update some process to openms dev

modules/local/diannconvert/main.nf

@@ -2,11 +2,11 @@ process DIANNCONVERT {
     tag "$meta.experiment_id"
     label 'process_medium'
 
-    conda "conda-forge::pandas_schema conda-forge::lzstring bioconda::pmultiqc=0.0.20"
+    conda "conda-forge::pandas_schema conda-forge::lzstring bioconda::pmultiqc=0.0.21"
     if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
-        container "https://depot.galaxyproject.org/singularity/pmultiqc:0.0.20--pyhdfd78af_0"
+        container "https://depot.galaxyproject.org/singularity/pmultiqc:0.0.21--pyhdfd78af_0"
     } else {
-        container "quay.io/biocontainers/pmultiqc:0.0.20--pyhdfd78af_0"
+        container "quay.io/biocontainers/pmultiqc:0.0.21--pyhdfd78af_0"
     }
 
     input:

modules/local/msstats/main.nf

@@ -2,11 +2,11 @@ process MSSTATS {
     tag "$msstats_csv_input.Name"
     label 'process_medium'
 
-    conda "bioconda::bioconductor-msstats=4.2.0"
+    conda "bioconda::bioconductor-msstats=4.8.3"
     if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
-        container "https://depot.galaxyproject.org/singularity/bioconductor-msstats:4.2.0--r41h619a076_1"
+        container "https://depot.galaxyproject.org/singularity/bioconductor-msstats:4.8.3--r43hf17093f_0"
     } else {
-        container "quay.io/biocontainers/bioconductor-msstats:4.2.0--r41h619a076_1"
+        container "quay.io/biocontainers/bioconductor-msstats:4.8.3--r43hf17093f_0"
     }
 
     input:

modules/local/msstatstmt/main.nf

@@ -2,11 +2,11 @@ process MSSTATSTMT {
     tag "$msstatstmt_csv_input.Name"
     label 'process_medium'
 
-    conda "bioconda::bioconductor-msstatstmt=2.2.0"
+    conda "bioconda::bioconductor-msstatstmt=2.8.0"
     if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
-        container "https://depot.galaxyproject.org/singularity/bioconductor-msstatstmt:2.2.0--r41hdfd78af_0"
+        container "https://depot.galaxyproject.org/singularity/bioconductor-msstatstmt:2.8.0--r43hdfd78af_0"
     } else {
-        container "quay.io/biocontainers/bioconductor-msstatstmt:2.2.0--r41hdfd78af_0"
+        container "quay.io/biocontainers/bioconductor-msstatstmt:2.8.0--r43hdfd78af_0"
     }
 
     input:

modules/local/openms/msstatsconverter/main.nf

@@ -2,10 +2,10 @@ process MSSTATSCONVERTER {
     tag "$exp_file.Name"
     label 'process_low'
 
-    conda "bioconda::openms=2.9.1"
+    conda "openms::openms-thirdparty=3.1.0"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/openms:2.9.1--h135471a_0' :
-        'quay.io/biocontainers/openms:2.9.1--h135471a_0' }"
+        'ghcr.io/openms/openms-executables-sif:latest' :
+        'ghcr.io/openms/openms-executables:latest' }"
 
     input:
     path consensusXML

modules/local/openms/proteininference/main.nf

@@ -1,10 +1,10 @@
 process PROTEININFERENCE {
     label 'process_medium'
 
-    conda "bioconda::openms=2.9.1"
+    conda "openms::openms-thirdparty=3.1.0"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/openms:2.9.1--h135471a_0' :
-        'quay.io/biocontainers/openms:2.9.1--h135471a_0' }"
+        'ghcr.io/openms/openms-executables-sif:latest' :
+        'ghcr.io/openms/openms-executables:latest' }"
 
     input:
     tuple val(meta), path(consus_file)

modules/local/openms/proteinquantifier/main.nf

@@ -2,10 +2,10 @@ process PROTEINQUANTIFIER {
     tag "${pro_quant_exp.baseName}"
     label 'process_medium'
 
-    conda "bioconda::openms=2.9.1"
+    conda "openms::openms-thirdparty=3.1.0"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/openms:2.9.1--h135471a_0' :
-        'quay.io/biocontainers/openms:2.9.1--h135471a_0' }"
+        'ghcr.io/openms/openms-executables-sif:latest' :
+        'ghcr.io/openms/openms-executables:latest' }"
 
     input:
     path epi_filt_resolve

modules/local/openms/proteomicslfq/main.nf

@@ -2,10 +2,10 @@ process PROTEOMICSLFQ {
     tag "${expdes.baseName}"
     label 'process_high'
 
