From 33d854675ed8812f3b35f822e5620a5ae51065bb Mon Sep 17 00:00:00 2001
From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com>
Date: Sat, 24 Jan 2026 02:45:10 +0000
Subject: [PATCH 1/3] Initial plan


From 92f543dd5f918c58037c857b4045771272c71002 Mon Sep 17 00:00:00 2001
From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com>
Date: Sat, 24 Jan 2026 02:48:23 +0000
Subject: [PATCH 2/3] Create Fastplong.sh handler with direct file
 concatenation

Co-authored-by: pmorrell <6227040+pmorrell@users.noreply.github.com>
---
 Handlers/Fastplong.sh | 190 ++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 190 insertions(+)
 create mode 100644 Handlers/Fastplong.sh

diff --git a/Handlers/Fastplong.sh b/Handlers/Fastplong.sh
new file mode 100644
index 0000000..0ddff6c
--- /dev/null
+++ b/Handlers/Fastplong.sh
@@ -0,0 +1,190 @@
+#!/bin/env bash
+
+#   This script performs long-read processing using fastplong
+#   which removes adapter sequences and filters by quality
+#   Please install fastplong before use.
+
+set -o pipefail
+
+#   What are the dependencies for Fastplong?
+declare -a Fastplong_Dependencies=(fastplong parallel)
+
+#   A function to detect if we should skip adapter trimming for PacBio HiFi reads
+function detect_pacbio_hifi() {
+    local sample_file="$1"
+    #   Check if this is a PacBio HiFi file (typically indicated by filename patterns or read structure)
+    #   PacBio HiFi reads are typically labeled with 'hifi' or 'ccs' in the filename
+    if [[ "${sample_file}" =~ hifi|ccs|HiFi|CCS ]]; then
+        echo "true"
+    else
+        echo "false"
+    fi
+}
+
+#   A function to process a sample using direct file concatenation
+function process_sample_direct() {
+    local sampleName="$1" # Name of the sample
+    local sampleFiles="$2" # Comma-separated list of sample files
+    local outDirectory="$3" # Output directory
+    local skipAdapter="$4" # Whether to skip adapter trimming (for PacBio HiFi)
+    local seqHand="$5" # The sequence_handling directory
+    
+    #   Make the output directories
+    mkdir -p "${outDirectory}/${sampleName}"
+    local out="${outDirectory}/${sampleName}"
+    local stats="${out}/stats"
+    mkdir -p "${stats}"
+    
+    #   Convert comma-separated list to array
+    IFS=',' read -ra fileArray <<< "${sampleFiles}"
+    
+    #   Create a temporary concatenated file
+    local tmpConcatFile="${out}/${sampleName}_concat_temp.fastq"
+    
+    #   Concatenate all input files
+    echo "Processing sample: ${sampleName}"
+    echo "Concatenating ${#fileArray[@]} file(s)..."
+    
+    #   Clear any existing temp file
+    true > "${tmpConcatFile}"
+    
+    #   Concatenate files, handling different compression formats
+    for file in "${fileArray[@]}"; do
+        if [[ ! -f "${file}" ]]; then
+            echo "Error: Input file not found: ${file}" >&2
+            exit 1
+        fi
+        
+        if [[ "${file}" =~ \.gz$ ]]; then
+            gzip -cd "${file}" >> "${tmpConcatFile}"
+        elif [[ "${file}" =~ \.bz2$ ]]; then
+            bzip2 -cd "${file}" >> "${tmpConcatFile}"
+        else
+            cat "${file}" >> "${tmpConcatFile}"
+        fi
+    done
+    
+    #   Verify concatenated file was created
+    if [[ ! -s "${tmpConcatFile}" ]]; then
+        echo "Error: Failed to create concatenated file for ${sampleName}" >&2
+        rm -f "${tmpConcatFile}"
+        exit 1
+    fi
+    
+    #   Prepare output file names
+    local outputFile="${out}/${sampleName}_filtered.fastq.gz"
+    
+    #   Run fastplong with appropriate options
+    echo "Running fastplong on ${sampleName}..."
+    
+    if [[ "${skipAdapter}" == "true" ]]; then
+        #   Skip adapter trimming for PacBio HiFi reads
+        if ! fastplong --skip-adapters --input "${tmpConcatFile}" --output "${outputFile}"; then
+            echo "Error: fastplong failed for sample ${sampleName}" >&2
+            rm -f "${tmpConcatFile}"
+            exit 1
+        fi
+    else
+        #   Standard processing with adapter trimming
+        if ! fastplong --input "${tmpConcatFile}" --output "${outputFile}"; then
+            echo "Error: fastplong failed for sample ${sampleName}" >&2
+            rm -f "${tmpConcatFile}"
+            exit 1
+        fi
+    fi
+    
+    #   Verify output file was created
+    if [[ ! -f "${outputFile}" ]]; then
+        echo "Error: Output file not created for ${sampleName}: ${outputFile}" >&2
+        rm -f "${tmpConcatFile}"
+        exit 1
+    fi
+    
+    #   Clean up temporary concatenated file
+    rm -f "${tmpConcatFile}"
+    
+    echo "Successfully processed ${sampleName}"
+}
+
+#   Export the function
+export -f process_sample_direct
+export -f detect_pacbio_hifi
+
+#   Main handler function for Fastplong processing
+function Fastplong() {
+    local sampleList="$1" # List of samples (one sample per line, with files separated by commas)
+    local outPrefix="$2" # Output directory prefix
+    local project="$3" # Project name
+    local seqHand="$4" # The sequence_handling directory
+    
+    #   Create the output directory
+    local outDirectory="${outPrefix}/Fastplong"
+    mkdir -p "${outDirectory}"
+    
+    #   Check if helper scripts directory exists
+    if [[ ! -d "${seqHand}"/HelperScripts ]]; then
+        echo "Cannot find directory with helper scripts, exiting..." >&2
+        exit 1
+    fi
+    
+    #   Read the sample list
+    if [[ ! -f "${sampleList}" ]]; then
+        echo "Error: Sample list file not found: ${sampleList}" >&2
+        exit 1
+    fi
+    
+    #   Process each sample
+    declare -a sampleNames=()
+    declare -a sampleFileLists=()
+    declare -a skipAdapterFlags=()
+    
+    #   Parse the sample list
+    while IFS= read -r line; do
+        #   Skip empty lines and comments
+        [[ -z "${line}" || "${line}" =~ ^# ]] && continue
+        
+        #   Extract sample name (first file basename without extension)
+        local firstFile
+        local sampleName
+        local skipAdapter
+        firstFile=$(echo "${line}" | cut -d',' -f1)
+        sampleName=$(basename "${firstFile}" | sed 's/\.[^.]*$//')
+        
+        #   Detect if we should skip adapter trimming
+        skipAdapter=$(detect_pacbio_hifi "${firstFile}")
+        
+        sampleNames+=("${sampleName}")
+        sampleFileLists+=("${line}")
+        skipAdapterFlags+=("${skipAdapter}")
+    done < "${sampleList}"
+    
+    #   Check if we have any samples to process
+    if [[ ${#sampleNames[@]} -eq 0 ]]; then
+        echo "Error: No samples found in sample list" >&2
+        exit 1
+    fi
+    
+    #   Process samples in parallel
+    echo "Processing ${#sampleNames[@]} sample(s)..."
+    if ! parallel --verbose --xapply process_sample_direct {1} {2} "${outDirectory}" {3} "${seqHand}" \
+        ::: "${sampleNames[@]}" \
+        ::: "${sampleFileLists[@]}" \
+        ::: "${skipAdapterFlags[@]}"; then
+        echo "Error: Parallel processing failed" >&2
+        exit 1
+    fi
+    
+    #   Create a list of output files
+    find "${outDirectory}" -name "*_filtered.fastq.gz" -type f | sort > "${outDirectory}/${project}_fastplong_filtered.txt"
+    
+    #   Verify the output list was created
+    if [[ ! -f "${outDirectory}/${project}_fastplong_filtered.txt" ]]; then
+        echo "Error: Failed to create output file list" >&2
+        exit 1
+    fi
+    
+    echo "Fastplong processing complete. Output list: ${outDirectory}/${project}_fastplong_filtered.txt"
+}
+
+#   Export the function
+export -f Fastplong

