WOMBAT-Pipelines

public public 1yr ago Version: Version 1 0 bookmarks
View Workflow
Report
wombat-pipelines
wombat-pipelines
wombat-pipelines
wombat-pipelines
View Workflow

Introduction

wombat-p pipelines is a bioinformatics analysis pipeline that bundles different workflow for the analysis of label-free proteomics data with the purpose of comparison and benchmarking. It allows using files from the proteomics metadata standard SDRF .

The pipeline is built using Nextflow , a workflow tool to run tasks across multiple compute infrastructures in a very portable manner. It uses Docker/Singularity containers making installation trivial and results highly reproducible. The Nextflow DSL2 implementation of this pipeline uses one container per process which makes it much easier to maintain and update software dependencies. We used one of the nf-core templates.

Pipeline summary

This work contains four major different workflows for the analysis or label-free proteomics data, originating from LC-MS experiments.

  1. MaxQuant + NormalyzerDE
  2. SearchGui + Proline + PolySTest
  3. Compomics tools + FlashLFQ + MSqRob
  4. Tools from the Trans-Proteomic Pipeline + ROTS

Initialization and parameterization of the workflows is based on tools from the SDRF pipelines , the ThermoRawFileParser with our own contributions and additional programs from the wombat-p organizaion [https://github.com/wombat-p/Utilities] as well as our fork . This includes setting a generalized set of data analysis parameters and the calculation of a multiple benchmarks.

Code Snippets

30
31
32
33
34
35
36
37
38
39
40
41
"""
echo '$foo' > params.json
cp "${fasta_file}" database.fasta
if [[ "${exp_design_file}" != "exp_design.txt" ]]
then
  cp "${exp_design_file}" exp_design.txt
fi
Rscript $baseDir/bin/CalcBenchmarks.R
mv benchmarks.json benchmarks_${workflow}.json
cp stand_pep_quant_merged.csv stand_pep_quant_merged${workflow}.csv
cp stand_prot_quant_merged.csv stand_prot_quant_merged${workflow}.csv
"""
NextFlow From line 30 of calcbenchmarks/main.nf 
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
"""
first_line=""
# avoid exp_design ending with .txt
mv "${exp_design}" exp_design.tsv
for file in *.txt
do
  echo \$file
  tail -n +2 "\$file" >> tlfq_ident.tabular
  first_line=\$(head -n1 "\$file")
done
# Use awk to add 3 new columns rep, frac, trep with ones to exp_design file
#awk 'NR==1{print \$0"\trep\tfrac\ttrep"} NR>1{print \$0"\t1\t1\t1"}' "exp_design.tsv" > ExperimentalDesign.tsv
cp exp_design.tsv ExperimentalDesign.tsv

# Remove .raw and .mzml from file names in first column of ExperimentalDesign.tsv
sed -i 's/.mzML//g' ExperimentalDesign.tsv
sed -i 's/.raw//g' ExperimentalDesign.tsv
sed       -i 's/.Raw//g' ExperimentalDesign.tsv
sed -i 's/.RAW//g' ExperimentalDesign.tsv
# Add first line to tlfq_ident.tabular
echo "\$first_line" | cat - tlfq_ident.tabular > lfq_ident.tabular
# Needed as path is overwritten when running with singularity
PATH=\$PATH:/usr/local/lib/dotnet:/usr/local/lib/dotnet/tools
CONDA_PREFIX=/usr/local FlashLFQ --idt "lfq_ident.tabular" --rep "./" --out ./ --mbr ${parameters.enable_match_between_runs} --ppm ${parameters.precursor_mass_tolerance} --sha ${protein_inference} --thr ${task.cpus}
"""
NextFlow Singularity Hub From line 38 of flashlfq/main.nf 
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
"""
first_line=""
# avoid exp_design ending with .txt
mv "${exp_design}" exp_design.tsv
for file in *.txt
do
  echo \$file
  tail -n +2 "\$file" >> tlfq_ident.tabular
  first_line=\$(head -n1 "\$file")
done
# Use awk to add 3 new columns rep, frac, trep with ones to exp_design file
#awk 'NR==1{print \$0"\trep\tfrac\ttrep"} NR>1{print \$0"\t1\t1\t1"}' "exp_design.tsv" > ExperimentalDesign.tsv
cp exp_design.tsv ExperimentalDesign.tsv

