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@@ -450,9 +450,9 @@ RUN apt-get update && \
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rm -rf /var/lib/apt/lists/*
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LABEL org.opencontainers.image.description="Companion container for running component io publish"
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LABEL org.opencontainers.image.created="2025-05-26T10:28:13Z"
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LABEL org.opencontainers.image.created="2025-05-28T11:02:51Z"
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LABEL org.opencontainers.image.source="https://github.com/viash-hub/demultiplex"
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LABEL org.opencontainers.image.revision="219bd5816e7e6a6c80b4d6f6c1d21b3ffe53c880"
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LABEL org.opencontainers.image.revision="6e71519815566a057711019a23a56a22479dd655"
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LABEL org.opencontainers.image.version="main"
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VIASHDOCKER
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@@ -579,9 +579,9 @@ function ViashHelp {
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echo " type: file, required parameter, file must exist"
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echo " Directory to write fastq data to"
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echo ""
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echo " --input_falco"
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echo " --input_sample_qc"
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echo " type: file, required parameter, multiple values allowed, file must exist"
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echo " Directory to write falco output to"
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echo " Directory to write sample QC output to"
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echo ""
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echo " --input_multiqc"
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echo " type: file, required parameter, file must exist"
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@@ -599,7 +599,7 @@ function ViashHelp {
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echo " type: file, output, file must exist"
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echo " default: fastq"
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echo ""
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echo " --output_falco"
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echo " --output_sample_qc"
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echo " type: file, output, file must exist"
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echo " default: qc/fastqc"
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echo ""
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@@ -676,20 +676,20 @@ while [[ $# -gt 0 ]]; do
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VIASH_PAR_INPUT=$(ViashRemoveFlags "$1")
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shift 1
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;;
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--input_falco)
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if [ -z "$VIASH_PAR_INPUT_FALCO" ]; then
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VIASH_PAR_INPUT_FALCO="$2"
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--input_sample_qc)
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if [ -z "$VIASH_PAR_INPUT_SAMPLE_QC" ]; then
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VIASH_PAR_INPUT_SAMPLE_QC="$2"
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else
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VIASH_PAR_INPUT_FALCO="$VIASH_PAR_INPUT_FALCO;""$2"
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VIASH_PAR_INPUT_SAMPLE_QC="$VIASH_PAR_INPUT_SAMPLE_QC;""$2"
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fi
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[ $# -lt 2 ] && ViashError Not enough arguments passed to --input_falco. Use "--help" to get more information on the parameters. && exit 1
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[ $# -lt 2 ] && ViashError Not enough arguments passed to --input_sample_qc. Use "--help" to get more information on the parameters. && exit 1
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shift 2
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;;
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--input_falco=*)
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if [ -z "$VIASH_PAR_INPUT_FALCO" ]; then
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VIASH_PAR_INPUT_FALCO=$(ViashRemoveFlags "$1")
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--input_sample_qc=*)
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if [ -z "$VIASH_PAR_INPUT_SAMPLE_QC" ]; then
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VIASH_PAR_INPUT_SAMPLE_QC=$(ViashRemoveFlags "$1")
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else
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VIASH_PAR_INPUT_FALCO="$VIASH_PAR_INPUT_FALCO;"$(ViashRemoveFlags "$1")
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VIASH_PAR_INPUT_SAMPLE_QC="$VIASH_PAR_INPUT_SAMPLE_QC;"$(ViashRemoveFlags "$1")
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fi
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shift 1
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;;
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@@ -737,15 +737,15 @@ while [[ $# -gt 0 ]]; do
