main.nf.rtf

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\f0\fs24 \cf0 /*\
vim: syntax=groovy\
-*- mode: groovy;-*-\
\
==============================\
IPAW: small open reading frame identification pipeline\
==============================\
@Authors\
Yafeng Zhu @yafeng\
\
https://github.com/yafeng/sorf_analysis\
\
- make sure conda install all excutive programs or scripts first\
- create a bin folder to store all scripts\
*/\
\
nf_required_version = '0.26.0'\
if( ! nextflow.version.matches(">= $\{nf_required_version\}") )\{\
  println("Nextflow version too old, $\{nf_required_version\} required")\
  exit(1)\
\}\
\
\
\
/* SET DEFAULT PARAMS */\
params.isobaric = false\
params.outdir = 'result'\
\
mods = file(params.mods)\
msgf_db = file(params.tdb)\
msgf_jar = file(params.msgfjar)\
converter = file(params.mzid2tsvConverter)\
\
params.PrecursorMassTolerance = '10ppm'\
params.FragmentMethodID = 3 // 3 for HCD spectra, 1 for CID, 2 for ETD\
params.inst = 3 // 0: Low-res LCQ/LTQ (Default), 1: Orbitrap/FTICR/Lumos, 2: TOF, 3: Q-Exactive\
plextype = params.isobaric ? params.isobaric.replaceFirst(/[0-9]+plex/, "") : false\
msgfprotocol = params.isobaric ? [tmt:4, itraq:2][plextype] : 0\
\
activationtype = [HCD:'High-energy collision-induced dissociation',CID:'Collision-induced dissociation',ETD:'Electron transfer dissociation',no:''][params.activationFilter]\
massshifts = [tmt:0.0013, itraq:0.00125, false:0]\
massshift = massshifts[plextype]\
\
params.qval = 0.05 \
params.MS2error = 0.02 // unit: Da\
\
params.novheaders = '^SEP;^decoy_SEP' \
params.noclassfdr = false\
novheaders = params.novheaders == true ? false : params.novheaders\
\
\
///////////////////\
\
println "PrecursorMassTolerance used in MSGF+:$\{params.PrecursorMassTolerance\}"\
println "q-value cutoff:$\{params.qval\}"\
println "MS2 error tolerance used in SpectrumAI:$\{params.MS2error\}"\
println "IsobaricAnalyzer filtered by activation:$\{params.activationFilter\}"\
println "InstrumentID used in MSGF+: $\{params.inst\}"\
println "FragmentMethodID used in MSGF+: $\{params.FragmentMethodID\}"\
println "ProtocolID used in MSGF+: $msgfprotocol"\
\
\
/* PIPELINE START */\
\
// Either feed an mzmldef file (tab separated lines with filepath\\tsetname)\
Channel\
  .from(file("$\{params.mzmldef\}").readLines())\
  .map \{ it -> it.tokenize('\\t') \}\
  .set \{ mzml_in \}\
\
\
mzml_in\
  .tap \{ sets \}\
  .map \{ it -> [ it[1], (it[0]=~/.*\\/(.+)\\..*$/)[0][1], file(it[0])]\} // create, set, samplename and file\
  .tap\{ mzmlfiles; mzml_msgf ; mzml_isobaric \}\
  .count()\
  .set\{ amount_mzml \}\
\
sets\
  .map\{ it -> it[1] \}\
  .unique()\
  .tap \{ sets_for_denoms \}\
  .collect()\
  .subscribe \{ println "Detected setnames: $\{it.join(', ')\}" \}\
\
\
// Get denominators if isobaric experiment\
// passed in form --denoms 'set1:126:128N set2:131 set4:129N:130C:131'\
\
if (params.isobaric && params.denoms) \{\
  setdenoms = [:]\
  params.denoms.tokenize(' ').each\{ it -> x=it.tokenize(':'); setdenoms.put(x[0], x[1..-1])\}\
  set_denoms = Channel.value(setdenoms)\
\
\}else if (params.isobaric) \{\
  setdenoms = [:]\