# Remove .raw and .mzml from file names in first column of ExperimentalDesign.tsv
sed -i 's/.mzML//g' ExperimentalDesign.tsv
sed -i 's/.raw//g' ExperimentalDesign.tsv
sed       -i 's/.Raw//g' ExperimentalDesign.tsv
sed -i 's/.RAW//g' ExperimentalDesign.tsv
# Add first line to tlfq_ident.tabular
echo "\$first_line" | cat - tlfq_ident.tabular > lfq_ident.tabular
FlashLFQ --idt "lfq_ident.tabular" --rep "./" --out ./ --mbr ${parameters.enable_match_between_runs} --ppm ${parameters.precursor_mass_tolerance} --sha ${protein_inference} --thr ${task.cpus}
"""
NextFlow From line 64 of flashlfq/main.nf 
22
23
24
"""
mzdb2mgf -i "${mzdbfile}" -o "${mzdbfile.baseName}.mgf" 
"""
NextFlow From line 22 of mzdb2mgf/main.nf 
31
32
33
34
35
"""
cp "proteinGroups.txt" protein_file.txt
cp "peptides.txt" peptide_file.txt
Rscript $baseDir/bin/runNormalyzer.R --comps="${params.comps}" --method="${parameters.normalization_method}" --exp_design="${exp_file}" --comp_file="${comp_file}"
"""
NextFlow From line 31 of normalyzerde/main.nf 
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
"""
convertProline=\$(which runPolySTestCLI.R)

echo \$convertProline
convertProline=\$(dirname \$convertProline)

echo \$convertProline
Rscript \${convertProline}/convertFromProline.R ${exp_design} ${proline_res}

sed -i "s/threads: 2/threads: ${task.cpus}/g" pep_param.yml
sed -i "s/threads: 2/threads: ${task.cpus}/g" prot_param.yml

runPolySTestCLI.R pep_param.yml
runPolySTestCLI.R prot_param.yml
"""
NextFlow From line 26 of run_polystest/main.nf 
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
    """
    if [[ "$map" != "params2sdrf.yml" ]]
    then
        cp "${map}" params2sdrf.yml
    fi
    if [[ "$sdrf" != "no_sdrf" ]] 
    then    
        if [[ "$sdrf" != "sdrf_local.tsv" ]]
        then
	    cp "${sdrf}" sdrf_local.tsv
        fi
    fi	
    if [[ "$exp_design" != "no_exp_design" ]] 
    then    
       if [[ "$exp_design" != "exp_design.txt" ]] 
       then
	     cp "${exp_design}" exp_design.txt
       fi
    else
        if [[ "$sdrf" == "no_sdrf" ]] 
        then
            printf "raw_file\texp_condition" >> exp_design.txt
	    for a in $raws
	    do
	        printf "\n\$a\tA" >> exp_design.txt
	    done
        else 
	    $baseDir/bin/sdrf2exp_design.py
        fi        
    fi
    if [[ "$sdrf" == "no_sdrf" ]] 
    then
	$baseDir/bin/exp_design2sdrf.py
    fi
    if [ "$raws" == "no_raws" ] && [ "$mzmls" == "no_mzmls" ]
    then
        # Download all files from column file uri		
        echo "Downloading raw files from column file uri\n"
	for a in \$(awk -F '\t' -v column_val='comment[file uri]' '{ if (NR==1) {val=-1; for(i=1;i<=NF;i++) { if (\$i == column_val) {val=i;}}} if(val != -1) { if (NR!=1) print \$val} } ' "$sdrf")
	do
            echo "Downloading \$a\n"
	    wget -c -T 100 -t 5 "\$a"
        done
    fi

