new module: stitchr

modules/nf-core/stitchr/Dockerfile

@@ -0,0 +1,26 @@
+# ---- Base image ----
+FROM python:3.14
+
+LABEL authors="Clara Bierwirth" \
+      description="Stitchr container with IMGT human and mouse data"
+
+# ---- Environment settings ----
+ENV PYTHONDONTWRITEBYTECODE=1 \
+    PYTHONUNBUFFERED=1 \
+    PATH="/usr/local/bin:${PATH}"
+
+# ---- System dependencies ----
+RUN apt-get update && apt-get install -y --no-install-recommends \
+      git \
+      build-essential \
+      wget \
+    && rm -rf /var/lib/apt/lists/*
+
+# ---- Install Stitchr and IMGTgeneDL ----
+RUN pip install --no-cache-dir --upgrade --force-reinstall \
+    stitchr==1.3.1 \
+    IMGTgeneDL==0.6.1
+
+# ---- Download human and mouse IMGT data ----
+RUN stitchrdl -s human
+RUN stitchrdl -s mouse

modules/nf-core/stitchr/thimble/main.nf

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+process STITCHR_THIMBLE {
+    tag "$meta.id"
+    label 'process_single'
+
+
+    container "ghcr.io/qbic-pipelines/stitchr:1.3.1"
+
+
+    input:
+    tuple val(meta), path(samplesheet)
+    tuple val(meta2), path(alt_codon_usage)
+    tuple val(meta3), path(allele_preferences)
+    val(species)
+
+
+    output:
+    tuple val(meta), path("${meta.id}.tsv"), emit: thimble
+    tuple val("${task.process}"), val('stitchr'), eval("stitchr --version"), topic: versions, emit: versions_stitchr
+    tuple val("${task.process}"), val('imgtgenedl'), val("0.6.1"), topic: versions, emit: versions_imgtgenedl
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    //optional files:
+    def codon_usage = alt_codon_usage ? "-cu ${alt_codon_usage}" : ""
+    def allele_preference = allele_preferences ? "-p ${allele_preferences}" : ""
+
+    """
+    thimble \
+        $args \
+        -in ${samplesheet} \
+        -o ${prefix}.tsv \
+        ${codon_usage} \
+        ${allele_preference} \
+        -s ${species}
+    """
+
+    stub:
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+
+    """
+    echo $args
+
+    touch ${prefix}.tsv
+    """
+}

modules/nf-core/stitchr/thimble/meta.yml

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+name: "stitchr_thimble"
+description: Automatic TCR nucleotide sequence generation from V, J and CDR3
+  information
+keywords:
+  - TCR
+  - sequence
+  - immunology
+tools:
+  - "stitchr":
+      description: "Automatic TCR nucleotide sequence generation from V, J and CDR3
+        information"
+      homepage: "https://github.com/JamieHeather/stitchr"
+      documentation: "https://jamieheather.github.io/stitchr/index.html"
+      tool_dev_url: "https://github.com/JamieHeather/stitchr"
+      doi: "10.1093/nar/gkac190"
+      licence:
+        - "MIT"
+      identifier: ""
+  - "imgtgenedl":
+      description: "provides access to TCR and IG genes stored in IMGT/GENE-DB"
+      homepage: "https://github.com/JamieHeather/IMGTgeneDL"
+      documentation: "https://github.com/JamieHeather/IMGTgeneDL/blob/main/README.md"
+      tool_dev_url: "https://github.com/JamieHeather/IMGTgeneDL"
+      doi: "10.1093/nar/gkab1136"
+      licence:
+        - "MIT"
+      identifier: ""
+input:
+  - - meta:
+        type: map
+        description: |
+          Groovy Map containing per sample information
+          e.g. `[ id:'sample1' ]`
+    - samplesheet:
+        type: file
+        description: tsv containing J,V and CDR3 information
+        pattern: "*.tsv"
+        ontologies:
+          - edam: http://edamontology.org/format_3475
+  - - meta2:
+        type: map
+        description: |
+          Information about codon usage
+    - alt_codon_usage:
+        type: file
+        description: txt containing alternative codon usage in kazusa-like format
+        pattern: "*.txt"
+        ontologies: []
+  - - meta3:
+        type: map
+        description: |
+          Information about non-standard allele preferences
+    - allele_preferences:
+        type: file
+        description: tsv containing alternative allele preferences
+        pattern: "*.tsv"
+        ontologies:
+          - edam: http://edamontology.org/format_3475
+  - species:
+      type: string
+      description: Species ("mouse" or "human")
+output:
+  thimble:
+    - - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. `[ id:'sample1' ]`
+      - ${meta.id}.tsv:
+          type: file
+          description: |
+            tsv containing full TCR sequences
+          ontologies: []
+  versions_stitchr:
+    - - ${task.process}:
+          type: string
+          description: The name of the process
+      - stitchr:
+          type: string
+          description: The name of the tool
+      - stitchr --version:
+          type: eval
+          description: The expression to obtain the version of the tool
+  versions_imgtgenedl:
+    - - ${task.process}:
+          type: string
+          description: The name of the process
+      - imgtgenedl:
+          type: string
+          description: The name of the tool
+      - 0.6.1:
+          type: string
+          description: The expression to obtain the version of the tool
+topics:
+  versions:
+    - - ${task.process}:
+          type: string
+          description: The name of the process
+      - stitchr:
+          type: string
+          description: The name of the tool
+      - stitchr --version:
+          type: eval
+          description: The expression to obtain the version of the tool
+    - - ${task.process}:
+          type: string
+          description: The name of the process
+      - imgtgenedl:
+          type: string
+          description: The name of the tool
+      - 0.6.1:
+          type: string
+          description: The expression to obtain the version of the tool
+authors:
+  - "@Clara0611"
+maintainers:
+  - "@Clara0611"

modules/nf-core/stitchr/thimble/tests/main.nf.test

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+nextflow_process {
+
+    name "Test Process STITCHR_THIMBLE"
+    script "../main.nf"
+    process "STITCHR_THIMBLE"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "stitchr"
+    tag "stitchr/thimble"
+
+    test("human - tsv") {
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test' ],
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/stitchr/stitchr_vdjdb.tsv', checkIfExists: true),
+                ]
+                  input[1] = [
+                    [ id: 'alt_codon_usage' ],
+                    []
+                ]
+                input[2] = [
+                    [ id: 'allele_preference' ],
+                    []
+                ]
+                input[3] = "human"
+                """
+            }
+        }
+
+        then {
+            assert process.success
+            assertAll(
+                { assert snapshot(
+                    process.out,
+                    process.out.findAll { key, val -> key.startsWith('versions') }
+                ).match() }
+            )
+        }
+
+    }
+
+    test("human - tsv - stub") {
+
+        options "-stub"
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test' ],
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/stitchr/stitchr_vdjdb.tsv', checkIfExists: true),
+                ]
+                 input[1] = [
+                    [ id: 'alt_codon_usage' ],
+                    []
+                ]
+                input[2] = [
+                    [ id: 'allele_preference' ],
+                    []
+                ]
+                input[3] = "human"
+                """
+            }
+        }
+
+        then {
+            assert process.success
+            assertAll(
+                { assert snapshot(
+                process.out,
+                process.out.findAll { key, val -> key.startsWith('versions') }
+                ).match() }
+            )
+        }
+
+    }
+
+}