Update presto filterseq module

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

@@ -4,4 +4,4 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-  - bioconda::presto=0.7.1
+  - bioconda::presto=0.7.9

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

@@ -4,16 +4,16 @@ process PRESTO_FILTERSEQ {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine in ['singularity', 'apptainer'] && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/presto:0.7.1--pyhdfd78af_0':
-        'quay.io/biocontainers/presto:0.7.1--pyhdfd78af_0' }"
+        '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(reads)
 
     output:
-    tuple val(meta), path("*_quality-pass.fastq"),  emit: reads
+    tuple val(meta), path("*_quality-pass.fastq.gz"),  emit: reads
     path "*_command_log.txt" , emit: logs
-    path "versions.yml" , emit: versions
+    tuple val("${task.process}"), val('presto'), eval('FilterSeq.py --version | grep -o "[0-9][0-9.]*" | head -n 1'), emit: versions_presto, topic: versions
     path "*.tab" , emit: log_tab
 
     when:
@@ -23,31 +23,25 @@ process PRESTO_FILTERSEQ {
     def args = task.ext.args ?: ''
     def args2 = task.ext.args2 ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
+    def log_prefix = reads.simpleName
     """
     FilterSeq.py quality \\
     -s $reads \\
     --outname ${prefix} \\
-    --log ${reads.baseName}.log \\
+    --log ${log_prefix}.log \\
     --nproc ${task.cpus} \\
     $args > ${prefix}_command_log.txt
 
-    ParseLog.py -l ${reads.baseName}.log $args2 -f ID QUALITY
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        presto: \$( FilterSeq.py --version | awk -F' '  '{print \$2}' )
-    END_VERSIONS
-    """
+    ParseLog.py -l ${log_prefix}.log $args2 -f ID QUALITY
+   """
 
     stub:
     def prefix = task.ext.prefix ?: "${meta.id}"
+    def log_prefix = reads.baseName.replaceFirst(/\.f(ast)?q$/, '')
     """
-    touch ${prefix}_quality-pass.fastq ${prefix}_quality-pass.fastq \\
-        ${prefix}_command_log.txt ${prefix}.log ${prefix}.tab
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        presto: \$( FilterSeq.py --version | awk -F' '  '{print \$2}' )
-    END_VERSIONS
+    touch ${prefix}_quality-pass.fastq.gz \\
+        ${prefix}_command_log.txt \\
+        ${log_prefix}.log \\
+        ${log_prefix}_table.tab
     """
 }

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

@@ -1,4 +1,3 @@
-# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/yaml-schema.json
 name: "presto_filterseq"
 description: Filter reads by quality score.
 keywords:
@@ -14,9 +13,9 @@ tools:
       documentation: "https://presto.readthedocs.io"
       tool_dev_url: "https://bitbucket.org/kleinstein/presto"
       doi: "10.1093/bioinformatics/btu138"
-      licence: ["AGPL v3"]
+      licence:
+        - "AGPL v3"
       identifier: biotools:presto-measure
-
 input:
   - - meta:
         type: map
@@ -25,42 +24,59 @@ input:
           e.g. `[ id:'test', single_end:false ]`
     - reads:
         type: file
-        description: fastq file
-        pattern: "*.{fastq}"
+        description: compressed fastq file
+        pattern: "*.{fastq.gz}"
         ontologies:
-          - edam: http://edamontology.org/format_1930 # FASTQ
+          - edam: http://edamontology.org/format_1930
 output:
   reads:
     - - meta:
           type: map
           description: |
             Groovy Map containing sample information
             e.g. `[ id:'test', single_end:false ]`
-      - "*_quality-pass.fastq":
+      - "*_quality-pass.fastq.gz":
           type: file
-          description: filtered fastq file
-          pattern: "*.{fastq}"
+          description: filtered fastq.gz file
+          pattern: "*.{fastq.gz}"
           ontologies:
-            - edam: http://edamontology.org/format_1930 # FASTQ
+            - edam: http://edamontology.org/format_1930
   logs:
     - "*_command_log.txt":
         type: file
         description: command logs
         pattern: "*.txt"
         ontologies: []
-  versions:
-    - versions.yml:
-        type: file
-        description: File containing software versions
-        pattern: "versions.yml"
-        ontologies:
-          - edam: http://edamontology.org/format_3750 # YAML
+  versions_presto:
+    - - ${task.process}:
+          type: string
+          description: The name of the process
+      - presto:
+          type: string
+          description: the name of the tool
+      - FilterSeq.py --version | grep -o "[0-9][0-9.]*" | head -n 1:
+          type: eval
+          description: The expression to obtain the version of the tool
   log_tab:
     - "*.tab":
         type: file
         description: parsed log table
         pattern: "*.tab"
         ontologies:
-          - edam: http://edamontology.org/format_3475 # TSV
+          - edam: http://edamontology.org/format_3475
+topics:
+  versions:
+    - - ${task.process}:
+          type: string
+          description: The name of the process
+      - presto:
+          type: string
+          description: the name of the tool
+      - FilterSeq.py --version | grep -o "[0-9][0-9.]*" | head -n 1:
+          type: eval
+          description: The expression to obtain the version of the tool
 authors:
   - "@ggabernet"
+maintainers:
+  - "@ggabernet"
+  - "@Vivian0105"