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VIASH_PAR_OUTPUT=$(ViashRemoveFlags "$1")
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shift 1
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;;
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--output_falco)
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[ -n "$VIASH_PAR_OUTPUT_FALCO" ] && ViashError Bad arguments for option \'--output_falco\': \'$VIASH_PAR_OUTPUT_FALCO\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
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VIASH_PAR_OUTPUT_FALCO="$2"
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[ $# -lt 2 ] && ViashError Not enough arguments passed to --output_falco. Use "--help" to get more information on the parameters. && exit 1
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--output_sample_qc)
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[ -n "$VIASH_PAR_OUTPUT_SAMPLE_QC" ] && ViashError Bad arguments for option \'--output_sample_qc\': \'$VIASH_PAR_OUTPUT_SAMPLE_QC\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
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VIASH_PAR_OUTPUT_SAMPLE_QC="$2"
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[ $# -lt 2 ] && ViashError Not enough arguments passed to --output_sample_qc. Use "--help" to get more information on the parameters. && exit 1
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shift 2
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;;
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--output_falco=*)
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[ -n "$VIASH_PAR_OUTPUT_FALCO" ] && ViashError Bad arguments for option \'--output_falco=*\': \'$VIASH_PAR_OUTPUT_FALCO\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
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VIASH_PAR_OUTPUT_FALCO=$(ViashRemoveFlags "$1")
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--output_sample_qc=*)
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[ -n "$VIASH_PAR_OUTPUT_SAMPLE_QC" ] && ViashError Bad arguments for option \'--output_sample_qc=*\': \'$VIASH_PAR_OUTPUT_SAMPLE_QC\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
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VIASH_PAR_OUTPUT_SAMPLE_QC=$(ViashRemoveFlags "$1")
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shift 1
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;;
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--output_multiqc)
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@@ -957,8 +957,8 @@ if [ -z ${VIASH_PAR_INPUT+x} ]; then
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ViashError '--input' is a required argument. Use "--help" to get more information on the parameters.
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exit 1
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fi
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if [ -z ${VIASH_PAR_INPUT_FALCO+x} ]; then
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ViashError '--input_falco' is a required argument. Use "--help" to get more information on the parameters.
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if [ -z ${VIASH_PAR_INPUT_SAMPLE_QC+x} ]; then
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ViashError '--input_sample_qc' is a required argument. Use "--help" to get more information on the parameters.
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exit 1
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fi
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if [ -z ${VIASH_PAR_INPUT_MULTIQC+x} ]; then
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@@ -1002,8 +1002,8 @@ fi
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if [ -z ${VIASH_PAR_OUTPUT+x} ]; then
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VIASH_PAR_OUTPUT="fastq"
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fi
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if [ -z ${VIASH_PAR_OUTPUT_FALCO+x} ]; then
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VIASH_PAR_OUTPUT_FALCO="qc/fastqc"
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if [ -z ${VIASH_PAR_OUTPUT_SAMPLE_QC+x} ]; then
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VIASH_PAR_OUTPUT_SAMPLE_QC="qc/fastqc"
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fi
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if [ -z ${VIASH_PAR_OUTPUT_MULTIQC+x} ]; then
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VIASH_PAR_OUTPUT_MULTIQC="qc/multiqc_report.html"
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@@ -1020,10 +1020,10 @@ if [ ! -z "$VIASH_PAR_INPUT" ] && [ ! -e "$VIASH_PAR_INPUT" ]; then
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ViashError "Input file '$VIASH_PAR_INPUT' does not exist."
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exit 1
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fi
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if [ ! -z "$VIASH_PAR_INPUT_FALCO" ]; then
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if [ ! -z "$VIASH_PAR_INPUT_SAMPLE_QC" ]; then
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IFS=';'
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set -f
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for file in $VIASH_PAR_INPUT_FALCO; do
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for file in $VIASH_PAR_INPUT_SAMPLE_QC; do
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unset IFS
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if [ ! -e "$file" ]; then
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ViashError "Input file '$file' does not exist."
