_META_MEMORY_KIB" =~ ^[-+]?[0-9]+$ ]]; then
|
|
ViashError 'memory_kib' has to be a long. Use "--help" to get more information on the parameters.
|
|
exit 1
|
|
fi
|
|
fi
|
|
if [[ -n "$VIASH_META_MEMORY_MIB" ]]; then
|
|
if ! [[ "$VIASH_META_MEMORY_MIB" =~ ^[-+]?[0-9]+$ ]]; then
|
|
ViashError 'memory_mib' has to be a long. Use "--help" to get more information on the parameters.
|
|
exit 1
|
|
fi
|
|
fi
|
|
if [[ -n "$VIASH_META_MEMORY_GIB" ]]; then
|
|
if ! [[ "$VIASH_META_MEMORY_GIB" =~ ^[-+]?[0-9]+$ ]]; then
|
|
ViashError 'memory_gib' has to be a long. Use "--help" to get more information on the parameters.
|
|
exit 1
|
|
fi
|
|
fi
|
|
if [[ -n "$VIASH_META_MEMORY_TIB" ]]; then
|
|
if ! [[ "$VIASH_META_MEMORY_TIB" =~ ^[-+]?[0-9]+$ ]]; then
|
|
ViashError 'memory_tib' has to be a long. Use "--help" to get more information on the parameters.
|
|
exit 1
|
|
fi
|
|
fi
|
|
if [[ -n "$VIASH_META_MEMORY_PIB" ]]; then
|
|
if ! [[ "$VIASH_META_MEMORY_PIB" =~ ^[-+]?[0-9]+$ ]]; then
|
|
ViashError 'memory_pib' has to be a long. Use "--help" to get more information on the parameters.
|
|
exit 1
|
|
fi
|
|
fi
|
|
|
|
# check whether value is belongs to a set of choices
|
|
if [ ! -z "$VIASH_PAR_UMITOOLS_EXTRACT_METHOD" ]; then
|
|
VIASH_PAR_UMITOOLS_EXTRACT_METHOD_CHOICES=("string;regex")
|
|
IFS=';'
|
|
set -f
|
|
if ! [[ ";${VIASH_PAR_UMITOOLS_EXTRACT_METHOD_CHOICES[*]};" =~ ";$VIASH_PAR_UMITOOLS_EXTRACT_METHOD;" ]]; then
|
|
ViashError '--umitools_extract_method' specified value of \'$VIASH_PAR_UMITOOLS_EXTRACT_METHOD\' is not in the list of allowed values. Use "--help" to get more information on the parameters.
|
|
exit 1
|
|
fi
|
|
set +f
|
|
unset IFS
|
|
fi
|
|
|
|
if [ ! -z "$VIASH_PAR_UMI_DISCARD_READ" ]; then
|
|
VIASH_PAR_UMI_DISCARD_READ_CHOICES=("0;1;2")
|
|
IFS=';'
|
|
set -f
|
|
if ! [[ ";${VIASH_PAR_UMI_DISCARD_READ_CHOICES[*]};" =~ ";$VIASH_PAR_UMI_DISCARD_READ;" ]]; then
|
|
ViashError '--umi_discard_read' specified value of \'$VIASH_PAR_UMI_DISCARD_READ\' is not in the list of allowed values. Use "--help" to get more information on the parameters.
|
|
exit 1
|
|
fi
|
|
set +f
|
|
unset IFS
|
|
fi
|
|
|
|
if [ ! -z "$VIASH_PAR_UMITOOLS_GROUPING_METHOD" ]; then
|
|
VIASH_PAR_UMITOOLS_GROUPING_METHOD_CHOICES=("unique;percentile;cluster;adjacency;directional")
|
|
IFS=';'
|
|
set -f
|
|
if ! [[ ";${VIASH_PAR_UMITOOLS_GROUPING_METHOD_CHOICES[*]};" =~ ";$VIASH_PAR_UMITOOLS_GROUPING_METHOD;" ]]; then
|
|
ViashError '--umitools_grouping_method' specified value of \'$VIASH_PAR_UMITOOLS_GROUPING_METHOD\' is not in the list of allowed values. Use "--help" to get more information on the parameters.