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

@@ -7,46 +7,31 @@ nextflow_process {
 
     tag "modules"
     tag "modules_nfcore"
-    tag "gunzip"
     tag "presto"
     tag "presto/filterseq"
 
     test("homo_sapiens - fastq") {
 
-        setup {
-
-            run("GUNZIP") {
-                script "../../../gunzip/main.nf"
-                process {
-                    """
-                    input[0] = [
-                    [ id:'test', single_end:false ], // meta map
-                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/fastq/test_airrseq_umi_R1.fastq.gz', checkIfExists: true)
-                    ]
-                    """
-                }
-            }
-        }
-
         when {
             process {
                 """
-                input[0] = GUNZIP.out.gunzip
+                    input[0] = [
+                    [ id:'test'], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/fastq/test_airrseq_umi_R1.fastq.gz', checkIfExists: true)
+                    ]
                 """
             }
         }
 
         then {
             assertAll(
                 { assert process.success },
-                { assert snapshot(process.out.versions,
-                                  process.out.reads,
-                                  process.out.log_tab).match() },
+                { assert snapshot(process.out.versions_presto).match("test_snap_versions") },
+                { assert snapshot(process.out.reads,
+                                  process.out.log_tab).match("test_snap_output") },
                 { assert path(process.out.log_tab.get(0)).getText().contains("QUALITY") },
                 { assert path(process.out.logs.get(0)).getText().contains("PASS") }
             )
         }
-
     }
-
 }

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

@@ -1,26 +1,38 @@
 {
-    "homo_sapiens - fastq": {
+    "test_snap_output": {
         "content": [
-            [
-                "versions.yml:md5,5f939545018a68e43b57c7dfc7ace1b8"
-            ],
             [
                 [
                     {
-                        "id": "test",
-                        "single_end": false
+                        "id": "test"
                     },
-                    "test_quality-pass.fastq:md5,36979cf434408b9cb5e8dc50692e2842"
+                    "test_quality-pass.fastq.gz:md5,ef29c77b26f2123a6db36bc1c9a40d7d"
                 ]
             ],
             [
-                "test_airrseq_umi_R1_table.tab:md5,3b3f6ff09d5fb8c01a25294e0522ec5f"
+                "test_airrseq_umi_R1_table.tab:md5,eefa8e36013b462cb9a37be2654d67eb"
+            ]
+        ],
+        "timestamp": "2026-06-30T13:44:26.505405459",
+        "meta": {
+            "nf-test": "0.9.5",
+            "nextflow": "26.04.4"
+        }
+    },
+    "test_snap_versions": {
+        "content": [
+            [
+                [
+                    "PRESTO_FILTERSEQ",
+                    "presto",
+                    "0.7.9"
+                ]
             ]
         ],
+        "timestamp": "2026-06-30T13:44:26.4964953",
         "meta": {
-            "nf-test": "0.9.2",
-            "nextflow": "24.10.3"
-        },
-        "timestamp": "2024-01-25T18:01:03.38558"
+            "nf-test": "0.9.5",
+            "nextflow": "26.04.4"
+        }
     }
 }