-    conda "bioconda::openms=2.9.1"
+    conda "openms::openms-thirdparty=3.1.0"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/openms:2.9.1--h135471a_0' :
-        'quay.io/biocontainers/openms:2.9.1--h135471a_0' }"
+        'ghcr.io/openms/openms-executables-sif:latest' :
+        'ghcr.io/openms/openms-executables:latest' }"
 
     input:
     path(mzmls)
@@ -30,6 +30,7 @@ process PROTEOMICSLFQ {
     script:
     def args = task.ext.args ?: ''
     def msstats_present = params.quantification_method == "feature_intensity" ? "-out_msstats ${expdes.baseName}_msstats_in.csv" : ""
+    def id_transfer_threshold = (params.quantification_method == "feature_intensity") && (transfer_ids != "off") ? "-id_transfer_threshold ${params.id_transfer_threshold}" : ""
     def triqler_present = (params.quantification_method == "feature_intensity") && (params.add_triqler_output) ? "-out_triqler ${expdes.baseName}_triqler_in.tsv" : ""
     def decoys_present = (params.quantify_decoys || ((params.quantification_method == "feature_intensity") && params.add_triqler_output)) ? '-PeptideQuantification:quantify_decoys' : ''
     def mzml_sorted = mzmls.collect().sort{ a, b -> a.name <=> b.name}

modules/local/pmultiqc/main.nf

@@ -1,11 +1,11 @@
 process PMULTIQC {
     label 'process_high'
 
-    conda "conda-forge::pandas_schema conda-forge::lzstring bioconda::pmultiqc=0.0.20"
+    conda "conda-forge::pandas_schema conda-forge::lzstring bioconda::pmultiqc=0.0.21"
     if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
-        container "https://depot.galaxyproject.org/singularity/pmultiqc:0.0.20--pyhdfd78af_0"
+        container "https://depot.galaxyproject.org/singularity/pmultiqc:0.0.21--pyhdfd78af_0"
     } else {
-        container "quay.io/biocontainers/pmultiqc:0.0.20--pyhdfd78af_0"
+        container "quay.io/biocontainers/pmultiqc:0.0.21--pyhdfd78af_0"
     }
 
     input:
@@ -23,6 +23,7 @@ process PMULTIQC {
     def args = task.ext.args ?: ''
     def disable_pmultiqc = (params.enable_pmultiqc) && (params.export_mztab) ? "" : "--disable_plugin"
     def disable_table_plots = (params.enable_pmultiqc) && (params.skip_table_plots) ? "--disable_table" : ""
+    def disable_idxml_index = (params.enable_pmultiqc) && (params.pmultiqc_idxml_skip) ? "--ignored_idxml" : ""
 
     """
     multiqc \\
@@ -31,6 +32,7 @@ process PMULTIQC {
         ${args} \\
         ${disable_pmultiqc} \\
         ${disable_table_plots} \\
+        ${disable_idxml_index} \\
         --quantification_method $params.quantification_method \\
         ./results \\
         -o .

nextflow.config

@@ -22,7 +22,6 @@ params {
     // Tools flags
     posterior_probabilities  = 'percolator'
     add_decoys               = false
-    enable_pmultiqc          = true
     search_engines           = 'comet'
     sage_processes           = 1
     run_fdr_cutoff           = 0.10
@@ -155,6 +154,7 @@ params {
     alignment_order          = 'star'
     add_triqler_output       = false
     quantify_decoys          = false
+    id_transfer_threshold    = 0.50 // only used if targeted_only is set to false (default)
 
     // DIA-NN
     diann_debug             = 3
@@ -190,9 +190,9 @@ params {
     msstatsiso_reference_normalization      = true
     msstats_plot_profile_qc                 = false
 
-    // PTXQC
-    enable_qc           = false
-    ptxqc_report_layout = null
+    // pmultiqc options
+    enable_pmultiqc          = true
+    pmultiqc_idxml_skip      = true
 
     // MultiQC options
     multiqc_config             = null

nextflow_schema.json

@@ -834,6 +834,12 @@
                     "default": true,
                     "fa_icon": "far fa-check-square"
                 },
+                "id_transfer_threshold": {
+                    "type": "number",
+                    "description": "The maximum percentage of samples that will be accepted for matching between runs (default: 0.5)",
+                    "default": 0.5,
+                    "fa_icon": "fas fa-filter"
+                },
                 "alignment_order": {
                     "type": "string",
                     "description": "The order in which maps are aligned. Star = all vs. the reference with most IDs (default). TreeGuided = an alignment tree is calculated first based on similarity measures of the IDs in the maps.",
@@ -1048,19 +1054,14 @@
             "description": "",
             "default": "",
             "properties": {
-                "enable_qc": {
+                "enable_pmultiqc": {
                     "type": "boolean",
-                    "description": "Enable generation of quality control report by PTXQC? default: 'false' since it is still unstable",
+                    "description": "Enable generation of pmultiqc report? default: 'false'",
                     "fa_icon": "fas fa-toggle-on"
                 },
-                "ptxqc_report_layout": {
-                    "type": "string",
-                    "description": "Specify a yaml file for the report layout (see PTXQC documentation) (TODO not yet fully implemented)",
-                    "fa_icon": "far fa-file"
-                },
-                "enable_pmultiqc": {
+                "pmultiqc_idxml_skip": {
                     "type": "boolean",
-                    "description": "Enable generation of pmultiqc report? default: 'false'",
+                    "description": "Skip idXML files (do not generate search engine scores) in pmultiqc report? default: 'true'",
                     "fa_icon": "fas fa-toggle-on"
                 }
             },