Added warnings to report and fixed issue where no plates are used

CODE_OF_CONDUCT.md

@@ -34,7 +34,7 @@ This Code of Conduct applies both within project spaces and in public spaces whe
 
 ## Enforcement
 
-Instances of abusive, harassing, or otherwise unacceptable behavior may be reported by contacting the project team on the [Gitter channel](https://gitter.im/nf-core/Lobby). The project team will review and investigate all complaints, and will respond in a way that it deems appropriate to the circumstances. The project team is obligated to maintain confidentiality with regard to the reporter of an incident. Further details of specific enforcement policies may be posted separately.
+The project team will review and investigate all complaints, and will respond in a way that it deems appropriate to the circumstances. The project team is obligated to maintain confidentiality with regard to the reporter of an incident. Further details of specific enforcement policies may be posted separately.
 
 Project maintainers who do not follow or enforce the Code of Conduct in good faith may face temporary or permanent repercussions as determined by other members of the project's leadership.
 

assets/report.html

@@ -150,6 +150,17 @@ <h5 class="title is-5">Site count</h5>
       </div>
       {% endif %}
 
+      {% if warnings|length %}
+      <h4 class="title is-4">Warnings</h4>
+      <div class="notification is-danger">
+        <ul>
+          {% for warn in warnings %}
+          <li>&bull; {{ warn }}</li>
+          {% endfor %}
+        </ul>
+      </div>
+      {% endif %}
+
     </div>
 
     <div id="rundatapage" class="mt-5 container">

bin/qc_protein.R

@@ -280,7 +280,6 @@ if (length(precursorcols) > 1) {
       parea$Set = sub('_MS1.*', '', parea$Set)
       parea$Set = sub('^X([^a-zA-Z])', '\\1', parea$Set)
       parea = parea[complete.cases(parea$ms1), ]
-      print(head(parea[c('Set', 'ms1')]))
       ggp = ggplot(parea) + 
         geom_boxplot(aes(Set, ms1)) + scale_y_log10() + coord_flip() + ylab("Intensity") + theme_bw() + theme(axis.title=element_text(size=15), axis.text=element_text(size=10), axis.title.y=element_blank())
     } else {

bin/qc_psms.R

@@ -5,7 +5,6 @@ library(tidyr)
 library(glue)
 library(stringr)
 
-# library(reshape2)
 args = commandArgs(trailingOnly=TRUE)
 has_fractions = args[1] == TRUE
 newmzmlfn = ifelse(args[2] == 'FALSE', '', args[2])
@@ -96,10 +95,8 @@ if (length(grep('plex', names(feats)))) {
 # Missed cleavages
 mcl = aggregate(get(scancol)~get(xcol)+get(miscleavcol), feats, length)
 colnames(mcl) = c(xcol, 'missed_cleavage', 'nrscan')
-#mcl$nrscan = as.factor(mcl$nrscan)
 mcl_am = subset(merge(mcl, amount_psms, by=xcol), missed_cleavage %in% c(0,1,2))
 mcl_am$percent = mcl_am$nrscan / mcl_am$"PSMs IDed" * 100
-# mcl_am$textycoord = ifelse(mcl_am$missed_cleavage!=0, mcl_am$percent, 10)
 mc_text_y = max(mcl_am$percent) * 2/6
 mcl_am$missed_cleavage = as.factor(mcl_am$missed_cleavage)
 
@@ -120,8 +117,6 @@ htmlwidgets::saveWidget(p, 'missed_cleavages.html', selfcontained=F)
 # Now the per-fraction or per-file stats
 if (has_fractions) {
   xcol = 'Fraction'
-  #  + plateID'
-  # plateID not necessary because we take subfeats?
 } else { 
   xcol = filenamecol
 }

bin/report_tables.py

@@ -4,7 +4,6 @@
 import os
 import sys
 import shutil
-import tomllib
 import argparse
 from glob import glob
 from collections import defaultdict
@@ -271,6 +270,15 @@ def get_plotly_html(fn):
         overlap[feattype] = False
 
