version fix

.nf-core.yml

@@ -1,6 +1,6 @@
 lint:
   files_unchanged:
-    - bin/scrape_software_versions.py
+    - .github/workflows/linting.yml
     - lib/NfcoreTemplate.groovy
   files_exist:
     - conf/igenomes.config

conf/modules.config

@@ -10,112 +10,192 @@
 ----------------------------------------------------------------------------------------
 */
 
-params {
-    modules {
-        'sdrfparsing' {
-            args    = 'convert-openms -t2 -l'
-        }
-        'decoydatabase' {
-            args    = ''
-            publish_files = ['log': 'logs']
-        }
-        'multiqc' {
-            args    = ''
-        }
-        'thermorawfileparser' {
-            args    = ''
-        }
-        'mzmlindexing' {
-            args    = ''
-            publish_files = ['log': '']
-        }
-        'openmspeakpicker' {
-            args    = ''
-            publish_files = ['log': '']
-        }
-        'isobaricanalyzer' {
-            args    = ''
-            publish_files = ['log': '']
-        }
-        'searchenginemsgf' {
-            args    = ''
-        }
-        'searchenginecomet' {
-            args    = ''
-        }
-        'indexpeptides' {
-            args    = ''
-            publish_files = ['log': '']
-        }
-        'extractpsmfeature' {
-            args    = ''
-            publish_files = ['log': '']
-        }
-        'percolator' {
-            args    = ''
-        }
-        'falsediscoveryrate' {
-            args    = ''
-        }
-        'idpep' {
-            args    = ''
-        }
-        'idscoreswitcher' {
-            args    = '-new_score_orientation lower_better'
-        }
-        'consensusid' {
-            args    = ''
-        }
-        'idfilter' {
-            args    = ''
-            suffix  = '.idXML'
-        }
-        'luciphoradapter' {
-            args    = ''
-            publish_files = ['log': '']
-        }
-        'idmapper' {
-            args    = ''
-            publish_files = ['log': '','consensusXML':'']
-        }
-        'filemerge' {
-            args    = ''
+process {
+
+    publishDir  = [
+        path: { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" },
+        mode: params.publish_dir_mode,
+        saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+    ]
+
+    // Local Subworkflows
+    // INPUT_CHECK
+    withName: 'NFCORE_QUANTMS:QUANTMS:INPUT_CHECK:SAMPLESHEET_CHECK' {
+        publishDir = [
+            path: { "${params.outdir}/pipeline_info" },
+            mode: 'copy',
+            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+        ]
+    }
+
+}
+
+// OPENMSPEAKPICKER
+if (params.openms_peakpicking){
+    process {
+            withName: 'NFCORE_QUANTMS:QUANTMS:.*:OPENMSPEAKPICKER' {
+            publishDir  = [
+                path: { "${params.outdir}/openmspeakpicker" },
+                mode: params.publish_dir_mode,
+                pattern: '*.log',
+                saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+            ]
         }
-        'epifany' {
-            args    = ''
-            publish_files = ['log': '']
+    }
+}
+
+// DECOYDATABASE
+if (params.add_decoys) {
+    process {
+        withName: 'NFCORE_QUANTMS:QUANTMS:.*:DECOYDATABASE' {
+            publishDir  = [
+                path: { "${params.outdir}/decoydatabase" },
+                mode: params.publish_dir_mode,
+                pattern: '*.log',
+                saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+            ]
         }
-        'proteininference' {
-            args    = ''
-            publish_files = ['log': '']
+    }
+}
+
+if (params.posterior_probabilities == "percolator") {
+    process {
+        // EXTRACTPSMFEATURE
+        withName: 'NFCORE_QUANTMS:QUANTMS:.*:EXTRACTPSMFEATURE' {
+            publishDir  = [
+                path: { "${params.outdir}/extractpsmfeature" },
+                mode: params.publish_dir_mode,
+                pattern: '*.log',
+                saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+            ]
         }
-        'idconflictresolver' {
-            args    = ''
+    }
+}
+
+if (params.search_engines.split(",").size() == 1) {
+    process {
+
+        // IDSCORESWITCHER
+        withName: 'NFCORE_QUANTMS:QUANTMS:.*:ID:PSMFDRCONTROL:IDSCORESWITCHER' {
+            ext.args    = [
+                "-new_score_orientation lower_better",
+                "-old_score \"Posterior Error Probability\"",
+                "-new_score_type q-value"
+            ].join(' ').trim()
+            publishDir  = [
+                path: { "${params.outdir}/idscoreswitcher" },
+                mode: params.publish_dir_mode,
+                saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+            ]
         }
-        'proteinquantifier' {
-            args    = ''
+    }
+}
+
+if (params.enable_mod_localization) {
+    process {
+
+        // IDSCORESWITCHERFORLUCIPHOR
+        withName: 'NFCORE_QUANTMS:QUANTMS:.*:ID:PHOSPHOSCORING:IDSCORESWITCHERFORLUCIPHOR' {
+            ext.args    = [
+                "-new_score_orientation lower_better",
+                "-old_score \"q-value\"",
+                "-new_score_type Posterior Error Probability"
+            ].join(' ').trim()
+            publishDir  = [
+                path: { "${params.outdir}/idscoreswitcherforluciphor" },
+                mode: params.publish_dir_mode,
+                saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+            ]
         }
-        'msstatsconverter' {
-            args    = ''
+    }
+}
+
+if (params.labelling_type){
+    if ( params.labelling_type.contains('tmt') | params.labelling_type.contains("itraq")){
+        process {
+            // ISOBARICANALYZER
+            withName: 'NFCORE_QUANTMS:QUANTMS:TMT:.*:ISOBARICANALYZER' {
+                publishDir  = [
+                    path: { "${params.outdir}/isobaricanalyzer" },
+                    mode: params.publish_dir_mode,
+                    pattern: '*.log',
+                    saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+                ]
+            }
+
+            // IDMAPPER
+            withName: 'NFCORE_QUANTMS:QUANTMS:TMT:.*:IDMAPPER' {
+                publishDir  = [
+                    path: { "${params.outdir}/idmapper" },
+                    mode: params.publish_dir_mode,
+                    pattern: '*.{log,consensusXML}',
+                    saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+                ]
+            }
+
+            // EPIFILTER
+            withName: 'NFCORE_QUANTMS:QUANTMS:.*:EPIFILTER' {
+                ext.args    = [
+                    "-score:prot \"$params.protein_level_fdr_cutoff\"",
+                    "-delete_unreferenced_peptide_hits",
+                    "-remove_decoys"
+                ].join(' ').trim()
+                ext.suffix  = '.consensusXML'
+                publishDir  = [
+                    path: { "${params.outdir}/epifilter" },
+                    mode: params.publish_dir_mode,
+                    saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+                ]
+            }
         }
-        'pmultiqc' {
-            args    = ''
+
+        if (params.protein_inference_bayesian) {
+            process {
+                // EPIFANY
+                withName: 'NFCORE_QUANTMS:QUANTMS:.*:EPIFANY' {
+                    publishDir  = [
+                        path: { "${params.outdir}/epifany" },
+                        mode: params.publish_dir_mode,
+                        pattern: '*.log',
+                        saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+                    ]
+                }
+            }
+        } else {
+            process {
+                // PROTEININFERENCER
+                withName: 'NFCORE_QUANTMS:QUANTMS:.*:PROTEININFERENCER' {
+                    publishDir  = [
+                        path: { "${params.outdir}/proteininferencer" },
+                        mode: params.publish_dir_mode,
+                        pattern: '*.log',
+                        saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+                    ]
+                }
+            }
         }
     }
 }
 