|
|
exit 1
|
|
fi
|
|
set +f
|
|
unset IFS
|
|
fi
|
|
|
|
if [ ! -z "$VIASH_PAR_TRIMMER" ]; then
|
|
VIASH_PAR_TRIMMER_CHOICES=("trimgalore;fastp")
|
|
IFS=';'
|
|
set -f
|
|
if ! [[ ";${VIASH_PAR_TRIMMER_CHOICES[*]};" =~ ";$VIASH_PAR_TRIMMER;" ]]; then
|
|
ViashError '--trimmer' specified value of \'$VIASH_PAR_TRIMMER\' is not in the list of allowed values. Use "--help" to get more information on the parameters.
|
|
exit 1
|
|
fi
|
|
set +f
|
|
unset IFS
|
|
fi
|
|
|
|
# create parent directories of output files, if so desired
|
|
if [ ! -z "$VIASH_PAR_QC_OUTPUT1" ] && [ ! -d "$(dirname "$VIASH_PAR_QC_OUTPUT1")" ]; then
|
|
mkdir -p "$(dirname "$VIASH_PAR_QC_OUTPUT1")"
|
|
fi
|
|
if [ ! -z "$VIASH_PAR_QC_OUTPUT2" ] && [ ! -d "$(dirname "$VIASH_PAR_QC_OUTPUT2")" ]; then
|
|
mkdir -p "$(dirname "$VIASH_PAR_QC_OUTPUT2")"
|
|
fi
|
|
if [ ! -z "$VIASH_PAR_FASTQC_HTML_1" ] && [ ! -d "$(dirname "$VIASH_PAR_FASTQC_HTML_1")" ]; then
|
|
mkdir -p "$(dirname "$VIASH_PAR_FASTQC_HTML_1")"
|
|
fi
|
|
if [ ! -z "$VIASH_PAR_FASTQC_HTML_2" ] && [ ! -d "$(dirname "$VIASH_PAR_FASTQC_HTML_2")" ]; then
|
|
mkdir -p "$(dirname "$VIASH_PAR_FASTQC_HTML_2")"
|
|
fi
|
|
if [ ! -z "$VIASH_PAR_FASTQC_ZIP_1" ] && [ ! -d "$(dirname "$VIASH_PAR_FASTQC_ZIP_1")" ]; then
|
|
mkdir -p "$(dirname "$VIASH_PAR_FASTQC_ZIP_1")"
|
|
fi
|
|
if [ ! -z "$VIASH_PAR_FASTQC_ZIP_2" ] && [ ! -d "$(dirname "$VIASH_PAR_FASTQC_ZIP_2")" ]; then
|
|
mkdir -p "$(dirname "$VIASH_PAR_FASTQC_ZIP_2")"
|
|
fi
|
|
if [ ! -z "$VIASH_PAR_TRIM_LOG_1" ] && [ ! -d "$(dirname "$VIASH_PAR_TRIM_LOG_1")" ]; then
|
|
mkdir -p "$(dirname "$VIASH_PAR_TRIM_LOG_1")"
|
|
fi
|
|
if [ ! -z "$VIASH_PAR_TRIM_LOG_2" ] && [ ! -d "$(dirname "$VIASH_PAR_TRIM_LOG_2")" ]; then
|
|
mkdir -p "$(dirname "$VIASH_PAR_TRIM_LOG_2")"
|
|
fi
|
|
if [ ! -z "$VIASH_PAR_TRIM_HTML_1" ] && [ ! -d "$(dirname "$VIASH_PAR_TRIM_HTML_1")" ]; then
|
|
mkdir -p "$(dirname "$VIASH_PAR_TRIM_HTML_1")"
|
|
fi
|
|
if [ ! -z "$VIASH_PAR_TRIM_HTML_2" ] && [ ! -d "$(dirname "$VIASH_PAR_TRIM_HTML_2")" ]; then
|
|
mkdir -p "$(dirname "$VIASH_PAR_TRIM_HTML_2")"
|
|
fi
|
|
if [ ! -z "$VIASH_PAR_TRIM_ZIP_1" ] && [ ! -d "$(dirname "$VIASH_PAR_TRIM_ZIP_1")" ]; then
|
|
mkdir -p "$(dirname "$VIASH_PAR_TRIM_ZIP_1")"
|
|
fi
|
|
if [ ! -z "$VIASH_PAR_TRIM_ZIP_2" ] && [ ! -d "$(dirname "$VIASH_PAR_TRIM_ZIP_2")" ]; then
|
|
mkdir -p "$(dirname "$VIASH_PAR_TRIM_ZIP_2")"
|
|
fi
|
|
if [ ! -z "$VIASH_PAR_SORTMERNA_LOG" ] && [ ! -d "$(dirname "$VIASH_PAR_SORTMERNA_LOG")" ]; then