    if [[ "$parameters" == "no_params" ]]
    then
	printf "params:\n  None:  \nrawfiles: None\nfastafile: None" >  params.yml
    elif [[ "$parameters" != "params.yml" ]] 
    then
        cp "${parameters}" params.yml
    fi
    echo "See workflow version" > prepare_files.version.txt
    cp sdrf_local.tsv sdrf_temp.tsv
    """
NextFlow From line 31 of prepare_files/main.nf 
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
"""
mkdir ./searchgui_results
for file in *.zip
do
unzip "\$file" -d ./searchgui_results/
mv \$(find ./ -type f \\( -name "*.t.xml.gz" -o -name "*.mzid" \\)) ./
gunzip *.t.xml.gz
rm -rf ./searchgui_results/*
done
touch import_file_list.txt
all_id_files=\$(find ./ -type f \\( -name "*.t.xml" -o -name "*.mzid" \\))
for file in \$all_id_files
do
echo "./\$file" >> import_file_list.txt
sed -i "s/PEPFDR/expected_fdr=${peptide_fdr}/g" "${param_file}"
sed -i "s/PROTFDR/expected_fdr=${protein_fdr}/g" "${param_file}"
sed -i "s/NUMPEPS/threshold=${parameters.min_num_peptides}/g" "${param_file}"
sed -i "s/moz_tol = 5/moz_tol=${prec_tol}/g" "${param_file}"
sed -i "s/moz_tol_unit = ppm/moz_tol_unit=${prec_ppm}/g" "${param_file}"
done
cp "${param_file}" lfq_param_file.txt
"""
NextFlow From line 30 of config_proline/main.nf 
29
30
31
32
"""
touch quant_exp_design.txt    
echo "${exp_design_text}" >> quant_exp_design.txt
"""
NextFlow From line 29 of exp_design_proline/main.nf 
34
35
36
37
38
39
40
41
42
43
44
"""
cp ${exp_design} quant_exp_design.txt
sed -i 's/raw_file/mzdb_file/g' quant_exp_design.txt
sed -i 's/.raw/.mzDB/g' quant_exp_design.txt
sed -i 's/.mzML/.mzDB/g' quant_exp_design.txt
sed -i 's/.mzml/.mzDB/g' quant_exp_design.txt
sed -i '2,\$s|^|./|' quant_exp_design.txt
# keep first two columns of quant_exp_design.txt
cut -f1,2 quant_exp_design.txt > quant_exp_design.txt.tmp
mv quant_exp_design.txt.tmp quant_exp_design.txt
"""
NextFlow From line 34 of exp_design_proline/main.nf 
20
21
22
23
"""
ls -la
thermo2mzdb -i "${rawfile}" -o "${rawfile.baseName}.mzDB" 
"""
NextFlow From line 20 of raw2mzdb/main.nf 
19
20
21
22
23
24
25
26
27
28
29
30
31
"""
# Check if the file is a mzML file
if [[ "${rawfile}" == *.{mzML,mzml} ]]
  then
      # check if same file
      if [[ "${rawfile}" != "${rawfile.baseName}.mzML" ]]
      then
        cp "${rawfile}" "${rawfile.baseName}.mzML"
      fi
  else
      thermorawfileparser -i "${rawfile}" -b "${rawfile.baseName}.mzML" -f 2
fi
"""
NextFlow From line 19 of raw2mzml/main.nf 
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
"""
parse_sdrf \\
convert-maxquant \\
-s "${sdrf}" \\
-f "PLACEHOLDER${fasta}" \\
-r PLACEHOLDER \\
-t PLACEHOLDERtemp \\
-o2 exp_design.tsv \\
-n ${task.cpus} 
echo "Preliminary" > sdrf_merge.version.txt

