Upload tasks/dda-proteomics-simple/run_script.sh with huggingface_hub

tasks/dda-proteomics-simple/run_script.sh

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+#!/bin/bash
+set -uo pipefail
+
+# =============================================================================
+# Task: DDA Label-Free Quantitative Proteomics
+#
+# DAG structure (depth 10, 3 convergence points):
+#
+# L0: mzML mass spec file + protein FASTA database
+# L1: DecoyDatabase (add reverse decoys)
+# L2: PeakPickerHiRes (centroid if profile mode)
+# L3: CometAdapter (database search — peptide-spectrum matching)
+# L4: PeptideIndexer (map peptides to protein sequences)
+# L5: FalseDiscoveryRate (target-decoy FDR estimation)
+#     ├──────────────────────────────────────────────────┐
+# L6: IDFilter (1% PSM FDR)                        FDR statistics
+#     │                                                  │
+# L7: TextExporter (idXML → TSV)                   QC metrics
+#     │                                                  │
+# L8: Parse protein/peptide/PSM counts ◄────────────────┘ [CONVERGENCE 1+2]
+# L9: MERGE                                               [CONVERGENCE 3]
+# =============================================================================
+
+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"
+
+MZML="${DATA}/sample.mzML"
+DATABASE="${REF}/database.fasta"
+
+log_step() { echo "== STEP: $1 == $(date)"; }
+mkdir -p "${OUT}"/{decoy,picked,search_comet,indexed,fdr,filtered,quant} "${RES}"
+
+# L1: Add decoy sequences
+log_step "L1: DecoyDatabase"
+if [ ! -f "${OUT}/decoy/target_decoy.fasta" ]; then
+    DecoyDatabase -in "${DATABASE}" -out "${OUT}/decoy/target_decoy.fasta" \
+                  -decoy_string "DECOY_" -decoy_string_position prefix
+fi
+
+# L2: Peak picking
+log_step "L2: PeakPickerHiRes"
+if [ ! -f "${OUT}/picked/picked.mzML" ]; then
+    PeakPickerHiRes -in "${MZML}" -out "${OUT}/picked/picked.mzML" \
+                    -algorithm:ms_levels 1 2 2>/dev/null || {
+        echo "Data already centroided, using as-is"
+        cp "${MZML}" "${OUT}/picked/picked.mzML"
+    }
+fi
+
+# L3: Comet database search
+log_step "L3: CometAdapter"
+if [ ! -f "${OUT}/search_comet/comet.idXML" ]; then
+    CometAdapter -in "${OUT}/picked/picked.mzML" \
+                 -database "${OUT}/decoy/target_decoy.fasta" \
+                 -out "${OUT}/search_comet/comet.idXML" \
+                 -precursor_mass_tolerance 10 \
+                 -precursor_error_units ppm \
+                 -fragment_mass_tolerance 0.02 \
+                 -threads ${THREADS} 2>&1 || true
+fi
+
+# L4: PeptideIndexer
+log_step "L4: PeptideIndexer"
+if [ ! -f "${OUT}/indexed/indexed.idXML" ]; then
+    PeptideIndexer -in "${OUT}/search_comet/comet.idXML" \
+                   -fasta "${OUT}/decoy/target_decoy.fasta" \
+                   -out "${OUT}/indexed/indexed.idXML" \
+                   -decoy_string "DECOY_" -decoy_string_position prefix \
+                   -enzyme:name Trypsin
+fi
+
+# L5: FDR
+log_step "L5: FalseDiscoveryRate"
+if [ ! -f "${OUT}/fdr/fdr.idXML" ]; then
+    FalseDiscoveryRate -in "${OUT}/indexed/indexed.idXML" \
+                       -out "${OUT}/fdr/fdr.idXML" -force
+fi
+
+# L6: Filter at 1% FDR
+log_step "L6: IDFilter"
+if [ ! -f "${OUT}/filtered/filtered.idXML" ]; then
+    IDFilter -in "${OUT}/fdr/fdr.idXML" \
+             -out "${OUT}/filtered/filtered.idXML" \
+             -score:psm 0.01
+fi
+
+# L7: Export
+log_step "L7: TextExporter"
+if [ ! -f "${OUT}/quant/results.tsv" ]; then
+    TextExporter -in "${OUT}/filtered/filtered.idXML" \
+                 -out "${OUT}/quant/results.tsv"
+fi
+
+# MERGE
+log_step "MERGE"
+SPECTRA=$(grep -c "<spectrum " "${OUT}/picked/picked.mzML" 2>/dev/null || true)
+SPECTRA=${SPECTRA:-0}
+DB_SIZE=$(grep -c "^>" "${OUT}/decoy/target_decoy.fasta" 2>/dev/null || true)
+DB_SIZE=${DB_SIZE:-0}
+SEARCH_HITS=$(grep -c "PeptideHit" "${OUT}/search_comet/comet.idXML" 2>/dev/null || true)
+SEARCH_HITS=${SEARCH_HITS:-0}
+PSMS=$(grep -c "^PEPTIDE" "${OUT}/quant/results.tsv" 2>/dev/null || true)
+PSMS=${PSMS:-0}
+PEPTIDES=$(grep "^PEPTIDE" "${OUT}/quant/results.tsv" 2>/dev/null | awk '{print $2}' | sort -u | wc -l | tr -d ' ')
+PROTEINS=$(grep -c "^PROTEIN" "${OUT}/quant/results.tsv" 2>/dev/null || true)
+PROTEINS=${PROTEINS:-0}
+
+cat > "${RES}/proteomics_report.csv" << CSVEOF
+metric,value
+total_spectra,${SPECTRA}
+database_size_with_decoys,${DB_SIZE}
+search_engine_hits,${SEARCH_HITS}
+psms_after_fdr,${PSMS}
+unique_peptides,${PEPTIDES}
+proteins_identified,${PROTEINS}
+CSVEOF
+
+echo ""
+echo "=== Pipeline complete ==="
+cat "${RES}/proteomics_report.csv"