Add the script of the pipeline

Fast5Pipeline

@@ -0,0 +1,162 @@
+#!/usr/bin/env bash
+# -*- coding: utf-8 -*-
+# Created on Fri June 23 14:31:04 2023    
+# @author: AlbertRockG
+
+# Function to display usage information
+usage() {
+    echo "Usage: $0 -c <guppy_config> -i <input_dir> -o <output_dir> -k <barcode_kits> -m <medaka_model> -b <batchsize>"
+    echo "Options:"
+    echo "  -c, --guppy-config     Guppy config file"
+    echo "  -i, --input-dir        Input directory"
+    echo "  -o, --output-dir       Output directory: different from the input directory"
+    echo "  -k, --barcode-kits     Barcode kits"
+    echo "  -m, --medaka-model     Medaka model: only high accuracy models supported"
+    echo "  -b, --batchsize        GPU memory control: controls memory use (default: 100)."
+    exit 1
+}
+
+# Function to concatenate fastq.gz files in a subfolder
+concatenate_fastq() {
+    local subfolder=$1
+
+    echo "Processing subfolder: $subfolder"
+
+    # Create the "joined" folder in the parent directory
+    parent_dir=$(dirname "$subfolder")
+    joined_folder="$parent_dir/joined"
+    mkdir -p "$joined_folder"
+
+    # Create output file name based on subfolder name
+    output_file="$joined_folder/$(basename "$subfolder").fastq.gz"
+
+    # Concatenate fastq.gz files into the output file
+    gunzip -c "$subfolder"/*.fastq.gz | gzip -c > "$output_file"
+
+    echo "Concatenated fastq.gz files into: $output_file"
+    echo ""
+}
+
+# Function to run flye on a joined_fastq file
+run_fly() {
+    local input_file=$1
+
+    echo "Processing file: $input_file"
+
+    # Create the "assembled" folder in the parent directory
+    parent_dir="${input_file%%/*}"
+    assembly_folder="$parent_dir/assembled"
+    mkdir -p "$assembly_folder"
+
+    # Create output file name based on subfolder name
+    output="$assembly_folder/$(basename "$input_file")"
+
+    # Run flye on the input file
+    flye -t "$(nproc)" --out-dir "$output" --nano-hq "$input_file"
+
+    echo "Flye analysis completed for: $input_file"
+    echo ""
+}
+
+# Function to run flye on a joined_fastq file
+run_medaka() {
+    local input_file=$1
+
+    echo "Processing file: $input_file"
+
+    # Create the "polished" folder in the parent directory
+    main_dir="${input_file%%/*}"
+    assembly_dir="$(basename "$input_file")"
+    polished_folder="$main_dir/polished"
+    mkdir -p "$polished_folder"
+
+    # Create output dir name based on the input file name
+    output="$polished_folder/$(basename "$input_file")"
+
+    # Run medaka on the input file
+    medaka_consensus -i "$input_file" \
+                 -d "$main_dir"/assembled/"$assembly_dir"/assembly.fasta \
+                 -o "$output" -m "$medaka_model" -t "$(nproc)" -b "$batchsize"
+
+    echo "Medaka analysis completed for: $input_file"
+    echo ""
+}
+
+
+# Parse command-line options
+while getopts ":c:i:o:k:m:b:" opt; do
+    case "${opt}" in
+        c)
+            guppy_config=${OPTARG}
+            ;;
+        i)
+            input_dir=${OPTARG}
+            ;;
+        o)
+            output_dir=${OPTARG}
+            ;;
+        k)
+            barcode_kits=${OPTARG}
+            ;;
+        m)
+            medaka_model=${OPTARG}
+            ;;
+        b)
+            batchsize=${OPTARG}
+            ;;
+        *)
+            usage
+            ;;
+    esac
+done
+
+# Check if all required options are provided
+if [[ -z $guppy_config || -z $input_dir || -z $output_dir || -z $barcode_kits || -z $medaka_model ]]; then
+    echo "Error: Missing required options"
+    usage
+fi
+
+# Step 1: Run guppy_basecaller
+guppy_basecaller --disable_pings -x auto \
+    -c "$guppy_config" \
+    -i "$input_dir" --recursive \
+    -s "$output_dir/basecalled"
+
+# Step 2: Run guppy_barcoder
+guppy_barcoder -t "$(nproc)" --disable_pings -x auto \
+    --barcode_kits "$barcode_kits" --enable_trim_barcodes \
+    -i "$output_dir/basecalled" --recursive \
+    -s "$output_dir/trimmed" --compress_fastq
+
+# Step 3: Join fastq.gz files
+
+# Loop through subfolders in the input folder
+for subfolder in "$output_dir"/trimmed/*; do
+    if [[ -d $subfolder ]]; then
+        concatenate_fastq "$subfolder"
+    fi
+done
+
+# Step 4: Run flye
+for input_file in "$output_dir"/joined/*.fastq.gz; do
+    if [[ -f $input_file ]]; then
+        run_flye "$input_file"
+    fi
+done
+
+# Step 6: Run medaka_consensus
+conda_env=medaka
+
+if conda info --envs | grep -wq "$conda_env"; then
+    # Activate conda environment
+    conda activate medaka
+
+    for input_file in "$output_dir"/joined/*.fastq.gz; do
+        if [[ -f $input_file ]]; then
+            run_medaka "$input_file"
+        fi
+    done
+
+    # Deactivate conda environment
+    conda deactivate
+fi