|
|
mkdir -p "$(dirname "$VIASH_PAR_SORTMERNA_LOG")"
|
|
fi
|
|
if [ ! -z "$VIASH_PAR_SALMON_QUANT_OUTPUT" ] && [ ! -d "$(dirname "$VIASH_PAR_SALMON_QUANT_OUTPUT")" ]; then
|
|
mkdir -p "$(dirname "$VIASH_PAR_SALMON_QUANT_OUTPUT")"
|
|
fi
|
|
if [ ! -z "$VIASH_PAR_TRIM_JSON" ] && [ ! -d "$(dirname "$VIASH_PAR_TRIM_JSON")" ]; then
|
|
mkdir -p "$(dirname "$VIASH_PAR_TRIM_JSON")"
|
|
fi
|
|
if [ ! -z "$VIASH_PAR_TRIM_HTML" ] && [ ! -d "$(dirname "$VIASH_PAR_TRIM_HTML")" ]; then
|
|
mkdir -p "$(dirname "$VIASH_PAR_TRIM_HTML")"
|
|
fi
|
|
if [ ! -z "$VIASH_PAR_MERGED_OUT" ] && [ ! -d "$(dirname "$VIASH_PAR_MERGED_OUT")" ]; then
|
|
mkdir -p "$(dirname "$VIASH_PAR_MERGED_OUT")"
|
|
fi
|
|
|
|
if [ "$VIASH_ENGINE_ID" == "native" ] ; then
|
|
if [ "$VIASH_MODE" == "run" ]; then
|
|
VIASH_CMD="bash"
|
|
else
|
|
ViashError "Engine '$VIASH_ENGINE_ID' does not support mode '$VIASH_MODE'."
|
|
exit 1
|
|
fi
|
|
fi
|
|
|
|
|
|
# set dependency paths
|
|
VIASH_DEP_FASTQC="$VIASH_META_RESOURCES_DIR/../../../nextflow/fastqc/main.nf"
|
|
VIASH_DEP_UMITOOLS_UMITOOLS_EXTRACT="$VIASH_META_RESOURCES_DIR/../../../nextflow/umitools/umitools_extract/main.nf"
|
|
VIASH_DEP_TRIMGALORE="$VIASH_META_RESOURCES_DIR/../../../nextflow/trimgalore/main.nf"
|
|
VIASH_DEP_BBMAP_BBSPLIT="$VIASH_META_RESOURCES_DIR/../../../nextflow/bbmap_bbsplit/main.nf"
|
|
VIASH_DEP_SORTMERNA="$VIASH_META_RESOURCES_DIR/../../../nextflow/sortmerna/main.nf"
|
|
VIASH_DEP_FQ_SUBSAMPLE="$VIASH_META_RESOURCES_DIR/../../../nextflow/fq_subsample/main.nf"
|
|
VIASH_DEP_UMI_TOOLS_UMI_TOOLS_EXTRACT="$VIASH_TARGET_DIR/dependencies/vsh/vsh/biobox/main/nextflow/umi_tools/umi_tools_extract/main.nf"
|
|
VIASH_DEP_FASTP="$VIASH_TARGET_DIR/dependencies/vsh/vsh/biobox/main/nextflow/fastp/main.nf"
|
|
VIASH_DEP_SALMON_SALMON_QUANT="$VIASH_TARGET_DIR/dependencies/vsh/vsh/biobox/main/nextflow/salmon/salmon_quant/main.nf"
|
|
|
|
ViashDebug "Running command: $(echo $VIASH_CMD)"
|
|
cat << VIASHEOF | eval $VIASH_CMD
|
|
set -e
|
|
tempscript=\$(mktemp "$VIASH_META_TEMP_DIR/viash-run-pre_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
|
|
workflow run_wf {
|
|
|
|
take:
|
|
input_ch
|
|
|
|
main:
|
|
output_ch = input_ch
|
|
|
|
| map { id, state ->
|
|
def input = state.fastq_2 ? [ state.fastq_1, state.fastq_2 ] : [ state.fastq_1 ]
|
|
def paired = input.size() == 2
|
|
[ id, state + [paired: paired, input: input] ]
|
|
}
|
|
|
|
// Perform QC on input fastq files
|
|
| fastqc.run (
|
|
