Added nf-core module presto/pairseq

modules/nf-core/presto/pairseq/environment.yml

@@ -0,0 +1,7 @@
+---
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
+channels:
+  - conda-forge
+  - bioconda
+dependencies:
+  - "bioconda::presto=0.7.9"

modules/nf-core/presto/pairseq/main.nf

@@ -0,0 +1,44 @@
+process PRESTO_PAIRSEQ {
+    tag "$meta.id"
+    label 'process_low'
+
+    conda "${moduleDir}/environment.yml"
+    container "${ workflow.containerEngine in ['singularity', 'apptainer'] && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/presto:0.7.9--pyhdfd78af_0':
+        'quay.io/biocontainers/presto:0.7.9--pyhdfd78af_0' }"
+
+    input:
+    tuple val(meta), path(R1_reads), path(R2_reads)
+    val(barcode_position)
+
+    output:
+    tuple val(meta), path("*_pair-pass.fastq.gz"), path("*_pair-pass.fastq.gz") , emit: reads
+    path "*_command_log.txt", emit: logs
+    tuple val("${task.process}"), val('presto'), eval('PairSeq.py --version | grep -o "[0-9][0-9.]*" | head -n 1'), emit: versions_presto, topic: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def copyfield = (barcode_position == 'R1')? '--1f BARCODE' : (barcode_position == 'R2')? '--2f BARCODE' : (barcode_position == 'R1R2')? '--1f BARCODE --2f BARCODE' : (barcode_position == 'clustersets')? '--1f CLUSTER --2f CLUSTER' : ''
+    def args = task.ext.args?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    PairSeq.py -1 ${R1_reads} \\
+               -2 ${R2_reads} \\
+               --outname ${prefix} \\
+               $copyfield \\
+               $args > ${prefix}_command_log.txt
+
+    """
+
+    stub:
+    def copyfield = (barcode_position == 'R1')? '--1f BARCODE' : (barcode_position == 'R2')? '--2f BARCODE' : (barcode_position == 'R1R2')? '--1f BARCODE --2f BARCODE' : (barcode_position == 'clustersets')? '--1f CLUSTER --2f CLUSTER' : ''
+    def args = task.ext.args?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    touch ${prefix}-1_pair-pass.fastq.gz \\
+          ${prefix}-2_pair-pass.fastq.gz \\
+          ${prefix}_command_log.txt 
+    """
+}

modules/nf-core/presto/pairseq/meta.yml

@@ -0,0 +1,89 @@
+name: "presto_pairseq"
+description: Sorts and matches sequence records with matching coordinates across
+  files
+keywords:
+  - immcantation
+  - airrseq
+  - genomics
+  - immunoinformatics
+tools:
+  - "presto":
+      description: "A bioinformatics toolkit for processing high-throughput lymphocyte
+        receptor sequencing data."
+      homepage: "https://immcantation.readthedocs.io"
+      documentation: "https://presto.readthedocs.io"
+      tool_dev_url: "https://bitbucket.org/kleinstein/presto"
+      doi: "10.1093/bioinformatics/btu138"
+      licence:
+        - "AGPL v3"
+      identifier: biotools:presto-measure
+input:
+  - - meta:
+        type: map
+        description: |
+          Groovy Map containing sample information
+          e.g. `[ id:'test']`
+    - R1_reads:
+        type: file
+        description: compressed fastq file
+        pattern: "*.{fastq.gz}"
+        ontologies:
+          - edam: http://edamontology.org/format_1930
+    - R2_reads:
+        type: file
+        description: compressed fastq file
+        pattern: "*.{fastq.gz}"
+        ontologies:
+          - edam: http://edamontology.org/format_1930
+  - barcode_position:
+      type: string
+      description: Barcode position. One of "R1, R2, R1R2 or clustersets". Default
+        is ""
+output:
+  reads:
+    - - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. `[ id:'test']`
+      - "*_pair-pass.fastq.gz": 
+          type: file
+          description: paired fastq.gz file of R1 reads
+          pattern: "*.{fastq.gz}"
+          ontologies:
+            - edam: http://edamontology.org/format_1930
+      - "*_pair-pass.fastq.gz": 
+          type: file
+          description: paired fastq.gz file of R2 reads
+          pattern: "*.{fastq.gz}"
+          ontologies:
+            - edam: http://edamontology.org/format_1930
+  logs:
+    - "*_command_log.txt":
+        type: file
+        description: command_logs
+        pattern: "*.txt"
+        ontologies: []
+  versions_presto:
+    - - ${task.process}:
+          type: string
+          description: The name of the process
+      - presto:
+          type: string
+          description: the name of the tool
+      - PairSeq.py --version | grep -o "[0-9][0-9.]*" | head -n 1:
+          type: eval
+          description: The expression to obtain the version of the tool
+topics:
+  versions:
+    - - ${task.process}:
+          type: string
+          description: The name of the process
+      - presto:
+          type: string
+          description: the name of the tool
+      - PairSeq.py --version | grep -o "[0-9][0-9.]*" | head -n 1:
+          type: eval
+          description: The expression to obtain the version of the tool
+authors:
+  - "@Vivian0105"

modules/nf-core/presto/pairseq/tests/main.nf.test

@@ -0,0 +1,42 @@
+nextflow_process {
+
+    name "Test Process PRESTO_PAIRSEQ"
+    script "../main.nf"
+    process "PRESTO_PAIRSEQ"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "presto"
+    tag "presto/pairseq"
+
+    test("homo_sapiens - fastq") {
+
+        when {
+            process {
+                """                
+                input[0] = [
+                    [ id:'test' ],
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/fastq/test_airrseq_umi_R1.fastq.gz', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/fastq/test_airrseq_R2.fastq.gz', checkIfExists: true),
+                ]
+                input[1] = ""
+                """
+            }
+        }
+
+        then {
+
+            assertAll(
+                { assert process.success},
+                { assert snapshot(
+                    process.out.reads.get(0).get(1),
+                    process.out.reads.get(0).get(2)
+                ).match("test_snap_out")},
+                { assert snapshot(
+                    process.out.versions_presto).match("test_snap_versions")
+                },  
+                { assert path(process.out.logs.get(0)).getText().contains("PASS") }
+            )
+        }
+    }
+}

modules/nf-core/presto/pairseq/tests/main.nf.test.snap

@@ -0,0 +1,35 @@
+{
+    "test_snap_out": {
+        "content": [
+            [
+                "test-1_pair-pass.fastq.gz:md5,7f98eefe4c7111d4632685680b6b9a4b",
+                "test-2_pair-pass.fastq.gz:md5,51220f557d95ab70c0819e9a3e8e593a"
+            ],
+            [
+                "test-1_pair-pass.fastq.gz:md5,7f98eefe4c7111d4632685680b6b9a4b",
+                "test-2_pair-pass.fastq.gz:md5,51220f557d95ab70c0819e9a3e8e593a"
+            ]
+        ],
+        "timestamp": "2026-07-01T11:37:32.233234794",
+        "meta": {
+            "nf-test": "0.9.5",
+            "nextflow": "26.04.4"
+        }
+    },
+    "test_snap_versions": {
+        "content": [
+            [
+                [
+                    "PRESTO_PAIRSEQ",
+                    "presto",
+                    "0.7.9"
+                ]
+            ]
+        ],
+        "timestamp": "2026-07-01T11:37:32.31243821",
+        "meta": {
+            "nf-test": "0.9.5",
+            "nextflow": "26.04.4"
+        }
+    }
+}