Upload tasks/downsampling-analysis/run_script.sh with huggingface_hub

tasks/downsampling-analysis/run_script.sh

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+#!/bin/bash
+set -e
+
+# =============================================================================
+# Task 27: Read Downsampling and Assembly Quality Titration
+#
+# DAG (depth 5, replicated fan-out):
+#
+# L0: PE reads + reference
+# L1: fastp (trim full dataset)
+# L2: ├── seqkit sample 25% → megahit → quast
+#     ├── seqkit sample 50% → megahit → quast
+#     └── seqkit sample 100% → megahit → quast
+# L3: Parse all three QUAST reports
+# L4: MERGE (titration report: how coverage affects assembly)
+# =============================================================================
+
+THREADS=$(( $(nproc) > 8 ? 8 : $(nproc) ))
+SCRIPT_DIR="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"
+DATA="${SCRIPT_DIR}/data"
+REF="${SCRIPT_DIR}/reference"
+OUT="${SCRIPT_DIR}/outputs"
+RES="${SCRIPT_DIR}/results"
+
+REFERENCE="${REF}/reference.fna"
+FRACTIONS=("0.25" "0.50" "1.00")
+
+log_step() {
+    echo "=================================================================="
+    echo "STEP: $1"
+    echo "$(date)"
+    echo "=================================================================="
+}
+
+mkdir -p "${OUT}/trimmed" "${RES}"
+
+# L1: Trim
+log_step "L1: fastp"
+if [ ! -f "${OUT}/trimmed/R1.fastq.gz" ]; then
+    fastp --in1 "${DATA}/reads_R1.fastq.gz" --in2 "${DATA}/reads_R2.fastq.gz" \
+          --out1 "${OUT}/trimmed/R1.fastq.gz" --out2 "${OUT}/trimmed/R2.fastq.gz" \
+          --detect_adapter_for_pe --thread ${THREADS} --json "${OUT}/trimmed/fastp.json"
+else echo "Skipping (exists)"; fi
+
+# L2: For each fraction, subsample + assemble + QC
+for FRAC in "${FRACTIONS[@]}"; do
+    FRAC_DIR="${OUT}/frac_${FRAC}"
+    mkdir -p "${FRAC_DIR}"
+
+    log_step "L2: Subsample ${FRAC} + assemble"
+    if [ ! -f "${FRAC_DIR}/assembly/final.contigs.fa" ]; then
+        if [ "${FRAC}" = "1.00" ]; then
+            cp "${OUT}/trimmed/R1.fastq.gz" "${FRAC_DIR}/R1.fastq.gz"
+            cp "${OUT}/trimmed/R2.fastq.gz" "${FRAC_DIR}/R2.fastq.gz"
+        else
+            seqkit sample -p "${FRAC}" -s 42 "${OUT}/trimmed/R1.fastq.gz" -o "${FRAC_DIR}/R1.fastq.gz"
+            seqkit sample -p "${FRAC}" -s 42 "${OUT}/trimmed/R2.fastq.gz" -o "${FRAC_DIR}/R2.fastq.gz"
+        fi
+        megahit -1 "${FRAC_DIR}/R1.fastq.gz" -2 "${FRAC_DIR}/R2.fastq.gz" \
+                -o "${FRAC_DIR}/assembly" -t ${THREADS} --min-contig-len 500
+    else echo "Skipping (exists)"; fi
+
+    log_step "L2: QUAST ${FRAC}"
+    if [ ! -f "${FRAC_DIR}/quast/report.tsv" ]; then
+        quast "${FRAC_DIR}/assembly/final.contigs.fa" -r "${REFERENCE}" \
+              -o "${FRAC_DIR}/quast" -t ${THREADS}
+    else echo "Skipping (exists)"; fi
+done
+
+# L3-L4: Parse + MERGE
+log_step "MERGE"
+
+echo "fraction,total_length,num_contigs,n50,largest_contig,genome_fraction,num_reads" > "${RES}/downsampling_report.csv"
+
+for FRAC in "${FRACTIONS[@]}"; do
+    FRAC_DIR="${OUT}/frac_${FRAC}"
+    TOTAL=$(grep "^Total length" "${FRAC_DIR}/quast/report.tsv" | head -1 | cut -f2)
+    NCTG=$(grep "^# contigs " "${FRAC_DIR}/quast/report.tsv" | head -1 | cut -f2)
+    N50=$(grep "^N50" "${FRAC_DIR}/quast/report.tsv" | cut -f2)
+    LARGEST=$(grep "^Largest contig" "${FRAC_DIR}/quast/report.tsv" | cut -f2)
+    GF=$(grep "^Genome fraction" "${FRAC_DIR}/quast/report.tsv" | cut -f2)
+    NREADS=$(zcat "${FRAC_DIR}/R1.fastq.gz" | wc -l | awk '{print $1/4}')
+    echo "${FRAC},${TOTAL},${NCTG},${N50},${LARGEST},${GF},${NREADS}" >> "${RES}/downsampling_report.csv"
+done
+
+echo ""
+echo "=== Pipeline complete ==="
+cat "${RES}/downsampling_report.csv"