3992 new module openmspeakpickerhires (nf-core#4207)

* add peakpickerhires module * Add peackpicker module with tests * prettier * fix falsely moved folder * Update meta.yml * fix prettier on other modules * Update environment.yml * Update environment.yml * Update environment.yml * Update environment.yml * Update environment.yml * Update environment.yml * Update environment.yml * Update environment.yml * Update environment.yml * Update environment.yml
adamrtalbot · Oct 25, 2023 · 4e2cbac · 4e2cbac
1 parent ec622d8
commit 4e2cbac
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diff --git a/modules/nf-core/openms/peakpickerhires/main.nf b/modules/nf-core/openms/peakpickerhires/main.nf
@@ -0,0 +1,49 @@
+process OPENMS_PEAKPICKERHIRES {
+    tag "$meta.id"
+    label 'process_low'
+
+    conda "bioconda::openms=3.0.0"
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/openms:3.0.0--h8964181_1' :
+        'biocontainers/openms:3.0.0--h8964181_1' }"
+
+    input:
+    tuple val(meta), path(mzml)
+
+    output:
+    tuple val(meta), path("*.mzML"), emit: mzml
+    path "versions.yml"            , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+
+    """
+    PeakPickerHiRes \\
+        -in $mzml \\
+        -out ${prefix}.mzML \\
+        -threads $task.cpus \\
+        $args
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        openms: \$(echo \$(FileInfo --help 2>&1) | sed 's/^.*Version: //; s/-.*\$//' | sed 's/ -*//; s/ .*\$//')
+    END_VERSIONS
+    """
+
+    stub:
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+
+    """
+    touch ${prefix}.mzML
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        openms: \$(echo \$(FileInfo --help 2>&1) | sed 's/^.*Version: //; s/-.*\$//' | sed 's/ -*//; s/ .*\$//')
+    END_VERSIONS
+    """
+}
diff --git a/modules/nf-core/openms/peakpickerhires/meta.yml b/modules/nf-core/openms/peakpickerhires/meta.yml
@@ -0,0 +1,46 @@
+name: "openms_peakpickerhires"
+description: A tool for peak detection in high-resolution profile data (Orbitrap or FTICR)
+keywords:
+  - peak picking
+  - mzml
+  - openms
+  - proteomics
+tools:
+  - "openms":
+      description: "OpenMS is an open-source software C++ library for LC-MS data management and analyses"
+      homepage: "https://openms.de"
+      documentation: "https://openms.readthedocs.io/en/latest/index.html"
+      tool_dev_url: "https://github.com/OpenMS/OpenMS"
+      doi: "10.1038/nmeth.3959"
+      licence: "['BSD']"
+
+input:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. `[ id:'test', single_end:false ]`
+  - mzml:
+      type: file
+      description: Mass spectrometer output file in mzML format
+      pattern: "*.{mzML}"
+
+output:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. `[ id:'test', single_end:false ]`
+  - versions:
+      type: file
+      description: File containing software versions
+      pattern: "versions.yml"
+  - mzml:
+      type: file
+      description: Peak-picked mass spectrometer output file in mzML format
+      pattern: "*.{mzML}"
+
+authors:
+  - "@jonasscheid"
+maintainers:
+  - "@jonasscheid"
diff --git a/tests/config/pytest_modules.yml b/tests/config/pytest_modules.yml
@@ -2580,6 +2580,10 @@ openms/idmerger:
   - modules/nf-core/openms/idmerger/**
   - tests/modules/nf-core/openms/idmerger/**
 
+openms/peakpickerhires:
+  - modules/nf-core/openms/peakpickerhires/**
+  - tests/modules/nf-core/openms/peakpickerhires/**
+
 optitype:
   - modules/nf-core/optitype/**
   - tests/modules/nf-core/optitype/**

diff --git a/tests/config/test_data.config b/tests/config/test_data.config
@@ -650,6 +650,7 @@ params {
             'msspectra' {
                 ups_file1                       = "${params.test_data_base}/data/proteomics/msspectra/OVEMB150205_12.raw"
                 ups_file2                       = "${params.test_data_base}/data/proteomics/msspectra/OVEMB150205_14.raw"
+                profile_spectra                 = "${params.test_data_base}/data/proteomics/msspectra/peakpicker_tutorial_1.mzML"
             }
             'database' {
                 yeast_ups                       = "${params.test_data_base}/data/proteomics/database/yeast_UPS.fasta"

diff --git a/tests/modules/nf-core/openms/peakpickerhires/main.nf b/tests/modules/nf-core/openms/peakpickerhires/main.nf
@@ -0,0 +1,15 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { OPENMS_PEAKPICKERHIRES } from '../../../../../modules/nf-core/openms/peakpickerhires/main.nf'
+
+workflow test_openms_peakpickerhires {
+
+    input = [
+        [ id:'test'], // meta map
+        file(params.test_data['proteomics']['msspectra']['profile_spectra'], checkIfExists: true)
+    ]
+
+    OPENMS_PEAKPICKERHIRES ( input )
+}
diff --git a/tests/modules/nf-core/openms/peakpickerhires/nextflow.config b/tests/modules/nf-core/openms/peakpickerhires/nextflow.config
@@ -0,0 +1,8 @@
+process {
+
+    publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+    withName: PEAKPICKERHIRES {
+        ext.args = '-algorithm:ms_levels 2'
+    }
+}
diff --git a/tests/modules/nf-core/openms/peakpickerhires/test.yml b/tests/modules/nf-core/openms/peakpickerhires/test.yml
@@ -0,0 +1,11 @@
+- name: openms peakpickerhires test_openms_peakpickerhires
+  command: nextflow run ./tests/modules/nf-core/openms/peakpickerhires -entry test_openms_peakpickerhires -c ./tests/config/nextflow.config
+  tags:
+    - openms/peakpickerhires
+    - openms
+  files:
+    - path: output/openms/test.mzML
+      # md5sums are not reproducible because PeakPickerHiRes saves the time of execution in the file
+      contains:
+        - '<cvParam cvRef="MS" accession="MS:1000294" name="mass spectrum" />'
+    - path: output/openms/versions.yml