runIf: { id, state -> !state.skip_qc && !state.skip_fastqc },
|
|
fromState: { id, state ->
|
|
def input = state.paired ? [ state.fastq_1, state.fastq_2 ] : [ state.fastq_1 ]
|
|
[ paired: state.paired,
|
|
input: input ]
|
|
},
|
|
toState: [
|
|
"fastqc_html_1": "fastqc_html_1",
|
|
"fastqc_html_2": "fastqc_html_2",
|
|
"fastqc_zip_1": "fastqc_zip_1",
|
|
"fastqc_zip_2": "fastqc_zip_2"
|
|
]
|
|
)
|
|
|
|
// Extract UMIs from fastq files and discard read 1 or read 2 if required
|
|
| umitools_extract.run (
|
|
runIf: { id, state -> state.with_umi && !state.skip_umi_extract },
|
|
fromState: { id, state ->
|
|
def input = state.paired ? [ state.fastq_1, state.fastq_2 ] : [ state.fastq_1 ]
|
|
def bc_pattern = state.paired ? [ state.umitools_bc_pattern, state.umitools_bc_pattern2 ] : [ state.umitools_bc_pattern ]
|
|
[ paired: state.paired,
|
|
input: input,
|
|
bc_pattern: bc_pattern,
|
|
umi_discard_read: state.umi_discard_read ]
|
|
},
|
|
toState: [
|
|
"fastq_1": "fastq_1",
|
|
"fastq_2": "fastq_2"
|
|
]
|
|
)
|
|
|
|
// Discard read if required
|
|
| map { id, state ->
|
|
def paired = state.paired
|
|
def fastq_2 = state.fastq_2
|
|
if (paired && state.with_umi && !state.skip_umi_extract && state.umi_discard_read != 0) {
|
|
fastq_2 = state.remove(state.fastq_2)
|
|
paired = false
|
|
}
|
|
[ id, state + [paired: paired, fastq_2: fastq_2] ]
|
|
}
|
|
|
|
// Trim reads using Trim galore!
|
|
| trimgalore.run (
|
|
runIf: { id, state -> !state.skip_trimming && state.trimmer == "trimgalore" },
|
|
fromState: { id, state ->
|
|
def input = state.paired ? [ state.fastq_1, state.fastq_2 ] : [ state.fastq_1 ]
|
|
[ paired: state.paired,
|
|
input: input,
|
|
min_trimmed_reads: state.min_trimmed_reads ]
|
|
},
|
|
toState: [
|
|
"fastq_1": "trimmed_r1",
|
|
"fastq_2": "trimmed_r2",
|
|
"trim_log_1": "trimming_report_r1",
|
|
"trim_log_2": "trimming_report_r2",
|
|
"trim_zip_1": "trimmed_fastqc_zip_1",
|
|
"trim_zip_2": "trimmed_fastqc_zip_2",
|
|
"trim_html_1": "trimmed_fastqc_html_1",
|
|
"trim_html_2": "trimmed_fastqc_html_2"
|
|
],
|
|
args: [gzip: true, fastqc: true]
|
|
)
|
|
|
|
// Trim reads using fastp
|
|
| fastp.run(
|
|
runIf: { id, state -> !state.skip_trimming && state.trimmer == "fastp" },
|
|
fromState: [
|
|
"in1": "fastq_1",
|
|
"in2": "fastq_2",
|
|
"merge": "fastp_save_merged",
|
|
"interleaved_in": "interleaved_reads",
|
|
"detect_adapter_for_pe": "fastp_pe_detect_adapter",
|
|
"adapter_fasta": "fastp_adapter_fasta"
|
|
],
|
|
toState: [
|
|
"fastq_1": "out1",