From aa6323575e94f2f5d0d0d9e885bc0a44bb591711 Mon Sep 17 00:00:00 2001
From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com>
Date: Sat, 24 Jan 2026 02:49:22 +0000
Subject: [PATCH 3/3] Address code review feedback: fix shebang and improve
 sample name extraction

Co-authored-by: pmorrell <6227040+pmorrell@users.noreply.github.com>
---
 Handlers/Fastplong.sh | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/Handlers/Fastplong.sh b/Handlers/Fastplong.sh
index 0ddff6c..d24b085 100644
--- a/Handlers/Fastplong.sh
+++ b/Handlers/Fastplong.sh
@@ -1,4 +1,4 @@
-#!/bin/env bash
+#!/bin/bash
 
 #   This script performs long-read processing using fastplong
 #   which removes adapter sequences and filters by quality
@@ -148,7 +148,8 @@ function Fastplong() {
         local sampleName
         local skipAdapter
         firstFile=$(echo "${line}" | cut -d',' -f1)
-        sampleName=$(basename "${firstFile}" | sed 's/\.[^.]*$//')
+        #   Remove common sequencing file extensions (.fastq.gz, .fq.gz, .fastq, .fq, etc.)
+        sampleName=$(basename "${firstFile}" | sed -e 's/\.fastq\.gz$//' -e 's/\.fq\.gz$//' -e 's/\.fastq\.bz2$//' -e 's/\.fq\.bz2$//' -e 's/\.fastq$//' -e 's/\.fq$//')
         
         #   Detect if we should skip adapter trimming
         skipAdapter=$(detect_pacbio_hifi "${firstFile}")