parse_sdrf \\
convert-normalyzerde \\
-s "${sdrf}" \\
-mq exp_design.tsv \\
-o Normalyzer_design.tsv \\
-oc Normalyzer_comparisons.txt
"""
NextFlow From line 24 of convert_maxquant/main.nf 
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
    """
    if [[ "$sdrf" != "sdrf.tsv" ]]
    then
	cp "${sdrf}" sdrf.tsv
    fi
    if [[ "$parameters" != "params.yml" ]] 
    then
        cp "${parameters}" params.yml
    fi
    if [[ "$map" != "params2sdrf.yml" ]]
    then
        cp "${map}" params2sdrf.yml
    fi
    # TODO change to package when available
    python $projectDir/bin/add_data_analysis_param.py > changed_params.txt
    python $projectDir/bin/sdrf2params.py
    """
NextFlow From line 34 of sdrfmerge/main.nf 
26
27
28
"""
searchgui eu.isas.searchgui.cmd.FastaCLI -in ${fasta} -decoy
"""
NextFlow From line 26 of create_decoy_database/main.nf 
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
"""
mkdir tmp
mkdir log
searchgui eu.isas.searchgui.cmd.PathSettingsCLI -temp_folder ./tmp -log ./log
searchgui eu.isas.searchgui.cmd.IdentificationParametersCLI -out searchgui \\
  -frag_tol ${frag_tol} -frag_ppm ${frag_ppm} -prec_tol ${prec_tol} -prec_ppm ${prec_ppm} -enzyme "${enzyme}" -mc ${parameters["allowed_miscleavages"]} \\
  -max_isotope ${parameters["isotope_error_range"]} \\
  ${fixed_mods} ${var_mods}\\
  -fi "${parameters["fions"]}" -ri "${parameters["rions"]}" -xtandem_quick_acetyl 0 -xtandem_quick_pyro 0 -peptide_fdr ${parameters["ident_fdr_peptide"]}\\
  -protein_fdr ${parameters["ident_fdr_protein"]} -psm_fdr ${parameters["ident_fdr_psm"]} \\
  -myrimatch_num_ptms ${parameters["max_mods"]} -ms_amanda_max_mod ${parameters["max_mods"]} -msgf_num_ptms ${parameters["max_mods"]} -meta_morpheus_max_mods_for_peptide\\
  ${parameters["max_mods"]} -directag_max_var_mods ${parameters["max_mods"]} -comet_num_ptms ${parameters["max_mods"]} \\#-tide_max_ptms ${parameters["max_mods"]}  \\
  -myrimatch_min_pep_length ${parameters["min_peptide_length"]} -myrimatch_max_pep_length ${parameters["max_peptide_length"]} -ms_amanda_min_pep_length ${parameters["min_peptide_length"]} \\
  -ms_amanda_max_pep_length ${parameters["max_peptide_length"]} -msgf_min_pep_length ${parameters["min_peptide_length"]} -msgf_max_pep_length ${parameters["max_peptide_length"]} \\
  -omssa_min_pep_length ${parameters["min_peptide_length"]} -omssa_max_pep_length ${parameters["max_peptide_length"]} -comet_min_pep_length ${parameters["min_peptide_length"]} \\
  -comet_max_pep_length ${parameters["max_peptide_length"]} -tide_min_pep_length ${parameters["min_peptide_length"]} -tide_max_pep_length ${parameters["max_peptide_length"]} \\
  -andromeda_min_pep_length ${parameters["min_peptide_length"]} -andromeda_max_pep_length ${parameters["max_peptide_length"]} -meta_morpheus_min_pep_length ${parameters["min_peptide_length"]} \\
  -meta_morpheus_max_pep_length ${parameters["max_peptide_length"]} -max_charge ${parameters.max_precursor_charge} -min_charge ${parameters.min_precursor_charge}
"""
NextFlow From line 67 of prepare_searchgui/main.nf 
30
31
32
33
34
35
36
37
38
39
40
41
42
"""
cat <<-END_VERSIONS > versions.yml
    "${task.process}":
        maxquant: \$(maxquant --version 2>&1 > /dev/null | cut -f2 -d\" \")
END_VERSIONS
sed \"s_<numThreads>.*_<numThreads>$task.cpus</numThreads>_\" ${paramfile} > mqpar_changed.xml
sed -i \"s|PLACEHOLDER|\$PWD/|g\" mqpar_changed.xml
mkdir temp
chmod -R a+rw *
maxquant mqpar_changed.xml
mv combined/txt/*.txt .
mv combined/proc/*unningTimes.txt runningTimes.txt
"""
NextFlow oschmod From line 30 of lfq/main.nf
ShowHide 15 more snippets with no or duplicated tags.

