merge origin

Author: jonasscheid

.prettierignore

@@ -12,6 +12,5 @@ testing*
 bin/
 .nf-test/
 ro-crate-metadata.json
-.nf-test/
 modules/nf-core/
 subworkflows/nf-core/

CHANGELOG.md

@@ -3,7 +3,15 @@
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/)
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
-## 3.2.0 - [releasename] - [date]
+## 3.2.0dev - [release name] - [date]
+
+### `Added`
+
+- Added support for single run quantification [#438](https://github.com/nf-core/mhcquant/pull/438)
+
+### `Fixed`
+
+- Fixed an issue where stripping the sequence in `SUMMARIZE_RESULTS` did not work for complex modifications [#436](https://github.com/nf-core/mhcquant/pull/436)
 
 ### `Changed`
 

bin/summarize_results.py

@@ -4,6 +4,7 @@
 
 import pandas as pd
 import numpy as np
+from pyopenms import AASequence
 from argparse import ArgumentParser
 import re
 from collections import Counter
@@ -87,6 +88,13 @@ def parse_multiTSV(file_path):
     df["psm"] = df["sequence"].map(psm)
     return df
 
+def strip_modifications(seq_with_mods: str) -> str:
+    try:
+        aa_seq = AASequence.fromString(seq_with_mods)
+        return aa_seq.toUnmodifiedString()
+    except Exception as e:
+        logging.warning(f"Could not parse sequence {seq_with_mods}: {e}")
+        return seq_with_mods
 
 def process_file(file, prefix, quantify, keep_cols):
     """Extract all the relevant information and write it to a TSV file for the MultiQC report
@@ -122,7 +130,7 @@ def process_file(file, prefix, quantify, keep_cols):
 
     # Remove modification information from the sequence column
     data["peptidoform"] = data["sequence"]
-    data["sequence"] = data["sequence"].apply(lambda seq: re.sub(r'\(.*?\)', '', seq))
+    data["sequence"] = data["sequence"].apply(strip_modifications)
 
     # ---------------------------------
     # Length distribution plot

conf/modules.config

@@ -255,6 +255,12 @@ process {
         ]
     }
 
+    withName: 'OPENMS_FILECONVERTER' {
+        publishDir  = [
+            enabled: false
+        ]
+    }
+
     withName: 'MULTIQC' {
         ext.args   = { params.multiqc_title ? "--title \"$params.multiqc_title\"" : '' }
         publishDir = [

conf/test_single_quant.config

@@ -0,0 +1,24 @@
+/*
+ * ----------------------------------------------------------------------------
+ *  Nextflow config file for running tests
+ * ----------------------------------------------------------------------------
+ * Defines bundled input files and everything required to run a fast and simple
+ * pipeline test. Use as follows:
+ *   nextflow run main.nf -profile test_single_quant,<docker/singularity>
+ *  */
+
+params {
+    config_profile_name        = 'Test single replicate profile'
+    config_profile_description = 'Test dataset to check pipeline function for single replicate'
+
+    // Limit resources so that this can run on GitHub Actions
+    max_cpus   = 2
+    max_memory = '6.GB'
+    max_time   = '6.h'
+
+    // Input data
+    input = params.pipelines_testdata_base_path + 'mhcquant/testdata/sample_sheet_single_quant.tsv'
+
+    // Pipeline settings
+    quantify = true
+}

modules/local/openms/fileconverter/environment.yml

@@ -0,0 +1,7 @@
+name: openms_fileconverter
+channels:
+  - conda-forge
+  - bioconda
+  - defaults
+dependencies:
+  - bioconda::openms=3.4.1

modules/local/openms/fileconverter/main.nf

@@ -0,0 +1,46 @@
+process OPENMS_FILECONVERTER {
+    tag "$meta.id"
+    label 'process_single'
+
+    conda "${moduleDir}/environment.yml"
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/openms:3.4.1--h81ffffe_1' :
+        'biocontainers/openms:3.4.1--h81ffffe_1' }"
+
+    input:
+    tuple val(meta), path(file), val(suffix)
+
+    output:
+    tuple val(meta), path("*.${suffix}"), emit: consensusxml
+    path "versions.yml"                    , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def prefix = task.ext.prefix ?: "${meta.id}"
+
+    """
+    FileConverter \\
+        -in $file \\
+        -out ${prefix}.${suffix} \\
+        -threads $task.cpus
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        openms: \$(echo \$(FileInfo --help 2>&1) | sed 's/^.*Version: //; s/-.*\$//' | sed 's/ -*//; s/ .*\$//')
+    END_VERSIONS
+    """
+
+    stub:
+    def prefix = task.ext.prefix ?: "${meta.id}"
+
+    """
+    touch ${prefix}.${suffix}
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        openms: \$(echo \$(FileInfo --help 2>&1) | sed 's/^.*Version: //; s/-.*\$//' | sed 's/ -*//; s/ .*\$//')
+    END_VERSIONS
+    """
+}