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new file mode 100644 index 0000000..3e6cefe --- /dev/null +++ b/input/HOPEproteome_TMT11workflow.workflow @@ -0,0 +1,327 @@ +# Workflow: HOPEproteome_TMT11workflow + + +# Please edit the following path to point to the correct location. +# In Windows, please replace single '\' with '\\' +database.db-path=/home/rstudio/fragpipe/input/decoys-contam-custom-canonical.fasta + +crystalc.run-crystalc=false +database.decoy-tag=rev_ +diann.fragpipe.cmd-opts= +diann.generate-msstats=true +diann.heavy= +diann.library= +diann.light= +diann.medium= +diann.q-value=0.01 +diann.quantification-strategy=3 +diann.quantification-strategy-2=QuantUMS (high accuracy) +diann.run-dia-nn=false +diann.run-dia-plex=false +diann.run-specific-protein-q-value=false +diann.unrelated-runs=false +diann.use-predicted-spectra=true +diaumpire.AdjustFragIntensity=true +diaumpire.BoostComplementaryIon=false +diaumpire.CorrThreshold=0 +diaumpire.DeltaApex=0.2 +diaumpire.ExportPrecursorPeak=false +diaumpire.Q1=true +diaumpire.Q2=true +diaumpire.Q3=true +diaumpire.RFmax=500 +diaumpire.RPmax=25 +diaumpire.RTOverlap=0.3 +diaumpire.SE.EstimateBG=false +diaumpire.SE.IsoPattern=0.3 +diaumpire.SE.MS1PPM=10 +diaumpire.SE.MS2PPM=20 +diaumpire.SE.MS2SN=1.1 +diaumpire.SE.MassDefectFilter=true +diaumpire.SE.MassDefectOffset=0.1 +diaumpire.SE.NoMissedScan=1 +diaumpire.SE.SN=1.1 +diaumpire.run-diaumpire=false +fpop.fpop-tmt=false +fpop.label_control= +fpop.label_fpop= +fpop.region_size=1 +fpop.run-fpop=false +fpop.subtract-control=false +freequant.mz-tol=10 +freequant.rt-tol=0.4 +freequant.run-freequant=false +ionquant.excludemods= +ionquant.heavy= +ionquant.imtol=0.05 +ionquant.ionfdr=0.01 +ionquant.light= +ionquant.locprob=0.75 +ionquant.maxlfq=1 +ionquant.mbr=0 +ionquant.mbrimtol=0.05 +ionquant.mbrmincorr=0 +ionquant.mbrrttol=1 +ionquant.mbrtoprun=10 +ionquant.medium= +ionquant.minfreq=0 +ionquant.minions=2 +ionquant.minisotopes=2 +ionquant.minscans=3 +ionquant.mztol=10 +ionquant.normalization=1 +ionquant.peptidefdr=1 +ionquant.proteinfdr=1 +ionquant.requantify=1 +ionquant.rttol=0.4 +ionquant.run-ionquant=true +ionquant.tp=0 +ionquant.uniqueness=0 +ionquant.use-labeling=false +ionquant.use-lfq=true +ionquant.writeindex=0 +msbooster.predict-rt=true +msbooster.predict-spectra=true +msbooster.run-msbooster=true +msbooster.use-correlated-features=false +msfragger.Y_type_masses= +msfragger.activation_types=all +msfragger.allowed_missed_cleavage_1=2 +msfragger.allowed_missed_cleavage_2=2 +msfragger.calibrate_mass=2 +msfragger.check_spectral_files=true +msfragger.clip_nTerm_M=true +msfragger.deisotope=1 +msfragger.delta_mass_exclude_ranges=(-1.5,3.5) +msfragger.deneutralloss=1 +msfragger.diagnostic_fragments= +msfragger.diagnostic_intensity_filter=0 +msfragger.digest_max_length=50 +msfragger.digest_min_length=8 +msfragger.fragment_ion_series=b,y +msfragger.fragment_mass_tolerance=20 +msfragger.fragment_mass_units=1 +msfragger.group_variable=0 +msfragger.intensity_transform=0 +msfragger.ion_series_definitions= +msfragger.isotope_error=-1/0/1/2/3 +msfragger.labile_search_mode=off +msfragger.localize_delta_mass=false +msfragger.mass_diff_to_variable_mod=0 +msfragger.mass_offsets=0 +msfragger.mass_offsets_detailed= +msfragger.max_fragment_charge=2 +msfragger.max_variable_mods_combinations=5000 +msfragger.max_variable_mods_per_peptide=3 +msfragger.min_fragments_modelling=2 +msfragger.min_matched_fragments=4 +msfragger.min_sequence_matches=2 +msfragger.minimum_peaks=15 +msfragger.minimum_ratio=0.01 +msfragger.misc.fragger.clear-mz-hi=131.5 +msfragger.misc.fragger.clear-mz-lo=125.5 +msfragger.misc.fragger.digest-mass-hi=5000 +msfragger.misc.fragger.digest-mass-lo=200 +msfragger.misc.fragger.enzyme-dropdown-1=lysc +msfragger.misc.fragger.enzyme-dropdown-2=trypsin +msfragger.misc.fragger.precursor-charge-hi=4 +msfragger.misc.fragger.precursor-charge-lo=1 +msfragger.misc.fragger.remove-precursor-range-hi=1.5 +msfragger.misc.fragger.remove-precursor-range-lo=-1.5 +msfragger.misc.slice-db=1 +msfragger.num_enzyme_termini=2 +msfragger.output_format=pepXML_pin +msfragger.output_max_expect=50 +msfragger.output_report_topN=1 +msfragger.output_report_topN_dda_plus=5 +msfragger.output_report_topN_dia1=5 +msfragger.override_charge=false +msfragger.precursor_mass_lower=-20 +msfragger.precursor_mass_mode=selected +msfragger.precursor_mass_units=1 +msfragger.precursor_mass_upper=20 +msfragger.precursor_true_tolerance=20 +msfragger.precursor_true_units=1 +msfragger.remainder_fragment_masses=-18.01056 79.96633 +msfragger.remove_precursor_peak=1 +msfragger.report_alternative_proteins=true +msfragger.require_precursor=true +msfragger.restrict_deltamass_to=all +msfragger.reuse_dia_fragment_peaks=false +msfragger.run-msfragger=true +msfragger.search_enzyme_cut_1=K +msfragger.search_enzyme_cut_2=KR +msfragger.search_enzyme_name_1=lysc +msfragger.search_enzyme_name_2=trypsin +msfragger.search_enzyme_nocut_1=P +msfragger.search_enzyme_nocut_2=P +msfragger.search_enzyme_sense_1=C +msfragger.search_enzyme_sense_2=C +msfragger.table.fix-mods=0.0,C-Term Peptide,true,-1; 0.0,N-Term Peptide,true,-1; 0.0,C-Term Protein,true,-1; 0.0,N-Term Protein,true,-1; 0.0,G (glycine),true,-1; 0.0,A (alanine),true,-1; 0.0,S (serine),true,-1; 0.0,P (proline),true,-1; 0.0,V (valine),true,-1; 0.0,T (threonine),true,-1; 57.02146,C (cysteine),true,-1; 0.0,L (leucine),true,-1; 0.0,I (isoleucine),true,-1; 0.0,N (asparagine),true,-1; 0.0,D (aspartic acid),true,-1; 0.0,Q (glutamine),true,-1; 229.16293,K (lysine),true,-1; 0.0,E (glutamic acid),true,-1; 0.0,M (methionine),true,-1; 0.0,H (histidine),true,-1; 0.0,F (phenylalanine),true,-1; 0.0,R (arginine),true,-1; 0.0,Y (tyrosine),true,-1; 0.0,W (tryptophan),true,-1; 0.0,B ,true,-1; 0.0,J,true,-1; 0.0,O,true,-1; 0.0,U,true,-1; 0.0,X,true,-1; 0.0,Z,true,-1 +msfragger.table.var-mods=15.9949,M,true,3; 42.0106,[^,true,1; 79.96633,STY,false,3; -17.0265,nQnC,false,1; -18.0106,nE,false,1; 229.16293,n^,true,1; 229.16293,S,true,1; 0.0,site_08,false,1; 0.0,site_09,false,1; 0.0,site_10,false,1; 0.0,site_11,false,1; 0.0,site_12,false,1; 0.0,site_13,false,1; 0.0,site_14,false,1; 0.0,site_15,false,1; 0.0,site_16,false,1 +msfragger.track_zero_topN=0 +msfragger.use_all_mods_in_first_search=false +msfragger.use_detailed_offsets=false +msfragger.use_topN_peaks=150 +msfragger.write_calibrated_mzml=false +msfragger.write_uncalibrated_mgf=false +msfragger.zero_bin_accept_expect=0 +msfragger.zero_bin_mult_expect=1 +opair.activation1=HCD +opair.activation2=ETD +opair.filterOxonium=true +opair.glyco_db= +opair.max_glycans=4 +opair.max_isotope_error=2 +opair.min_isotope_error=0 +opair.ms1_tol=20 +opair.ms2_tol=20 +opair.oxonium_filtering_file= +opair.oxonium_minimum_intensity=0.05 +opair.reverse_scan_order=false +opair.run-opair=false +opair.single_scan_type=false +peptide-prophet.cmd-opts=--decoyprobs --ppm --accmass --nonparam --expectscore +peptide-prophet.combine-pepxml=false +peptide-prophet.run-peptide-prophet=false +percolator.cmd-opts=--only-psms --no-terminate --post-processing-tdc +percolator.keep-tsv-files=false +percolator.min-prob=0.5 +percolator.run-percolator=true +phi-report.dont-use-prot-proph-file=false +phi-report.filter=--sequential --picked --prot 0.01 +phi-report.pep-level-summary=false +phi-report.philosoher-msstats=false +phi-report.print-decoys=false +phi-report.prot-level-summary=false +phi-report.remove-contaminants=false +phi-report.run-report=true +protein-prophet.cmd-opts=--maxppmdiff 2000000 --minprob 0.5 +protein-prophet.run-protein-prophet=true +ptmprophet.cmdline= +ptmprophet.run-ptmprophet=false +ptmshepherd.adv_params=false +ptmshepherd.annotation-common=true +ptmshepherd.annotation-custom=false +ptmshepherd.annotation-glyco=false +ptmshepherd.annotation-unimod=false +ptmshepherd.annotation_file= +ptmshepherd.annotation_tol=0.01 +ptmshepherd.cap_y_ions= +ptmshepherd.decoy_type=1 +ptmshepherd.diag_ions= +ptmshepherd.diagmine_diagMinFoldChange=3.0 +ptmshepherd.diagmine_diagMinSpecDiff=00.2 +ptmshepherd.diagmine_fragMinFoldChange=3.0 +ptmshepherd.diagmine_fragMinPropensity=00.1 +ptmshepherd.diagmine_fragMinSpecDiff=00.1 +ptmshepherd.diagmine_minIonsPerSpec=2 +ptmshepherd.diagmine_minPeps=25 +ptmshepherd.diagmine_pepMinFoldChange=3.0 +ptmshepherd.diagmine_pepMinSpecDiff=00.2 +ptmshepherd.glyco_adducts= +ptmshepherd.glyco_fdr=1.00 +ptmshepherd.glyco_isotope_max=3 +ptmshepherd.glyco_isotope_min=-1 +ptmshepherd.glyco_ppm_tol=50 +ptmshepherd.glycodatabase= +ptmshepherd.histo_smoothbins=2 +ptmshepherd.iontype_a=false +ptmshepherd.iontype_b=true +ptmshepherd.iontype_c=false +ptmshepherd.iontype_x=false +ptmshepherd.iontype_y=true +ptmshepherd.iontype_z=false +ptmshepherd.localization_allowed_res= +ptmshepherd.localization_background=4 +ptmshepherd.max_adducts=0 +ptmshepherd.n_glyco=true +ptmshepherd.normalization-psms=true +ptmshepherd.normalization-scans=false +ptmshepherd.output_extended=false +ptmshepherd.peakpicking_mass_units=0 +ptmshepherd.peakpicking_minPsm=10 +ptmshepherd.peakpicking_promRatio=0.3 +ptmshepherd.peakpicking_width=0.002 +ptmshepherd.precursor_mass_units=0 +ptmshepherd.precursor_tol=0.01 +ptmshepherd.print_decoys=false +ptmshepherd.prob_dhexOx=2,0.5,0.1 +ptmshepherd.prob_dhexY=2,0.5 +ptmshepherd.prob_neuacOx=2,0.05,0.2 +ptmshepherd.prob_neugcOx=2,0.05,0.2 +ptmshepherd.prob_phosphoOx=2,0.05,0.2 +ptmshepherd.prob_regY=5,0.5 +ptmshepherd.prob_sulfoOx=2,0.05,0.2 +ptmshepherd.remainder_masses= +ptmshepherd.remove_glycan_delta_mass=true +ptmshepherd.run-shepherd=false +ptmshepherd.run_diagextract_mode=false +ptmshepherd.run_diagmine_mode=false +ptmshepherd.run_glyco_mode=false +ptmshepherd.spectra_maxfragcharge=2 +ptmshepherd.spectra_ppmtol=20 +ptmshepherd.varmod_masses= +quantitation.run-label-free-quant=false +run-psm-validation=true +run-validation-tab=true +saintexpress.fragpipe.cmd-opts= +saintexpress.max-replicates=3 +saintexpress.run-saint-express=true +saintexpress.virtual-controls=100 +speclibgen.easypqp.extras.max_delta_ppm=15 +speclibgen.easypqp.extras.max_delta_unimod=0.02 +speclibgen.easypqp.extras.rt_lowess_fraction=0 +speclibgen.easypqp.fragment.a=false +speclibgen.easypqp.fragment.b=true +speclibgen.easypqp.fragment.c=false +speclibgen.easypqp.fragment.x=false +speclibgen.easypqp.fragment.y=true +speclibgen.easypqp.fragment.z=false +speclibgen.easypqp.im-cal=Automatic selection of a run as reference IM +speclibgen.easypqp.neutral_loss=false +speclibgen.easypqp.rt-cal=noiRT +speclibgen.easypqp.select-file.text= +speclibgen.easypqp.select-im-file.text= +speclibgen.keep-intermediate-files=false +speclibgen.run-speclibgen=false +tab-run.delete_calibrated_mzml=false +tab-run.delete_temp_files=false +tab-run.sub_mzml_prob_threshold=0.5 +tab-run.write_sub_mzml=false +tmtintegrator.add_Ref=-1 +tmtintegrator.aggregation_method=0 +tmtintegrator.allow_overlabel=true +tmtintegrator.allow_unlabeled=false +tmtintegrator.best_psm=true +tmtintegrator.channel_num=TMT-11 +tmtintegrator.extraction_tool=IonQuant +tmtintegrator.glyco_qval=-1 +tmtintegrator.groupby=-1 +tmtintegrator.log2transformed=true +tmtintegrator.max_pep_prob_thres=0.9 +tmtintegrator.min_ntt=0 +tmtintegrator.min_pep_prob=0.9 +tmtintegrator.min_percent=0.05 +tmtintegrator.min_purity=0.5 +tmtintegrator.min_site_prob=-1 +tmtintegrator.mod_tag=none +tmtintegrator.ms1_int=true +tmtintegrator.outlier_removal=true +tmtintegrator.print_RefInt=false +tmtintegrator.prot_exclude=none +tmtintegrator.prot_norm=1 +tmtintegrator.psm_norm=false +tmtintegrator.quant_level=2 +tmtintegrator.ref_tag=Reference +tmtintegrator.run-tmtintegrator=true +tmtintegrator.tolerance=20 +tmtintegrator.top3_pep=true +tmtintegrator.unique_gene=0 +tmtintegrator.unique_pep=false +tmtintegrator.use_glycan_composition=false +workflow.description=

Basic TMT 10-plex workflow, with identification and quantification from high mass accuracy MS2. Met oxidation, protein N-term Acetyl, n-term TMT, and TMT on S ("overlabeling") are specified as variable modifications. TMT-Integrator with virtual reference approach, median-centering normalization, data summarization at the gene level. If a reference/bridge sample is available, specify the corresponding channel/sample name tag in the annotation file(s) and in TMT-Integrator tab.

+workflow.input.data-type.im-ms=false +workflow.input.data-type.regular-ms=true +workflow.misc.save-sdrf=true +workflow.saved-with-ver=21.1 diff --git a/run_fragpipe.sh b/run_fragpipe.sh index b3ae2b2..4fa6e92 100644 --- a/run_fragpipe.sh +++ b/run_fragpipe.sh @@ -1,5 +1,3 @@ -#!/bin/bash - set -e set -o pipefail @@ -7,6 +5,38 @@ set -o pipefail input_dir=input tools_dir=/fragpipe_bin/fragPipe-22.0/fragpipe/tools +#Initialize variables +cohort="" +run_subset=FALSE + +# define parameter variables +while [ $# -gt 0 ]; do + case "$1" in + --cohort) + if [[ "$1" != *=* ]]; then shift; fi # Value is next arg if no `=` + cohort="${1#*=}" + ;; + --run_subset) + run_subset=TRUE # Set run_subset to true when the flag is provided + ;; + --help|-h) + echo "Usage: $0 [--run_subset] [--cohort [cptac|hope]]" + echo "" + echo "Options:" + echo " --run_subset Run fragpipe on first experiment in cohort only" + echo " --cohort Cohort, cptac or hope" + echo " -h/--help Display usage information" + exit 0 + ;; + *) + >&2 printf "Error: Invalid argument\n" + exit 1 + ;; + esac + shift +done + + # Error out if no custom.fasta is provided if [ ! -e "$input_dir/custom.fasta" ]; then echo "Error: must supply a custom.fasta file in the input directory ($input_dir)" @@ -29,9 +59,29 @@ $tools_dir/Philosopher/philosopher-v5.1.1 workspace --clean # Return to the previous directory cd - -# set cavatica directory -cavatica_dir=(/home/rstudio/fragpipe/data/projects/harenzaj/proteomics) +# set cavatica directory based on --cohort argument +if [[ -n "$cohort" ]]; then + + # Check if the next argument is "hope" or "cptac" + if [[ "$cohort" == "hope" ]]; then + echo "Fragpipe will be run on HOPE cohort" + cavatica_dir=(/home/rstudio/fragpipe/data/projects/harenzaj/hope-proteomics/HOPE_TotalProteome_mzML) + + elif [[ "$cohort" == "cptac" ]]; then + echo "Fragpipe will be run on CPTAC cohort" + cavatica_dir=(/home/rstudio/fragpipe/data/projects/harenzaj/proteomics) + + else + echo "Error: Invalid cohort. Use 'hope' or 'cptac'." + exit 1 + fi +else + echo "Error: Missing --cohort argument." + echo "Usage: bash run_fragpipe.sh --cohort [hope|cptac]" + exit 1 +fi +# check that cavatica project directory path exists if [ ! -d $cavatica_dir ]; then echo "Error: path to cavatica project directory does not exist. Confirm that proteomics cavatica project is mounted to data/ directory" exit 1 @@ -49,32 +99,62 @@ fi rm -rf $tmp_dir/* # copy mzML files to temporary directory, maintaining directory structure -echo "copying mzML files to temporary directory..." + echo "copying mzML files to temporary directory..." + + if [[ "$cohort" == "cptac" ]]; then -if ! [[ " $* " == *" --run_subset "* ]]; then + if [ "$run_subset" = TRUE ]; then -cp -R $cavatica_dir/*CBTTC_PBT_Proteome* /home/rstudio/fragpipe/tmp/ + cp -R $cavatica_dir/*01CBTTC_PBT_Proteome* /home/rstudio/fragpipe/tmp/ + + else -else + cp -R $cavatica_dir/*CBTTC_PBT_Proteome* /home/rstudio/fragpipe/tmp/ + + fi + + # unzip mzML files, force overwrite if files exist + echo "unzipping mzML files..." + gunzip -f /home/rstudio/fragpipe/tmp/*CBTTC_PBT_Proteome*/*mzML.gz + + else -cp -R $cavatica_dir/01CBTTC_PBT_Proteome* /home/rstudio/fragpipe/tmp/ + if [ "$run_subset" = TRUE ]; then + cp -R $cavatica_dir/*01CPTAC_AYA_Proteome* /home/rstudio/fragpipe/tmp/ + + else + + cp -R $cavatica_dir/*CPTAC_AYA_Proteome* /home/rstudio/fragpipe/tmp/ + + fi + # unzip mzML files, force overwrite if files exist + echo "unzipping mzML files..." + gunzip -f /home/rstudio/fragpipe/tmp/*CPTAC_AYA_Proteome*/*mzML.gz + fi -# unzip mzML files, force overwrite if files exist -echo "unzipping mzML files..." -gunzip -f /home/rstudio/fragpipe/tmp/*CBTTC_PBT_Proteome*/*mzML.gz # set workflow, manifest, results and tools directories echo "Starting Fragpipe run..." -wf=/home/rstudio/fragpipe/input/PDC000180customworkflow.workflow -manifest=/home/rstudio/fragpipe/input/PDC000180filesmanifest.fp-manifest +# set manifest and workflow paths based on cohort +if [[ "$cohort" == "cptac" ]]; then + + wf=/home/rstudio/fragpipe/input/PDC000180customworkflow.workflow + manifest=/home/rstudio/fragpipe/input/PDC000180filesmanifest.fp-manifest + +else + + wf=/home/rstudio/fragpipe/input/HOPEproteome_TMT11workflow.workflow + manifest=/home/rstudio/fragpipe/input/HOPE-files-manifest.fp-manifest + +fi -if [[ " $* " == *" --run_subset "* ]]; then +if [[ "$run_subset" = TRUE ]]; then -grep "01CBTTC_" $manifest > /home/rstudio/fragpipe/input/PDC000180filesmanifest.fp-manifest_sub -manifest=/home/rstudio/fragpipe/input/PDC000180filesmanifest.fp-manifest_sub +grep "01C" $manifest > /home/rstudio/fragpipe/input/manifest.fp-manifest_sub +manifest=/home/rstudio/fragpipe/input/manifest.fp-manifest_sub fi