Create ZIP file of selected nf-flu results

nf-flu-zip-package.sh

#!/bin/bash

set -euo pipefail

SAMPLESHEET="samplesheet.csv"
OUTPUT_DIR="results"
ZIP_PACKAGE_DIR="$(date -I)-nf-flu-results"
VERBOSE=false
OVERWRITE=false

# Help message
print_help() {
    echo "Usage: $0 -s <samplesheet> -o <output_dir> -d <zip_package_dir>"
    echo
    echo "Create a zip package of selected nf-flu results given a samplesheet CSV"
    echo
    echo "Options:"
    echo "  -s SAMPLESHEET      Samplesheet file in CSV format. Used for getting sample names. First column should contain sample names (default: $SAMPLESHEET)"
    echo "  -o OUTPUT_DIR       Output directory containing the nf-flu results (default: $OUTPUT_DIR)"
    echo "  -d ZIP_PACKAGE_DIR  Directory to store the zip package (default: $ZIP_PACKAGE_DIR)"
    echo "  -O                  Overwrite output files (default: $OVERWRITE)"
    echo "  -v                  Verbose output"
    echo "  -h                  Display this help message"
}

# Parse command line options
while getopts "s:o:d:Ohv" opt; do
    case $opt in
        s) SAMPLESHEET=$OPTARG ;;
        o) OUTPUT_DIR=$OPTARG ;;
        d) ZIP_PACKAGE_DIR=$OPTARG ;;
        O) OVERWRITE=true ;;
        v) VERBOSE=true ;;
        h) print_help; exit 0 ;;
        \?) echo "Invalid option: -$OPTARG" >&2 ;;
    esac
done


error_handler() {
    echo -e "\n\033[1;31mError on line $1\033[0m"
    # Perform any cleanup or logging here
}

cleanup() {
    echo "Cleaning up before exiting..."
    echo "Removing temporary directory at $ZIP_PACKAGE_DIR"
    rm -rf "$ZIP_PACKAGE_DIR"
}

handle_interrupt() {
    echo -e "\n\033[1;31mERROR:\033[1m Script interrupted...\033[0m"
    cleanup
    exit 1
}

# Trap ERR signal to handle errors
trap 'error_handler $LINENO' ERR

# Trap EXIT signal to perform cleanup
trap cleanup EXIT

# Trap SIGINT and SIGTERM to handle interruptions
trap handle_interrupt SIGINT SIGTERM

error() {
  echo -e "$(date -Is)  \033[1;31mERROR: \033[0m\033[1m$1\033[0m"
}

warning() {
  echo -e "$(date -Is)  \033[1;33mWARNING: \033[0m\033[1m$1\033[0m"
}

info() {
  echo -e "$(date -Is)  \033[1;32mINFO: \033[0m\033[1m$1\033[0m"
}

if [[ ! -f "$SAMPLESHEET" ]]; then
    error "Samplesheet not found at $SAMPLESHEET"
    exit 1
fi

if [[ ! -d "$OUTPUT_DIR" ]]; then
    error "Output directory not found at $OUTPUT_DIR"
    exit 1
fi

if [[ -d "$ZIP_PACKAGE_DIR" ]]; then
    error "Directory already exists at $ZIP_PACKAGE_DIR"
    if [[ $OVERWRITE == false ]]; then
        exit 1
    fi
fi

info "Reading samplesheet from $SAMPLESHEET"
info "Output directory: $OUTPUT_DIR"
info "Creating temporary directory at $ZIP_PACKAGE_DIR"

# from samplesheet.csv read column after header in first row into Bash array
samples=($(awk -F, 'NR>1 {print $1}' "$SAMPLESHEET" | uniq))

# join sample names with ; delimiter
samples_joined=$(printf "; %s" "${samples[@]}")
info "Found the following samples: ${samples_joined:2}"

# Create a temporary directory to store the results
mkdir -p "$ZIP_PACKAGE_DIR"

if [ -f "$ZIP_PACKAGE_DIR.zip" ]; then
    error "Zip package already exists at $ZIP_PACKAGE_DIR.zip!"
    if [[ $OVERWRITE == false ]]; then
        exit 1
    fi
fi

subtyping_report=$(realpath "$OUTPUT_DIR/nf-flu-subtyping-report.xlsx")
if [[ -z "$subtyping_report" ]]; then
    error "Subtyping report not found"
else
    if [[ $VERBOSE == true ]]; then
        info "Found subtyping report at $subtyping_report"
    fi
    ln -s "$subtyping_report" "$ZIP_PACKAGE_DIR/nf-flu-subtyping-report.xlsx"
fi
nextclade_tsv=$(realpath "$OUTPUT_DIR/nextclade/nextclade.tsv")
if [[ -z "$nextclade_tsv" ]]; then
    error "Nextclade TSV not found"
else
    if [[ $VERBOSE == true ]]; then
        info "Found subtyping report at $nextclade_tsv"
    fi
    ln -s "$nextclade_tsv" "$ZIP_PACKAGE_DIR/nextclade.tsv"
fi
flumut_outputs=($(realpath "$OUTPUT_DIR/flumut/"*))
if [[ $VERBOSE == true ]]; then
    info "Found ${#flumut_outputs[@]} Flumut outputs"
    info "1st Flumut output: ${flumut_outputs[0]}"
    info "1st Flumut output realpath: $(realpath ${flumut_outputs[0]})"
fi

mkdir -p "$ZIP_PACKAGE_DIR/FluMut"
for flumut_out in "${flumut_outputs[@]}"; do
    ln -s "$flumut_out" "$ZIP_PACKAGE_DIR/FluMut/$(basename $flumut_out)"
done