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@@ -1123,8 +1123,8 @@ fi
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if [ ! -z "$VIASH_PAR_OUTPUT" ] && [ ! -d "$(dirname "$VIASH_PAR_OUTPUT")" ]; then
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mkdir -p "$(dirname "$VIASH_PAR_OUTPUT")"
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fi
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if [ ! -z "$VIASH_PAR_OUTPUT_FALCO" ] && [ ! -d "$(dirname "$VIASH_PAR_OUTPUT_FALCO")" ]; then
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mkdir -p "$(dirname "$VIASH_PAR_OUTPUT_FALCO")"
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if [ ! -z "$VIASH_PAR_OUTPUT_SAMPLE_QC" ] && [ ! -d "$(dirname "$VIASH_PAR_OUTPUT_SAMPLE_QC")" ]; then
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mkdir -p "$(dirname "$VIASH_PAR_OUTPUT_SAMPLE_QC")"
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fi
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if [ ! -z "$VIASH_PAR_OUTPUT_MULTIQC" ] && [ ! -d "$(dirname "$VIASH_PAR_OUTPUT_MULTIQC")" ]; then
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mkdir -p "$(dirname "$VIASH_PAR_OUTPUT_MULTIQC")"
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@@ -1152,16 +1152,16 @@ if [ ! -z "$VIASH_PAR_INPUT" ]; then
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VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$VIASH_PAR_INPUT")" )
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VIASH_PAR_INPUT=$(ViashDockerAutodetectMount "$VIASH_PAR_INPUT")
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fi
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if [ ! -z "$VIASH_PAR_INPUT_FALCO" ]; then
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VIASH_TEST_INPUT_FALCO=()
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if [ ! -z "$VIASH_PAR_INPUT_SAMPLE_QC" ]; then
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VIASH_TEST_INPUT_SAMPLE_QC=()
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IFS=';'
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for var in $VIASH_PAR_INPUT_FALCO; do
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for var in $VIASH_PAR_INPUT_SAMPLE_QC; do
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unset IFS
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VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$var")" )
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var=$(ViashDockerAutodetectMount "$var")
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VIASH_TEST_INPUT_FALCO+=( "$var" )
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VIASH_TEST_INPUT_SAMPLE_QC+=( "$var" )
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done
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VIASH_PAR_INPUT_FALCO=$(IFS=';' ; echo "${VIASH_TEST_INPUT_FALCO[*]}")
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VIASH_PAR_INPUT_SAMPLE_QC=$(IFS=';' ; echo "${VIASH_TEST_INPUT_SAMPLE_QC[*]}")
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fi
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if [ ! -z "$VIASH_PAR_INPUT_MULTIQC" ]; then
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VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$VIASH_PAR_INPUT_MULTIQC")" )
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@@ -1180,10 +1180,10 @@ if [ ! -z "$VIASH_PAR_OUTPUT" ]; then
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VIASH_PAR_OUTPUT=$(ViashDockerAutodetectMount "$VIASH_PAR_OUTPUT")
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VIASH_CHOWN_VARS+=( "$VIASH_PAR_OUTPUT" )
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fi
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if [ ! -z "$VIASH_PAR_OUTPUT_FALCO" ]; then
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VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$VIASH_PAR_OUTPUT_FALCO")" )
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VIASH_PAR_OUTPUT_FALCO=$(ViashDockerAutodetectMount "$VIASH_PAR_OUTPUT_FALCO")
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VIASH_CHOWN_VARS+=( "$VIASH_PAR_OUTPUT_FALCO" )
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if [ ! -z "$VIASH_PAR_OUTPUT_SAMPLE_QC" ]; then
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VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$VIASH_PAR_OUTPUT_SAMPLE_QC")" )
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VIASH_PAR_OUTPUT_SAMPLE_QC=$(ViashDockerAutodetectMount "$VIASH_PAR_OUTPUT_SAMPLE_QC")
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VIASH_CHOWN_VARS+=( "$VIASH_PAR_OUTPUT_SAMPLE_QC" )
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fi
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if [ ! -z "$VIASH_PAR_OUTPUT_MULTIQC" ]; then
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VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$VIASH_PAR_OUTPUT_MULTIQC")" )
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@@ -1270,12 +1270,12 @@ cat > "\$tempscript" << 'VIASHMAIN'
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## VIASH START
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# The following code has been auto-generated by Viash.
