Merge pull request #604 from MaLLLiYA/isobaric_workflow

add IsobaricWorkflow to TMT workflow

Author: ypriverol

conf/modules/modules.config

@@ -64,7 +64,7 @@ process {
     }
 
     // Result tables from multiple pipelines including LFQ, TMT, DIA, DDA
-    withName: '.*:PROTEOMICSLFQ|PROTEIN_QUANTIFIER|MSSTATS_CONVERTER|FINAL_QUANTIFICATION|CONVERT_RESULTS' {
+    withName: '.*:PROTEOMICSLFQ|PROTEIN_QUANTIFIER|MSSTATS_CONVERTER|FINAL_QUANTIFICATION|CONVERT_RESULTS|ISOBARIC_WORKFLOW' {
         publishDir = [
             path: { "${params.outdir}/quant_tables" },
             mode: 'copy',

modules/local/openms/isobaric_workflow/main.nf

@@ -0,0 +1,64 @@
+process ISOBARIC_WORKFLOW {
+    tag "${expdes.baseName}"
+    label 'process_high'
+    label 'openms'
+
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'oras://ghcr.io/bigbio/openms-tools-thirdparty-sif:2025.04.14' :
+        'ghcr.io/bigbio/openms-tools-thirdparty:2025.04.14' }"
+
+    input:
+    path(mzmls)
+    path(id_files)
+    path(expdes)
+
+    output:
+    path "${expdes.baseName}_openms.mzTab", emit: out_mztab
+    path "${expdes.baseName}_openms.consensusXML", emit: out_consensusXML
+    path "*.log", emit: log
+    path "versions.yml", emit: versions
+
+    script:
+    def args = task.ext.args ?: ''
+    def extractBaseName = { filename ->
+        def name = filename.toString()
+        name = name.replaceAll(/\.mzML$/, '')
+
+        if (name.endsWith('.idXML')) {
+            name = name.replaceAll(/\.idXML$/, '')
+            name = name.replaceAll(/_(comet|msgf|sage|consensus)(_perc)?(_filter)?(_fdr)?$/, '')
+        }
+        return name
+    }
+
+    def mzml_sorted = mzmls.collect().sort{ a, b ->
+        extractBaseName(a.name) <=> extractBaseName(b.name)
+    }
+    def id_sorted = id_files.collect().sort{ a, b ->
+        extractBaseName(a.name) <=> extractBaseName(b.name)
+    }
+
+    """
+    IsobaricWorkflow \\
+        -threads ${task.cpus} \\
+        -in ${mzml_sorted.join(' ')} \\
+        -in_id ${id_sorted.join(' ')} \\
+        -exp_design ${expdes} \\
+        -type ${params.type} \\
+        -inference_method ${params.protein_inference_method} \\
+        -protein_quantification ${params.protein_quant} \\
+        -psmFDR ${params.psm_level_fdr_cutoff} \\
+        -proteinFDR ${params.protein_level_fdr_cutoff} \\
+        -picked_fdr ${params.picked_fdr} \\
+        -picked_decoy_string ${params.decoy_string} \\
+        -out ${expdes.baseName}_openms.consensusXML \\
+        -out_mzTab ${expdes.baseName}_openms.mzTab \\
+        $args \\
+        2>&1 | tee isobaricworkflow.log
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        IsobaricWorkflow: \$(IsobaricWorkflow 2>&1 | grep -E '^Version(.*)' | sed 's/Version: //g' | cut -d ' ' -f 1)
+    END_VERSIONS
+    """
+}

modules/local/openms/isobaric_workflow/meta.yml

@@ -0,0 +1,42 @@
+name: isobaric_workflow
+description: Extracts and normalizes isobaric labeling information from an LC-MS/MS experiment.
+keywords:
+  - OpenMS
+  - quantification
+tools:
+  - IsobaricWorkflow:
+      description: |
+        Extracts and normalizes isobaric labeling information from an LC-MS/MS experiment.
+      homepage: https://abibuilder.cs.uni-tuebingen.de/archive/openms/Documentation/release/latest/html/TOPP_IsobaricWorkflow.html
+      documentation: https://abibuilder.cs.uni-tuebingen.de/archive/openms/Documentation/release/latest/html/TOPP_IsobaricWorkflow.html
+  - mzmls:
+      type: file
+      description: Input Spectra in mzML format
+      pattern: "*.mzML"
+  - id_files:
+      type: file
+      description: Identifications in idXML or mzIdentML format with posterior error probabilities as score type.
+      pattern: "*.idXML"
+  - expdes:
+      type: file
+      description: An experimental design file
+      pattern: "*.tsv"
+output:
+  - out_mztab:
+      type: file
+      description: mzTab file with analysis results
+      pattern: "*.mzTab"
+  - out_consensusXML:
+      type: file
+      description: ConsensusXML file for visualization and further processing in OpenMS.
+      pattern: "*.consensusXML"
+  - log:
+      type: file
+      description: log file
+      pattern: "*.log"
+  - version:
+      type: file
+      description: File containing software version
+      pattern: "versions.yml"
+authors:
+  - "@MaLLLiYA"

nextflow.config

@@ -178,6 +178,9 @@ params {
     add_triqler_output       = false
     quantify_decoys          = false
 