 
+warnings = []
+for fn in glob('warnings*'):
+    if os.path.exists(fn):
+        with open(fn) as fp:
+            for line in fp:
+                if warn := line.strip():
+                    warnings.append(warn)
+
+
 # Write to template
 with open('report_groovy_template.html', 'w') as fp:
     fp.write(template.render(reportdate=date,
@@ -293,4 +301,5 @@ def get_plotly_html(fn):
         ptmplots=ptmplots,
         ptmtables=ptmtables,
         ptmtitles=ptm_headers,
+        warnings=warnings,
         ))

main.nf

@@ -19,69 +19,6 @@ include { REPORTING } from './workflows/reporting.nf'
 ----------------------------------------------------------------------------------------
 */
 
-
-def multifile_format(fileparam) {
-    if (!fileparam) {
-        return false
-    }
-    sum_fn = file(fileparam)
-    if (!(sum_fn instanceof List)) {
-      sum_fn = [sum_fn]
-    }
-    return sum_fn.join(', ')
-}
-
-
-def create_workflow_summary(summary) {
-
-    def yaml_file = workDir.resolve('workflow_summary_mqc.yaml')
-    yaml_file.text  = """
-    id: 'lehtiolab-ddamsproteomics-summary'
-    description: " - this information is collected when the pipeline is started."
-    section_name: 'lehtiolab/ddamsproteomics Workflow Summary'
-    section_href: 'https://github.com/lehtiolab/ddamsproteomics'
-    plot_type: 'html'
-    data: |
-        <dl class=\"dl-horizontal\">
-${summary.collect { k,v -> "            <dt>$k</dt><dd><samp>${v ?: '<span style=\"color:#999999;\">N/A</a>'}</samp></dd>" }.join("\n")}
-        </dl>
-    """.stripIndent()
-
-   return yaml_file
-}
-
-
-/*
- * Parse software version numbers
- */
-process get_software_versions {
-
-    publishDir "${params.outdir}", mode: 'copy', overwrite: true
-
-    output:
-    file 'software_versions.yaml' into software_versions_qc
-
-    script:
-    noms1 = params.noms1quant || params.noquant
-    """
-    echo $workflow.manifest.version > v_pipeline.txt
-    echo $workflow.nextflow.version > v_nextflow.txt
-    echo 2023.01.1202 > v_msgf.txt
-    ${!noms1 && !params.hardklor ? 'dinosaur | head -n2 | grep Dinosaur > v_dino.txt || true' : ''}
-    ${!noms1 && params.hardklor ? 'hardklor | head -n1 > v_hk.txt || true' : ''}
-    kronik | head -n2 | tr -cd '[:digit:],\\.' > v_kr.txt || true
-    #luciphor2 |& grep Version > v_luci.txt # incorrect version from binary (2014), echo below
-    echo Version: 2020_04_03 > v_luci.txt # deprecate when binary is correct
-    echo 3.5 > v_perco.txt
-    msstitch --version > v_mss.txt
-    echo 2.9.1 > v_openms.txt
-    Rscript <(echo "packageVersion('DEqMS')") > v_deqms.txt
-    scrape_software_versions.py > software_versions.yaml
-    """
-}
-
-
-
 process createTargetDecoyFasta {
   label 'msstitch'
 
@@ -108,12 +45,6 @@ def fr_or_file(it, length) {
   return it.size() > length ? it[length] : "${file(it[0]).baseName}.${file(it[0]).extension}"
 }
 
-def plate_or_no(it, length) {
-  return it.size() > 3 ? it[3] : "no_plate"
-}
-
-
-
 