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$( if [ ! -z ${VIASH_PAR_INPUT+x} ]; then echo "${VIASH_PAR_INPUT}" | sed "s#'#'\"'\"'#g;s#.*#par_input='&'#" ; else echo "# par_input="; fi )
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$( if [ ! -z ${VIASH_PAR_INPUT_FALCO+x} ]; then echo "${VIASH_PAR_INPUT_FALCO}" | sed "s#'#'\"'\"'#g;s#.*#par_input_falco='&'#" ; else echo "# par_input_falco="; fi )
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$( if [ ! -z ${VIASH_PAR_INPUT_SAMPLE_QC+x} ]; then echo "${VIASH_PAR_INPUT_SAMPLE_QC}" | sed "s#'#'\"'\"'#g;s#.*#par_input_sample_qc='&'#" ; else echo "# par_input_sample_qc="; fi )
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$( if [ ! -z ${VIASH_PAR_INPUT_MULTIQC+x} ]; then echo "${VIASH_PAR_INPUT_MULTIQC}" | sed "s#'#'\"'\"'#g;s#.*#par_input_multiqc='&'#" ; else echo "# par_input_multiqc="; fi )
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$( if [ ! -z ${VIASH_PAR_INPUT_RUN_INFORMATION+x} ]; then echo "${VIASH_PAR_INPUT_RUN_INFORMATION}" | sed "s#'#'\"'\"'#g;s#.*#par_input_run_information='&'#" ; else echo "# par_input_run_information="; fi )
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$( if [ ! -z ${VIASH_PAR_INPUT_DEMULTIPLEXER_LOGS+x} ]; then echo "${VIASH_PAR_INPUT_DEMULTIPLEXER_LOGS}" | sed "s#'#'\"'\"'#g;s#.*#par_input_demultiplexer_logs='&'#" ; else echo "# par_input_demultiplexer_logs="; fi )
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$( if [ ! -z ${VIASH_PAR_OUTPUT+x} ]; then echo "${VIASH_PAR_OUTPUT}" | sed "s#'#'\"'\"'#g;s#.*#par_output='&'#" ; else echo "# par_output="; fi )
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$( if [ ! -z ${VIASH_PAR_OUTPUT_FALCO+x} ]; then echo "${VIASH_PAR_OUTPUT_FALCO}" | sed "s#'#'\"'\"'#g;s#.*#par_output_falco='&'#" ; else echo "# par_output_falco="; fi )
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$( if [ ! -z ${VIASH_PAR_OUTPUT_SAMPLE_QC+x} ]; then echo "${VIASH_PAR_OUTPUT_SAMPLE_QC}" | sed "s#'#'\"'\"'#g;s#.*#par_output_sample_qc='&'#" ; else echo "# par_output_sample_qc="; fi )
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$( if [ ! -z ${VIASH_PAR_OUTPUT_MULTIQC+x} ]; then echo "${VIASH_PAR_OUTPUT_MULTIQC}" | sed "s#'#'\"'\"'#g;s#.*#par_output_multiqc='&'#" ; else echo "# par_output_multiqc="; fi )
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$( if [ ! -z ${VIASH_PAR_OUTPUT_RUN_INFORMATION+x} ]; then echo "${VIASH_PAR_OUTPUT_RUN_INFORMATION}" | sed "s#'#'\"'\"'#g;s#.*#par_output_run_information='&'#" ; else echo "# par_output_run_information="; fi )
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$( if [ ! -z ${VIASH_PAR_OUTPUT_DEMULTIPLEXER_LOGS+x} ]; then echo "${VIASH_PAR_OUTPUT_DEMULTIPLEXER_LOGS}" | sed "s#'#'\"'\"'#g;s#.*#par_output_demultiplexer_logs='&'#" ; else echo "# par_output_demultiplexer_logs="; fi )
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@@ -1326,12 +1326,12 @@ do
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ls "\$output_location"
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done
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echo "Grouping output from \$par_input_falco into \$par_output_falco"
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mkdir -p "\$par_output_falco"
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IFS=";" read -ra falco_inputs <<< \$par_input_falco
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for falco_dir in "\${falco_inputs[@]}"; do
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echo "Copying contents of \$falco_dir"
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find -H -D exec "\$falco_dir" -type f -maxdepth 1 -exec cp -t "\$par_output_falco" {} +
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echo "Grouping output from \$par_input_sample_qc into \$par_output_sample_qc"
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mkdir -p "\$par_output_sample_qc"
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IFS=";" read -ra sample_qc_inputs <<< \$par_input_sample_qc
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for qc_dir in "\${sample_qc_inputs[@]}"; do
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echo "Copying contents of \$qc_dir"
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find -H -D exec "\$qc_dir" -type f -maxdepth 1 -exec cp -t "\$par_output_sample_qc" {} +
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done
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VIASHMAIN
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bash "\$tempscript" &
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@@ -1346,18 +1346,18 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then