+    // IsobaricWorkflow flags
+    type                     = 'itraq4plex'
+
     // ProteomicsLFQ MBR parameters
     targeted_only            = true // If false MBR will be applied for quantification of all proteins
     feature_with_id_min_score = 0.10

workflows/tmt.nf

@@ -7,15 +7,13 @@
 //
 // MODULES: Local to the pipeline
 //
-include { FILE_MERGE  } from '../modules/local/openms/file_merge/main'
 include { MSSTATS_TMT } from '../modules/local/msstats/msstats_tmt/main'
+include { ISOBARIC_WORKFLOW } from '../modules/local/openms/isobaric_workflow/main'
+include { MSSTATS_CONVERTER } from '../modules/local/openms/msstats_converter/main'
 
 //
 // SUBWORKFLOWS: Consisting of a mix of local and nf-core/modules
 //
-include { FEATURE_MAPPER    } from '../subworkflows/local/feature_mapper/main'
-include { PROTEIN_INFERENCE } from '../subworkflows/local/protein_inference/main'
-include { PROTEIN_QUANT     } from '../subworkflows/local/protein_quant/main'
 include { ID                } from '../subworkflows/local/id/main'
 
 /*
@@ -41,35 +39,32 @@ workflow TMT {
     ch_software_versions = ch_software_versions.mix(ID.out.versions)
 
     //
-    // SUBWORKFLOW: FEATUREMAPPER
+    // SUBWORKFLOW: ISOBARIC_WORKFLOW
     //
-    FEATURE_MAPPER(ch_file_preparation_results, ID.out.id_results)
-    ch_software_versions = ch_software_versions.mix(FEATURE_MAPPER.out.versions)
+    ch_file_preparation_results.join(ID.out.id_results)
+        .multiMap { it ->
+            mzmls: pmultiqc_mzmls: it[1]
+            ids: it[2]
+        }
+        .set{ ch_iso_workflow }
+    ISOBARIC_WORKFLOW(ch_iso_workflow.mzmls.collect(),
+                ch_iso_workflow.ids.collect(),
+                ch_expdesign
+            )
+    ch_software_versions = ch_software_versions.mix(ISOBARIC_WORKFLOW.out.versions)
 
     //
-    // MODULE: FILEMERGE
+    // MODULE: MSSTATS_CONVERTER
     //
-    FILE_MERGE(FEATURE_MAPPER.out.id_map.collect())
-    ch_software_versions = ch_software_versions.mix(FILE_MERGE.out.versions)
-
-    //
-    // SUBWORKFLOW: PROTEININFERENCE
-    //
-    PROTEIN_INFERENCE(FILE_MERGE.out.id_merge)
-    ch_software_versions = ch_software_versions.mix(PROTEIN_INFERENCE.out.versions)
-
-    //
-    // SUBWORKFLOW: PROTEINQUANT
-    //
-    PROTEIN_QUANT(PROTEIN_INFERENCE.out.epi_idfilter, ch_expdesign)
-    ch_software_versions = ch_software_versions.mix(PROTEIN_QUANT.out.versions)
+    MSSTATS_CONVERTER(ISOBARIC_WORKFLOW.out.out_consensusXML, ch_expdesign, "ISO")
+    ch_software_versions = ch_software_versions.mix(MSSTATS_CONVERTER.out.versions)
 
     //
     // MODULE: MSSTATSTMT
     //
     ch_msstats_out = Channel.empty()
     if(!params.skip_post_msstats){
-        MSSTATS_TMT(PROTEIN_QUANT.out.msstats_csv)
+        MSSTATS_TMT(MSSTATS_CONVERTER.out.out_msstats)
         ch_msstats_out = MSSTATS_TMT.out.msstats_csv
         ch_software_versions = ch_software_versions.mix(MSSTATS_TMT.out.versions)
     }
@@ -85,8 +80,8 @@ workflow TMT {
     emit:
     ch_pmultiqc_ids         = ch_pmultiqc_ids
     ch_pmultiqc_consensus   = ch_pmultiqc_consensus
-    final_result            = PROTEIN_QUANT.out.out_mztab
-    msstats_in              = PROTEIN_QUANT.out.msstats_csv
+    final_result            = ISOBARIC_WORKFLOW.out.out_mztab
+    msstats_in              = MSSTATS_CONVERTER.out.out_msstats
     msstats_out             = ch_msstats_out
     versions                = ch_software_versions
 }