Login to post a comment if you would like to share your experience with this workflow.

Do you know this workflow well? If so, you can request seller status , and start supporting this workflow.

Free

Created: 1yr ago
Updated: 1yr ago
Maitainers: public
URL: https://github.com/wombat-p/WOMBAT-Pipelines
Name: wombat-pipelines
Version: Version 1
Badge:
workflow icon

Insert copied code into your website to add a link to this workflow.

Downloaded: 0
Copyright: Public Domain
License: MIT License
  • Future updates

Related Workflows

psychip_snakemake
Show Details View Workflow
ENCODE pipeline for histone marks developed for the psychENCODE project
public

public

psychip pipeline is an improved version of the ENCODE pipeline for histone marks developed for the psychENCODE project. The o...
raw sequence reads Alignment Sequence alignment report macs2 ucsc-bedclip bedGraphToBigWig BEDTools BWA Picard SAMtools Snakemake
Free
74
ncov_2
Show Details View Workflow
Near-real time tracking of SARS-CoV-2 in Connecticut
public

public

Repository containing scripts to perform near-real time tracking of SARS-CoV-2 in Connecticut using genomic data. This pipeli...
JSON nextclade Augur Biopython FOCUS Pandas Snakemake bs4 epiweeks geopy matplotlib numpy pycountry pycountry-convert uszipcode
Free
28
cellranger-snakemake-gke
Show Details View Workflow
snakemake workflow to run cellranger on a given bucket using gke.
public

public

A Snakemake workflow for running cellranger on a given bucket using Google Kubernetes Engine. The usage of this workflow ...
macs2 ucsc-bedclip bedGraphToBigWig BEDTools BWA Picard SAMtools Snakemake
Free
74
atlas
Show Details View Workflow
ATLAS - Three commands to start analyzing your metagenome data
public

public

Metagenome-atlas is a easy-to-use metagenomic pipeline based on snakemake. It handles all steps from QC, Assembly, Binning, t...
raw sequence reads Genome assembly Annotation track checkm2 gunc prodigal snakemake-wrapper-utils MEGAHIT Atlas BBMap Biopython BioRuby Bwa-mem2 cd-hit CheckM DAS Diamond eggNOG-mapper v2 MetaBAT 2 Minimap2 MMseqs MultiQC Pandas Picard pyfastx SAMtools SemiBin Snakemake SPAdes SqueezeMeta TADpole VAMB CONCOCT ete3 gtdbtk h5py networkx numpy plotly psutil utils metagenomics
Free
175
rna-seq-star-deseq2
Show Details View Workflow
RNA-seq workflow using STAR and DESeq2
public

public

This workflow performs a differential gene expression analysis with STAR and Deseq2. The usage of this workflow is described ...
raw sequence reads Gene expression profiling ID list snakemake-wrapper-utils biomaRt PCAtools BiocParallel BWA Cutadapt DESeq2 GFFutils MultiQC Pandas SAMtools Snakemake STAR cli stringr tidyverse RNA-Seq
Free
41
dna-seq-gatk-variant-calling
Show Details View Workflow
This Snakemake pipeline implements the GATK best-practices workflow
public

public

This Snakemake pipeline implements the GATK best-practices workflow for calling small germline variants. The usage of thi...
VCF raw sequence reads Variant calling genetic variants gatk rust-bio-tools snakemake-wrapper-utils tabix BCFtools BWA FastQC MultiQC Pandas Picard SAMtools Snakemake Trimmomatic Variant Effect Predictor (VEP) common matplotlib numpy seaborn DNA
Free
57