# Symlink selected results to the temporary directory
for sample in "${samples[@]}"; do
    if [[ $VERBOSE == true ]]; then
        info "Symlinking sample '$sample' results to $ZIP_PACKAGE_DIR"
    fi
    # Find the consensus sequence for the sample getting the absolute path
    consensus=$(find "$OUTPUT_DIR/consensus/bcftools" -name "${sample}.consensus.fasta")
    if [[ -z "$consensus" ]]; then
        warning "Consensus sequence not found for sample '$sample'"
    else
        if [[ $VERBOSE == true ]]; then
            info "Found consensus sequence for sample '$sample' at $consensus"
        fi
        mkdir -p "$ZIP_PACKAGE_DIR/$sample/"{Annotations,FluMut,Variants,GenoFLU}
        ln -sf $(realpath "$consensus") "$ZIP_PACKAGE_DIR/$sample/${sample}.consensus.fasta"
        ln -sf $(realpath "$subtyping_report") "$ZIP_PACKAGE_DIR/$sample/${sample}-nf-flu-subtyping-report.xlsx"
        for flumut_out in "${flumut_outputs[@]}"; do
            # if FluMut output file extension is '.fasta', skip it
            if [[ $(basename "$flumut_out") == *.fasta ]]; then
                continue
            fi
            ln -sf "$flumut_out" "$ZIP_PACKAGE_DIR/$sample/FluMut/${sample}-$(basename $flumut_out)"
        done
        vcfs=($(find "$OUTPUT_DIR/variants/" \( -name "${sample}.*.clair3.vcf.gz" -o -name "${sample}.*.freebayes.vcf" \) | uniq))
        if [[ $VERBOSE == true ]]; then
            info "Found ${#vcfs[@]} VCF files for sample '$sample'"
            info "1st VCF: ${vcfs[0]}"
            info "1st VCF realpath: $(realpath ${vcfs[0]})"
        fi
        for vcf in "${vcfs[@]}"; do
            ln -sf $(realpath "$vcf") "$ZIP_PACKAGE_DIR/$sample/Variants/$(basename $vcf)"
        done
        if [[ -d "$OUTPUT_DIR/annotation/$sample" ]]; then
            annotations=()
            annotations+=($(find "$OUTPUT_DIR/annotation/$sample" -name "${sample}.*" | uniq))
            if [[ -d "$OUTPUT_DIR/annotation/bcftools/$sample" ]]; then
                annotations+=($(find "$OUTPUT_DIR/annotation/bcftools/$sample" -name "${sample}.*" | uniq))
            fi
            for annotation in "${annotations[@]}"; do
                ln -sf $(realpath "$annotation") "$ZIP_PACKAGE_DIR/$sample/Annotations/$(basename $annotation)"
            done
        fi
        if [[ -d "$OUTPUT_DIR/mismatch_report" ]]; then
            mismatch_report=$(find "$OUTPUT_DIR/mismatch_report" -name "${sample}-blastn-report.xlsx" | uniq | head -n1)
            if [[ -z "$mismatch_report" ]]; then
                warning "BLASTN mismatch report not found for sample '$sample'"
            else
                if [[ $VERBOSE == true ]]; then
                    info "Found mismatch report for sample '$sample' at '$mismatch_report'"
                fi
                ln -sf $(realpath "$mismatch_report") "$ZIP_PACKAGE_DIR/$sample/$(basename $mismatch_report)"
            fi
        fi
        if [[ -d "$OUTPUT_DIR/genoflu" ]]; then
            genoflu_out=($(find "$OUTPUT_DIR/genoflu/" -name "${sample}.*" | uniq))
            if [[ -z "$genoflu_out" ]]; then
                warning "GenoFLU output not found for sample '$sample'"
            else
                if [[ $VERBOSE == true ]]; then
                    info "Found GenoFLU output for sample '$sample' at '$genoflu_out'"
                fi
                mkdir -p "$ZIP_PACKAGE_DIR/$sample/GenoFLU"
            fi
            for genoflu_out in "${genoflu_out[@]}"; do
                ln -sf $(realpath "$genoflu_out") "$ZIP_PACKAGE_DIR/$sample/GenoFLU/$(basename $genoflu_out)"
            done
        fi
        if [[ -d "$OUTPUT_DIR/nextclade" && -f "$OUTPUT_DIR/nextclade/nextclade.tsv" ]]; then
            ln -sf $(realpath "$OUTPUT_DIR/nextclade/nextclade.tsv") "$ZIP_PACKAGE_DIR/$sample/${sample}.nextclade.tsv"
        fi
    fi
done

if [[ $VERBOSE == true ]]; then
    info "Listing files in $ZIP_PACKAGE_DIR"
    tree "$ZIP_PACKAGE_DIR" || true
fi

info "Creating zip package '$ZIP_PACKAGE_DIR.zip'..."
zip -r "$ZIP_PACKAGE_DIR.zip" "$ZIP_PACKAGE_DIR"
info "Created zip package at $(realpath "$ZIP_PACKAGE_DIR.zip")"

info "Creating tar.gz '${ZIP_PACKAGE_DIR}.tar.gz'"
tar --dereference -czf "${ZIP_PACKAGE_DIR}.tar.gz" "$ZIP_PACKAGE_DIR"
info "Created tar.gz package at $(realpath "$ZIP_PACKAGE_DIR.tar.gz")"