Snakemake workflow to perform tandem mass tag (TMT) analysis using the Trans Proteomic Pipeline (TPP)

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Snakemake workflow to perform tandem mass tag (TMT) analysis using the Trans Proteomic Pipeline (TPP)

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Code Snippets

shell:
    "decoyFastaGenerator.pl {params.i} DECOY {params.o}"

SnakeMake From line 77 of main/Snakefile

shell:
    "sed 's/SAMPLE_NAME/{wildcards.sample}/g' {params.t} > {wildcards.sample}_tandem.params && "
    "sed 's/OUTPUT_DIR/" + basename(OUT_DIR) + "/g' {params.x} > taxonomy_{wildcards.sample}.xml && "
    "tandem {wildcards.sample}_tandem.params > {params.l} 2>&1 && "
    "mv {wildcards.sample}.tandem " + basename(OUT_DIR) + "/tandem/ &&"
    "rm {wildcards.sample}_tandem.params taxonomy_{wildcards.sample}.xml"

SnakeMake From line 105 of main/Snakefile

shell:
    "Tandem2XML {params.i} {params.o} > {params.l} 2>&1"

SnakeMake From line 132 of main/Snakefile

    shell:
        'comet'
        ' -P{params.t}'
        ' -D{params.d}'
        ' -N{wildcards.sample}'
        ' {params.i}'
        ' > {params.l} 2>&1'
        ' && mv {wildcards.sample}.pep.xml ' + join('/data', basename(OUT_DIR), 'comet')

##--------------------------------------------------------------------------------------##
##--------------------------------------------------------------------------------------##

rule PeptideProphet:
    input:
        pepXML = expand(join(OUT_DIR, '{engine}', '{sample}.pep.xml'), sample = SAMPLES, engine = ENGINES)
    output:
        PepProph = join(OUT_DIR, '{engine}', 'PepProph', 'xinteract.pep.xml')
    params:
        o = join('/data', basename(OUT_DIR), '{engine}', 'PepProph', 'xinteract.pep.xml'),
        l = join('/data', basename(OUT_DIR), basename(LOGS_DIR), '{engine}_PepProph.log'),
        d = join('/data', basename(OUT_DIR), 'database_plus_decoy.fa'),
        c = "/data/params/condition.xml"
    singularity:
        "docker://spctools/tpp"
    message:
        """  ------  Runing PeptideProphet search for combined mzMLs from {wildcards.engine} ------  """
    threads:
        16
    resources:
        mem_mb=32000
    shell:
        'xinteract'
        ' -N{params.o}'
        ' -p0.0'
        ' -l7'
        ' -PPM'
        ' -OAP'

SnakeMake From line 159 of main/Snakefile

shell:
    'InterProphetParser'
    ' THREADS=8'
    ' DECOY={params.d}'
    ' {params.i}'
    ' {params.o}'
    ' > {params.l} 2>&1'

SnakeMake From line 224 of main/Snakefile

shell:
    'ProteinProphet'
    ' {params.i}'
    ' {params.o}'
    ' IPROPHET'
    ' NOGROUPWTS'
    ' PLOTPNG'
    ' EXCELPEPS'
    ' EXCEL.90'
    ' LIBRA{params.c}'
    ' > {params.l} 2>&1'
    ' && mv quantitation.tsv {params.q}'

SnakeMake From line 255 of main/Snakefile

shell:
    'InterProphetParser'
    ' THREADS=8'
    ' DECOY={params.d}'
    ' {params.ic}'
    ' {params.it}'
    ' {params.o}'
    ' > {params.l} 2>&1'

SnakeMake From line 288 of main/Snakefile

shell:
    'ProteinProphet'
    ' {params.i}'
    ' {params.o}'
    ' IPROPHET'
    ' NOGROUPWTS'
    ' PLOTPNG'
    ' EXCELPEPS'
    ' EXCEL.90'
    ' LIBRA{params.c}'
    ' > {params.l} 2>&1'
    ' && mv quantitation.tsv {params.q}'