remove posterior_probabilities parameter.

modules/local/openms/extractpsmfeatures/main.nf

@@ -0,0 +1,43 @@
+process EXTRACTPSMFEATURES {
+    tag "$meta.mzml_id"
+    label 'process_very_low'
+    label 'process_single'
+    label 'openms'
+
+    conda "bioconda::openms-thirdparty=3.2.0"
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/openms-thirdparty:3.2.0--h9ee0642_4' :
+        'biocontainers/openms-thirdparty:3.2.0--h9ee0642_4' }"
+
+    input:
+    tuple val(meta), path(id_file), path(extra_feat)
+
+    output:
+    tuple val(meta), path("${id_file.baseName}_feat.idXML"), emit: id_files_feat
+    path "versions.yml", emit: versions
+    path "*.log", emit: log
+
+    script:
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.mzml_id}"
+
+    feature = ""
+    if (params.ms2rescore && params.id_only) {
+        feature = "-extra \$(awk 'NR > 1 && \$1 !~ /psm_file/ {printf \"%s \", \$2}' ${extra_feat})"
+    }
+
+    """
+    PSMFeatureExtractor \\
+        -in ${id_file} \\
+        -out ${id_file.baseName}_feat.idXML \\
+        -threads $task.cpus \\
+        ${feature} \\
+        $args \\
+        2>&1 | tee ${id_file.baseName}_extract_psm_feature.log
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        PSMFeatureExtractor: \$(PSMFeatureExtractor 2>&1 | grep -E '^Version(.*)' | sed 's/Version: //g' | cut -d ' ' -f 1)
+    END_VERSIONS
+    """
+}

modules/local/openms/extractpsmfeatures/meta.yml

@@ -0,0 +1,40 @@
+name: extracpsmfeatures
+description: Computes extra features for each input PSM.
+keywords:
+  - PSM
+  - feature
+  - OpenMS
+tools:
+  - PSMFeatureExtractor:
+      description: |
+        Computes extra features for each input PSM.
+      homepage: https://abibuilder.cs.uni-tuebingen.de/archive/openms/Documentation/nightly/html/UTILS_PSMFeatureExtractor.html
+      documentation: https://abibuilder.cs.uni-tuebingen.de/archive/openms/Documentation/nightly/html/UTILS_PSMFeatureExtractor.html
+input:
+  - meta:
+      type: map
+      description: Groovy Map containing sample information
+  - id_file:
+      type: file
+      description: |
+        Input idXML file containing the identifications.
+      pattern: "*.idXML"
+output:
+  - meta:
+      type: map
+      description: Groovy Map containing sample information
+  - id_files_feat:
+      type: file
+      description: |
+        Output file in idXML format
+      pattern: "*.idXML"
+  - log:
+      type: file
+      description: log file
+      pattern: "*.log"
+  - version:
+      type: file
+      description: File containing software version
+      pattern: "versions.yml"
+authors:
+  - "@daichengxin"