Upload tasks/mapping-qc/run_script.sh with huggingface_hub

tasks/mapping-qc/run_script.sh

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+#!/bin/bash
+set -e
+
+# =============================================================================
+# Task 23: Genome Coverage and Mapping Quality Analysis
+#
+# DAG (depth 5):
+#
+# L0: PE reads + reference
+# L1: fastp (trim)
+# L2: bwa mem (align)
+#     ├──────────────────────────────────────┐
+# L3: samtools stats/flagstat      mosdepth (coverage)
+#     │                                │
+# L4: samtools idxstats          ├── per-base coverage
+#     (per-contig mapping)       └── per-window coverage
+#     │                                │
+#     └── bedtools genomecov     deeptools bamCoverage
+#         (coverage histogram)    (normalized signal)
+# L5: MERGE
+# =============================================================================
+
+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"
+
+log_step() {
+    echo "=================================================================="
+    echo "STEP: $1"
+    echo "$(date)"
+    echo "=================================================================="
+}
+
+mkdir -p "${OUT}"/{trimmed,aligned,stats,coverage} "${RES}"
+
+# ===========================================================================
+# L1: Trimming
+# ===========================================================================
+log_step "L1: fastp"
+if [ ! -f "${OUT}/trimmed/R1.fastq" ]; then
+    fastp --in1 "${DATA}/reads_R1.fastq" --in2 "${DATA}/reads_R2.fastq" \
+          --out1 "${OUT}/trimmed/R1.fastq" --out2 "${OUT}/trimmed/R2.fastq" \
+          --detect_adapter_for_pe --thread ${THREADS} \
+          --json "${OUT}/trimmed/fastp.json"
+else echo "Skipping (exists)"; fi
+
+# ===========================================================================
+# L2: Alignment
+# ===========================================================================
+log_step "L2: bwa mem"
+if [ ! -f "${OUT}/aligned/reads.sorted.bam" ]; then
+    bwa index "${REFERENCE}" 2>/dev/null
+    bwa mem -t ${THREADS} -R "@RG\tID:sample\tSM:sample\tPL:ILLUMINA" \
+            "${REFERENCE}" "${OUT}/trimmed/R1.fastq" "${OUT}/trimmed/R2.fastq" \
+        | samtools sort -@ ${THREADS} -o "${OUT}/aligned/reads.sorted.bam"
+    samtools index "${OUT}/aligned/reads.sorted.bam"
+else echo "Skipping (exists)"; fi
+BAM="${OUT}/aligned/reads.sorted.bam"
+
+# ===========================================================================
+# L3-A: samtools stats + flagstat
+# ===========================================================================
+log_step "L3-A: samtools stats"
+if [ ! -f "${OUT}/stats/samtools_stats.txt" ]; then
+    samtools stats "${BAM}" > "${OUT}/stats/samtools_stats.txt"
+    samtools flagstat "${BAM}" > "${OUT}/stats/flagstat.txt"
+    samtools idxstats "${BAM}" > "${OUT}/stats/idxstats.txt"
+else echo "Skipping (exists)"; fi
+
+# ===========================================================================
+# L3-B: mosdepth coverage analysis
+# ===========================================================================
+log_step "L3-B: mosdepth"
+if [ ! -f "${OUT}/coverage/sample.mosdepth.summary.txt" ]; then
+    mosdepth -t ${THREADS} --by 1000 "${OUT}/coverage/sample" "${BAM}"
+else echo "Skipping (exists)"; fi
+
+# ===========================================================================
+# L4-A: bedtools genomecov (coverage histogram)
+# ===========================================================================
+log_step "L4-A: bedtools genomecov"
+if [ ! -f "${OUT}/coverage/genomecov.txt" ]; then
+    bedtools genomecov -ibam "${BAM}" > "${OUT}/coverage/genomecov.txt"
+else echo "Skipping (exists)"; fi
+
+# ===========================================================================
+# L4-B: deeptools bamCoverage (normalized signal)
+# ===========================================================================
+log_step "L4-B: deeptools bamCoverage"
+if [ ! -f "${OUT}/coverage/sample.bw" ]; then
+    bamCoverage --bam "${BAM}" --outFileName "${OUT}/coverage/sample.bw" \
+                --binSize 100 --normalizeUsing RPGC \
+                --effectiveGenomeSize 2900000 \
+                --numberOfProcessors ${THREADS} 2>/dev/null || true
+else echo "Skipping (exists)"; fi
+
+# ===========================================================================
+# L5: MERGE
+# ===========================================================================
+log_step "L5-MERGE"
+
+# Parse samtools stats
+TOTAL_READS=$(grep "^SN" "${OUT}/stats/samtools_stats.txt" | grep "raw total sequences" | cut -f3)
+MAPPED_READS=$(grep "^SN" "${OUT}/stats/samtools_stats.txt" | grep "reads mapped:" | cut -f3)
+MAPPED_PCT=$(grep "mapped (" "${OUT}/stats/flagstat.txt" | head -1 | grep -oP '[\d.]+%' | tr -d '%')
+PROPERLY_PAIRED=$(grep "properly paired" "${OUT}/stats/flagstat.txt" | grep -oP '[\d.]+%' | tr -d '%')
+AVG_QUALITY=$(grep "^SN" "${OUT}/stats/samtools_stats.txt" | grep "average quality" | cut -f3)
+AVG_INSERT=$(grep "^SN" "${OUT}/stats/samtools_stats.txt" | grep "insert size average" | cut -f3)
+ERROR_RATE=$(grep "^SN" "${OUT}/stats/samtools_stats.txt" | grep "error rate" | cut -f3)
+
+# Parse mosdepth
+MEAN_COV=$(awk '$1=="total" {print $4}' "${OUT}/coverage/sample.mosdepth.summary.txt")
+MIN_COV=$(awk '$1=="total" {print $5}' "${OUT}/coverage/sample.mosdepth.summary.txt")
+MAX_COV=$(awk '$1=="total" {print $6}' "${OUT}/coverage/sample.mosdepth.summary.txt")
+
+# Coverage breadth from genomecov (% bases with >=1x coverage)
+BREADTH=$(awk '$1=="genome" && $2==0 {print 100-$5*100}' "${OUT}/coverage/genomecov.txt" | head -1)
+
+cat > "${RES}/mapping_qc_report.csv" << CSVEOF
+metric,value
+total_reads,${TOTAL_READS}
+mapped_reads,${MAPPED_READS}
+mapping_rate,${MAPPED_PCT}
+properly_paired_rate,${PROPERLY_PAIRED}
+average_base_quality,${AVG_QUALITY}
+average_insert_size,${AVG_INSERT}
+error_rate,${ERROR_RATE}
+mean_coverage,${MEAN_COV}
+min_coverage,${MIN_COV}
+max_coverage,${MAX_COV}
+coverage_breadth_pct,${BREADTH}
+CSVEOF
+
+echo ""
+echo "=== Pipeline complete ==="
+cat "${RES}/mapping_qc_report.csv"
+echo ""
+ls -lh "${RES}/"