 // Parse mzML input to get files and sample names etc
 // get setname, sample name (baseName), input mzML file. 
@@ -156,7 +87,6 @@ process isobaricQuant {
   activationtype = [auto: 'auto', any: 'any', hcd:'beam-type collision-induced dissociation', cid:'Collision-induced dissociation', etd:'Electron transfer dissociation'][params.activation]
   plextype = isobtype ? isobtype.replaceFirst(/[0-9]+plex/, "") : 'false'
   massshift = [tmt:0.0013, itraq:0.00125, false:0][plextype]
-  //(is_stripped, parsed_infile) = stripchars_infile(infile)
   """
   ${isobtype ? "IsobaricAnalyzer -type $isobtype -in \"${infile}\" -out \"${infile.baseName}.consensusXML\" -extraction:select_activation \"$activationtype\" -extraction:reporter_mass_shift $massshift -extraction:min_precursor_intensity 1.0 -extraction:keep_unannotated_precursor true -quantification:isotope_correction true" : ''}
   """
@@ -165,12 +95,6 @@ process isobaricQuant {
 
 
 process dinosaur {
-container 'lehtiolab/ddamsproteomics:2.18'
-// Biocontainers arent working with dinosaur tests, FIXME create auto build of it
-
-//  container "${workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-//    'https://depot.galaxyproject.org/singularity/dinosaur:1.2.0--0' :
-//    'quay.io/biocontainers/dinosaur:1.2.0--0'}"
 
   input:
   tuple val(sample), path(infile)
@@ -686,28 +610,13 @@ if (params.sampletable) {
     // .map { it -> [it[2].replaceAll('[ ]+$', '').replaceAll('^[ ]+', ''), file(it[0]).baseName.replaceAll(regex_specialchars, '_'), file(it[0]), it[1], plate_or_no(it, 3), fr_or_file(it, 4)] }
 
   mzml_in
-// FIXME clean out
     // Prepare mzml files (sort, collect) for processes that need all of them
     .toList()
     .map { it.sort( {a, b -> a.sample <=> b.sample}) } // sort on sample for consistent .sh script in -resume
     .map { it -> [it.collect() { it.setname }, it.collect() { it.mzmlfile }, it.collect() { it.plate }, it.collect() { it.fraction } ] } // lists: [sets], [mzmlfiles], [plates], [fractions]
-    //.tap { mzmlfiles_psmqc } // FIXME this prevents completion of the pipeline somehow
     .map { it -> it[0..2] } // remove basenames, fractions
     .set { mzmlfiles_all_sort }
 
-
-/*
-// FIXME this needed still?
-  if (!is_rerun) {
-    mzml_in 
-      .count()
-      .subscribe { println "$it mzML files in analysis" }
-      .into { mzmlcount_psm; mzmlcount_percolator }
-  } else {
-    Channel.value(0).into { mzmlcount_psm; mzmlcount_percolator }
-  }
-*/
-
   // Spec lookup prep if needed
   do_quant = false
   if (is_rerun) {
@@ -816,10 +725,9 @@ if (params.sampletable) {
     | set { specquant_lookups }
   }
 
-
   tdb = Channel.fromPath(params.tdb)
   createTargetDecoyFasta(tdb)
-  // bothdbs.into { psmdbs; fdrdbs; ptmdbs }
+
   if (!is_rerun) {
     search_mods = [params.mods ? params.mods : false,
       params.ptms ?: false,
@@ -902,8 +810,6 @@ if (params.sampletable) {
   } else {
     totalproteome_ch = Channel.empty()
   }
-println(params.genes)
-println(params.onlypeptides)
   if (params.genes) {
     totalprot_col = 'Gene Name'
   } else if (params.onlypeptides) {
@@ -939,9 +845,11 @@ println(params.onlypeptides)
       do_ms1,
       !params.onlypeptides
     )
-    ptm_ch = PTMANALYSIS.out
+    ptm_ch = PTMANALYSIS.out.ptms
+    ptmwarn_ch = PTMANALYSIS.out.warnings
   } else {
     ptm_ch = Channel.empty()
+    ptmwarn_ch = Channel.empty()
   }
 