|
|
"fastq_2": "out2",
|
|
"failed_trim": "failed_out",
|
|
"failed_trim_unpaired1": "unpaired1",
|
|
"failed_trim_unpaired2": "unpaired2",
|
|
"trim_json": "json",
|
|
"trim_html": "html",
|
|
"trim_merged_out": "merged_out"
|
|
]
|
|
)
|
|
|
|
// Perform FASTQC on reads trimmed using fastp
|
|
| fastqc.run(
|
|
runIf: { id, state -> !state.skip_trimming && state.trimmer == "fastp" },
|
|
fromState: { id, state ->
|
|
def input = state.paired ? [ state.fastq_1, state.fastq_2 ] : [ state.fastq_1 ]
|
|
[ paired: state.paired,
|
|
input: input ]
|
|
},
|
|
toState: [
|
|
"trim_html_1": "fastqc_html_1",
|
|
"trim_html_2": "fastqc_html_2",
|
|
"trim_zip_1": "fastqc_zip_1",
|
|
"trim_zip_2": "fastqc_zip_2"
|
|
],
|
|
key: "fastqc_trimming"
|
|
)
|
|
|
|
// Filter out contaminant RNA
|
|
| bbmap_bbsplit.run (
|
|
runIf: { id, state -> !state.skip_bbsplit },
|
|
fromState: { id, state ->
|
|
def input = state.paired ? [ state.fastq_1, state.fastq_2 ] : [ state.fastq_1 ]
|
|
[ paired: state.paired,
|
|
input: input,
|
|
built_bbsplit_index: state.bbsplit_index ]
|
|
},
|
|
args: ["only_build_index": false],
|
|
toState: [
|
|
"fastq_1": "fastq_1",
|
|
"fastq_2": "fastq_2"
|
|
]
|
|
)
|
|
|
|
// Sort reads by rRNA and non-rRNA
|
|
| sortmerna.run (
|
|
runIf: { id, state -> state.remove_ribo_rna },
|
|
fromState: { id, state ->
|
|
def input = state.paired ? [ state.fastq_1, state.fastq_2 ] : [ state.fastq_1 ]
|
|
def filePaths = state.ribo_database_manifest.readLines()
|
|
def refs = filePaths.collect { it }
|
|
[ paired: state.paired,
|
|
input: input,
|
|
ribo_database_manifest: refs ]
|
|
},
|
|
toState: [
|
|
"fastq_1": "fastq_1",
|
|
"fastq_2": "fastq_2",
|
|
"sortmerna_log": "sortmerna_log"
|
|
]
|
|
)
|
|
|
|
// Sub-sample FastQ files and pseudo-align with Salmon to auto-infer strandedness
|
|
| fq_subsample.run (
|
|
runIf: { id, state -> state.strandedness == 'auto' },
|
|
fromState: { id, state ->
|
|
def input = state.paired ? [ state.fastq_1, state.fastq_2 ] : [ state.fastq_1 ]
|
|
[
|
|
input: input,
|
|
extra_args: state.extra_fq_subsample_args
|
|
]
|
|
},
|
|
toState: [
|
|
"subsampled_fastq_1": "output_1",
|
|
"subsampled_fastq_2": "output_2"
|
|
]
|
|
)
|
|
|
|
// Infer lib-type for salmon quant
|
|
| map { id, state ->
|
|
def lib_type = (state.paired) ?
|
|
(
|
|
(state.strandedness == "forward") ?
|
|
"ISF" :
|
|
(
|
|
(state.strandedness == "reverse") ? "ISR" : "IU"
|
|
)
|
|
)
|
|
: (
|
|
(state.strandedness == "forward") ?