 process {
 
-    publishDir = [
-        path: { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" },
-        mode: 'copy',
-        saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
-    ]
+    // INDEXPEPTIDES
+    withName: 'NFCORE_QUANTMS:QUANTMS:.*:INDEXPEPTIDES' {
+        publishDir  = [
+            path: { "${params.outdir}/indexpeptides" },
+            mode: params.publish_dir_mode,
+            pattern: '*.log',
+            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+        ]
+    }
 
-    withName: SAMPLESHEET_CHECK {
-        publishDir = [
-            path: { "${params.outdir}/pipeline_info" },
-            mode: 'copy',
+    // IDFILTER
+    withName: 'NFCORE_QUANTMS:QUANTMS:.*:ID:PSMFDRCONTROL:IDFILTER' {
+        ext.args    = "-score:pep \"$params.psm_pep_fdr_cutoff\""
+        ext.suffix  = '.idXML'
+        publishDir  = [
+            path: { "${params.outdir}/idfilter" },
+            mode: params.publish_dir_mode,
             saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
         ]
     }
@@ -127,5 +207,4 @@ process {
             pattern: '*_versions.yml'
         ]
     }
-
 }

conf/test.config

@@ -22,13 +22,12 @@ params {
     // Input data
     input = 'https://raw.githubusercontent.com/daichengxin/quantms/dev/assets/PXD000001.sdrf.tsv'
 
-    quant_method = 'ISO'
     database = 'https://raw.githubusercontent.com/daichengxin/proteomicstmt/dev/tmt_testdata/erwinia_carotovora.fasta'
     posterior_probabilities = "percolator"
     search_engines = "msgf"
     protein_level_fdr_cutoff = 0.01
     decoy_string = "rev"
-    label = 'tmt6plex'
+    labelling_type = 'tmt6plex'
     fragment_method = 'HCD'
     add_decoys = true
     protocol = 'TMT'

conf/test_lfq.config

@@ -16,7 +16,7 @@ params {
   max_time = 48.h
 
   // Input data
-  quant_method = "LFQ"
+  labelling_type = "label free sample"
   input = 'https://raw.githubusercontent.com/nf-core/test-datasets/proteomicslfq/testdata/BSA_design_urls.tsv'
   database = 'https://raw.githubusercontent.com/nf-core/test-datasets/proteomicslfq/testdata/18Protein_SoCe_Tr_detergents_trace_target_decoy.fasta'
   posterior_probabilities = "fit_distributions"

docs/README.md

@@ -1,6 +1,6 @@
-# nf-core/proteomicslfq: Documentation
+# nf-core/quantms: Documentation
 
-The nf-core/proteomicslfq documentation is split into the following pages:
+The nf-core/quantms documentation is split into the following pages:
 
 * [Usage](usage.md)
     * An overview of how the pipeline works, how to run it and a description of all of the different command-line flags.