  sets_for_denoms.reduce(setdenoms)\{ a, b -> a.put(b, ['_126']); return a \}.set\{ set_denoms \}\
\}\
\
\
process IsobaricQuant \{\
\
  when: params.isobaric\
\
  input:\
  set val(setname), val(sample), file(infile) from mzml_isobaric\
\
  output:\
  set val(sample), file("$\{infile\}.consensusXML") into isobaricxml\
\
  """\
  source activate openms-2.4.0\
  IsobaricAnalyzer  -type $params.isobaric -in $infile -out "$\{infile\}.consensusXML" -extraction:select_activation "$activationtype" -extraction:reporter_mass_shift $massshift -extraction:min_precursor_intensity 1.0 -extraction:keep_unannotated_precursor true -quantification:isotope_correction true \
  """\
\}\
\
isobaricamount = params.isobaric ? amount_mzml.value : 1\
\
isobaricxml\
  .ifEmpty(['NA', 'NA'])\
  .buffer(size: isobaricamount)\
  .flatMap \{ it.sort(\{a, b -> a[0] <=> b[0]\}) \}\
  .map \{ it -> it[1] \}\
  .collect()\
  .set \{ sorted_isoxml \}\
\
mzmlfiles\
  .tap \{ groupset_mzmls \}\
  .buffer(size: amount_mzml.value)\
  .map \{ it.sort( \{a, b -> a[1] <=> b[1]\}) \}  //to sort by the first element of a tuple in descending order\
  .map \{ it -> [it.collect() \{ it[0] \}, it.collect() \{ it[2] \}] \}\
  .set\{ mzmlfiles_all \}\
\
process createSpectraLookup \{\
\
  input:\
  file(isobxmls) from sorted_isoxml \
  set val(setnames), file(mzmlfiles) from mzmlfiles_all\
  \
  output:\
  file('mslookup_db.sqlite') into spec_lookup\
\
  script:\
  if(params.isobaric)\
  """\
  source activate nf-core-ddamsproteomics-1.0.0\
  msslookup spectra -i $\{mzmlfiles.join(' ')\} --setnames $\{setnames.join(' ')\}\
  msslookup isoquant --dbfile mslookup_db.sqlite -i $\{isobxmls.join(' ')\} --spectra $\{mzmlfiles.join(' ')\}\
  """\
  else\
  """\
  msslookup spectra -i $\{mzmlfiles.join(' ')\} --setnames $\{setnames.join(' ')\}\
  """\
\}\
\
process msgfPlus \{\
\
  input:\
  set val(setname), val(sample), file(x) from mzml_msgf\
\
  output:\
  set val(setname), val(sample), file("$\{sample\}.mzid") into mzids\
  \
  """\
  java -Xmx8000M -jar $msgf_jar -tasks 1 -thread 1 -d $msgf_db -s $x -o "$\{sample\}.mzid" -mod $mods -tda 1 -t $\{params.PrecursorMassTolerance\} -ti -1,2 -m $\{params.FragmentMethodID\} -inst $\{params.inst\} -e 1 -protocol $\{msgfprotocol\} -ntt 2 -minLength 8 -maxLength 40 -minCharge 2 -maxCharge 4 -maxMissedCleavages 2 -n 1 -addFeatures 1\
  """\
\}\
\
process ConvertmzidTotsv \{\
\
  input:\
  set val(setname), val(sample), file(x) from mzids\
  \
  output:\
  set val(setname), file('out.mzid.tsv') into mzidtsvs \
\
  """\
  source activate mono\
  mono $converter -mzid:$x -tsv:temp.tsv -showDecoy\
  cut_extra_aa.py temp.tsv out.mzid.tsv\
  rm -f temp.tsv\
  """\
\}\
\
mzidtsvs\
  .groupTuple()\
  .set \{mzidtsvs_byset\}\
\
process MergeTSVbyset \{\
\
  publishDir "$\{params.outdir\}", mode: 'copy', overwrite: true\
\
  input:\
  set val(setname), file('tsv?') from mzidtsvs_byset\
\
  output:\
  file("$\{setname\}_allpsms.txt") into merged_tsvs\
  """\
  head -1 tsv1 > psmheader  \
  tail -q -n +2 tsv* > psmmerge\
  cat psmheader psmmerge > $\{setname\}_allpsms.txt\
  """\
\}}