|
|
"SF" :
|
|
(
|
|
(state.strandedness == "reverse") ? "SR" : "U"
|
|
)
|
|
)
|
|
[ id, state + [lib_type: lib_type] ]
|
|
}
|
|
| salmon_quant.run (
|
|
runIf: { id, state -> state.strandedness == 'auto' },
|
|
fromState: { id, state ->
|
|
def unmated_reads = !state.paired ? state.subsampled_fastq_1 : null
|
|
def mates1 = state.paired ? state.subsampled_fastq_1 : null
|
|
def mates2 = state.paired ? state.subsampled_fastq_2 : null
|
|
[ unmated_reads: unmated_reads,
|
|
mates1: mates1,
|
|
mates2: mates2,
|
|
gene_map: state.gtf,
|
|
index: state.salmon_index,
|
|
lib_type: state.lib_type ]
|
|
},
|
|
args: [ "skip_quant": true ],
|
|
toState: [ "salmon_quant_output": "output" ]
|
|
)
|
|
|
|
| map { id, state ->
|
|
def mod_state = (!state.paired) ?
|
|
[trim_log_2: state.remove(state.trim_log_2), trim_zip_2: state.remove(state.trim_zip_2), trim_html_2: state.remove(state.trim_html_2), failed_trim_unpaired2: state.remove(state.failed_trim_unpaired2)] :
|
|
[]
|
|
[ id, state + mod_state ]
|
|
}
|
|
|
|
| map { id, state ->
|
|
def mod_state = state.findAll { key, value -> value instanceof java.nio.file.Path && value.exists() }
|
|
[ id, mod_state ]
|
|
}
|
|
|
|
| setState (
|
|
"fastqc_html_1": "fastqc_html_1",
|
|
"fastqc_html_2": "fastqc_html_2",
|
|
"fastqc_zip_1": "fastqc_zip_1",
|
|
"fastqc_zip_2": "fastqc_zip_2",
|
|
"qc_output1": "fastq_1",
|
|
"qc_output2": "fastq_2",
|
|
"trim_log_1": "trim_log_1",
|
|
"trim_log_2": "trim_log_2",
|
|
"trim_zip_1": "trim_zip_1",
|
|
"trim_zip_2": "trim_zip_2",
|
|
"trim_html_1": "trim_html_1",
|
|
"trim_html_2": "trim_html_2",
|
|
"sortmerna_log": "sortmerna_log",
|
|
"failed_trim": "failed_trim",
|
|
"failed_trim_unpaired1": "failed_trim_unpaired1",
|
|
"failed_trim_unpaired2": "failed_trim_unpaired2",
|
|
"trim_json": "trim_json",
|
|
"trim_html": "trim_html",
|
|
"trim_merged_out": "trim_merged_out",
|
|
"salmon_quant_output": "salmon_quant_output"
|
|
)
|
|
|
|
emit:
|
|
output_ch
|
|
}
|
|
VIASHMAIN
|
|
nextflow run . -main-script "\$tempscript" &
|
|
wait "\$!"
|
|
|
|
VIASHEOF
|
|
|
|
|
|
# check whether required files exist
|
|
if [ ! -z "$VIASH_PAR_SALMON_QUANT_OUTPUT" ] && [ ! -e "$VIASH_PAR_SALMON_QUANT_OUTPUT" ]; then
|
|
ViashError "Output file '$VIASH_PAR_SALMON_QUANT_OUTPUT' does not exist."
|
|
exit 1
|
|
fi
|
|
if [ ! -z "$VIASH_PAR_TRIM_JSON" ] && [ ! -e "$VIASH_PAR_TRIM_JSON" ]; then
|
|
ViashError "Output file '$VIASH_PAR_TRIM_JSON' does not exist."
|
|
exit 1
|
|
fi
|
|
if [ ! -z "$VIASH_PAR_TRIM_HTML" ] && [ ! -e "$VIASH_PAR_TRIM_HTML" ]; then
|
|
ViashError "Output file '$VIASH_PAR_TRIM_HTML' does not exist."
|
|
exit 1
|
|
fi
|
|
if [ ! -z "$VIASH_PAR_MERGED_OUT" ] && [ ! -e "$VIASH_PAR_MERGED_OUT" ]; then
|
|
ViashError "Output file '$VIASH_PAR_MERGED_OUT' does not exist."
|
|
exit 1
|
|
fi
|
|
|
|
|
|
exit 0
|