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if [ ! -z "$VIASH_PAR_INPUT" ]; then
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VIASH_PAR_INPUT=$(ViashDockerStripAutomount "$VIASH_PAR_INPUT")
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fi
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if [ ! -z "$VIASH_PAR_INPUT_FALCO" ]; then
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unset VIASH_TEST_INPUT_FALCO
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if [ ! -z "$VIASH_PAR_INPUT_SAMPLE_QC" ]; then
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unset VIASH_TEST_INPUT_SAMPLE_QC
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IFS=';'
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for var in $VIASH_PAR_INPUT_FALCO; do
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for var in $VIASH_PAR_INPUT_SAMPLE_QC; do
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unset IFS
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if [ -z "$VIASH_TEST_INPUT_FALCO" ]; then
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VIASH_TEST_INPUT_FALCO="$(ViashDockerStripAutomount "$var")"
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if [ -z "$VIASH_TEST_INPUT_SAMPLE_QC" ]; then
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VIASH_TEST_INPUT_SAMPLE_QC="$(ViashDockerStripAutomount "$var")"
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else
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VIASH_TEST_INPUT_FALCO="$VIASH_TEST_INPUT_FALCO;""$(ViashDockerStripAutomount "$var")"
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VIASH_TEST_INPUT_SAMPLE_QC="$VIASH_TEST_INPUT_SAMPLE_QC;""$(ViashDockerStripAutomount "$var")"
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fi
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done
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VIASH_PAR_INPUT_FALCO="$VIASH_TEST_INPUT_FALCO"
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VIASH_PAR_INPUT_SAMPLE_QC="$VIASH_TEST_INPUT_SAMPLE_QC"
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fi
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if [ ! -z "$VIASH_PAR_INPUT_MULTIQC" ]; then
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VIASH_PAR_INPUT_MULTIQC=$(ViashDockerStripAutomount "$VIASH_PAR_INPUT_MULTIQC")
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@@ -1371,8 +1371,8 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then
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if [ ! -z "$VIASH_PAR_OUTPUT" ]; then
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VIASH_PAR_OUTPUT=$(ViashDockerStripAutomount "$VIASH_PAR_OUTPUT")
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fi
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if [ ! -z "$VIASH_PAR_OUTPUT_FALCO" ]; then
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VIASH_PAR_OUTPUT_FALCO=$(ViashDockerStripAutomount "$VIASH_PAR_OUTPUT_FALCO")
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if [ ! -z "$VIASH_PAR_OUTPUT_SAMPLE_QC" ]; then
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VIASH_PAR_OUTPUT_SAMPLE_QC=$(ViashDockerStripAutomount "$VIASH_PAR_OUTPUT_SAMPLE_QC")
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fi
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if [ ! -z "$VIASH_PAR_OUTPUT_MULTIQC" ]; then
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VIASH_PAR_OUTPUT_MULTIQC=$(ViashDockerStripAutomount "$VIASH_PAR_OUTPUT_MULTIQC")
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@@ -1403,8 +1403,8 @@ if [ ! -z "$VIASH_PAR_OUTPUT" ] && [ ! -e "$VIASH_PAR_OUTPUT" ]; then
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ViashError "Output file '$VIASH_PAR_OUTPUT' does not exist."
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exit 1
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fi
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if [ ! -z "$VIASH_PAR_OUTPUT_FALCO" ] && [ ! -e "$VIASH_PAR_OUTPUT_FALCO" ]; then
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ViashError "Output file '$VIASH_PAR_OUTPUT_FALCO' does not exist."
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if [ ! -z "$VIASH_PAR_OUTPUT_SAMPLE_QC" ] && [ ! -e "$VIASH_PAR_OUTPUT_SAMPLE_QC" ]; then
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ViashError "Output file '$VIASH_PAR_OUTPUT_SAMPLE_QC' does not exist."
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exit 1
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fi
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if [ ! -z "$VIASH_PAR_OUTPUT_MULTIQC" ] && [ ! -e "$VIASH_PAR_OUTPUT_MULTIQC" ]; then
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