   splitpsms_ch
@@ -1036,92 +944,13 @@ println(params.onlypeptides)
     params.proteinconflvl,
     all_setnames,
     ptm_ch,
+    psmwarnings_ch
+      .concat(MSGFPERCO.out.warnings)
+      .concat(ptmwarn_ch)
+      .toList().toList()
+      .filter { it[0] }
+      .ifEmpty(nofile),
   )
-
-
-/*
-
-  // QC for PSMs
-
-  // FIXME allplates could go as file into R QC directly?
-  if (fractionation) {
-    countMS2sPerPlate.out.allplates
-      .splitText()
-      .map { it -> it.trim() }
-      .toList()
-      .map { it -> [it] }
-      .set { allplates_split }
-    countMS2sPerPlate.out.counted
-      .combine(allplates_split)
-      .set { scans_result }
-  } else {
-    countMS2sPerPlate.out.counted
-    | map { it -> [it[0], 'NA', ['noplates']] }
-    | set { scans_result }
-    //| into { scans_platecount; scans_result }
-  }
-  psm_result // From createPSMTable
-    .filter { it[0] == 'target' }
-    .combine(scans_result)
-    .map { it -> [it[0], it[1], it[2], it[3], it[4].unique()] }
-    .set { targetpsm_result }
-
-
-
-
-mzmlfiles_all_count
-// Count lookup can be spectra if needed quant
-  .merge(countlookup)
-  .set { specfilein }
-
-
-process countMS2perFile {
-
-  input:
-  set val(setnames), file(mzmlfiles), val(platenames), file(speclookup) from specfilein
-
-/// The following is maybe OK?
-
-if (complementary_run) {
-  oldnewsets
-    .splitText()
-    .map { it -> it.trim() }
-    .toList()
-    .set { allsetnames }
-  cleaned_psms
-    .flatMap { it -> [['target', it[0]], ['decoy', it[1]]] }
-    .set { td_oldpsms }
-} else {
-  mzml_in
-    .map { it -> it[2] } 
-    .unique()
-    .toList()
-    .set { allsetnames }
-
-  // if not using this youll have a combine on an open channel without
-  // anything from complement cleaner. Will not run createPTMLookup then
-  cleaned_ptmpsms = Channel.value('NA')
-}
-
-/// until here - we can investigate later
-
-// Set names are first item in input lists, collect them for PSM tables and QC purposes
-// FIXME just reuse channels
-allsetnames 
-  .into { setnames_featqc; setnames_psms; setnames_psmqc; setnames_ptms }
-
-
-
-if (!params.quantlookup) {
-  ptm_lookup_old
-    .concat(ptm_lookup_new)
-// PTM lookup needs not to have quant, can be spectra
-    .set { ptm_lookup_in }
-}
-
-*/
-
-//  publishDir "${params.outdir}", mode: 'copy', overwrite: true, saveAs: {["target_psmlookup.sql", "decoy_psmlookup.sql", "target_psmtable.txt", "decoy_psmtable.txt"].contains(it) && (is_rerun || !no_psms) ? it : null}
 
   target_psmtable.map { it[1] }
   .concat(psmtables_ch | filter { it[0] == 'decoy' } | map { it[1] })

nextflow.config

@@ -11,18 +11,11 @@ nextflow.enable.configProcessNamesValidation = false
 params {
   help = false
   outdir = './results'
-  igenomes_base = "./iGenomes"
   tracedir = "${params.outdir}/pipeline_info"
   clusterOptions = false
-  awsqueue = false
-  awsregion = 'eu-west-1'
   external_config_version = 'master'
 
   name = false
-  email = false
-  plaintext_email = false
-
-  mzmls = false
   input = false
   tdb = false
   mods = false
@@ -226,6 +219,8 @@ process {
     container = containers['openms'][engine]
   }
   withName: dinosaur {
+    // Biocontainers arent working with dinosaur tests
+    // this container is our own DDA container with conda
     container = containers['dinosaur'][engine]
   }
   withName: hardklor {