Added evigene/tr2aacds

modules/nf-core/evigene/tr2aacds/environment.yml

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+---
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
+name: "evigene_tr2aacds"
+channels:
+  - conda-forge
+  - bioconda
+  - defaults
+dependencies:
+  - "bioconda::evigene=23.7.15"

modules/nf-core/evigene/tr2aacds/main.nf

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+process EVIGENE_TR2AACDS {
+    tag "$meta.id"
+    label 'process_medium'
+
+    conda "${moduleDir}/environment.yml"
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/evigene:23.7.15--hdfd78af_1':
+        'biocontainers/evigene:23.7.15--hdfd78af_1' }"
+
+    input:
+    tuple val(meta), path(fasta)
+
+    output:
+    tuple val(meta), path("dropset")    , emit: dropset
+    tuple val(meta), path("okayset")    , emit: okayset
+    path "versions.yml"                 , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args        = task.ext.args     ?: ''
+    def prefix      = task.ext.prefix   ?: "${meta.id}"
+
+    def max_memory  = 7*1024
+    if (!task.memory) {
+        log.info '[evigene] Available memory not known - defaulting to 7GB. Specify process memory requirements to change this.'
+    } else {
+        max_memory  = (task.memory.mega*0.8).intValue()
+    }
+
+    def simple_name = fasta.simpleName
+    def rename_files= ( simple_name != prefix ) ? 'yes' : 'no'
+    """
+    # Nextflow changes the container --entrypoint to /bin/bash (container default entrypoint: /usr/local/env-execute)
+    # Check for container variable initialisation script and source it.
+    if [ -f "/usr/local/env-activate.sh" ]; then
+        set +u  # Otherwise, errors out because of various unbound variables
+        . "/usr/local/env-activate.sh"
+        set -u
+    fi
+
+    \$EVIGENEHOME/scripts/prot/tr2aacds.pl \\
+        $args \\
+        -NCPU=$task.cpus \\
+        -MAXMEM=$max_memory \\
+        -cdnaseq $fasta
+
+    if [ "$rename_files" = "yes" ]; then
+        find \\
+            dropset \\
+            -type f \\
+            -exec sh -c 'mv "\$1" "\$(echo \$1 | sed s/$simple_name/$prefix/)"' sh {} \\;
+
+        find \\
+            okayset \\
+            -type f \\
+            -exec sh -c 'mv "\$1" "\$(echo \$1 | sed s/$simple_name/$prefix/)"' sh {} \\;
+    fi
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        tr2aacds: \$(cat \$EVIGENEHOME/scripts/prot/tr2aacds.pl | sed -n 's/use constant VERSION =>  \\([^;]*\\);.*/\\1/p')
+    END_VERSIONS
+    """
+
+    stub:
+    def args        = task.ext.args ?: ''
+    def prefix      = task.ext.prefix ?: "${meta.id}"
+    def max_memory  = 7*1024
+    if (!task.memory) {
+        log.info '[evigene] Available memory not known - defaulting to 7GB. Specify process memory requirements to change this.'
+    }
+    """
+    # Nextflow changes the container --entrypoint to /bin/bash (container default entrypoint: /usr/local/env-execute)
+    # Check for container variable initialisation script and source it.
+    if [ -f "/usr/local/env-activate.sh" ]; then
+        set +u  # Otherwise, errors out because of various unbound variables
+        . "/usr/local/env-activate.sh"
+        set -u
+    fi
+
+    mkdir dropset
+    touch dropset/${prefix}.drop.aa
+    touch dropset/${prefix}.drop.cds
+    touch dropset/${prefix}.drop.tr
+
+    mkdir okayset
+    touch okayset/${prefix}.ann.txt
+    touch okayset/${prefix}.cull.aa
+    touch okayset/${prefix}.cull.cds
+    touch okayset/${prefix}.cull.mrna
+    touch okayset/${prefix}.genesum.txt
+    touch okayset/${prefix}.mainalt.tab
+    touch okayset/${prefix}.okay.aa
+    touch okayset/${prefix}.okay.cds
+    touch okayset/${prefix}.okay.mrna
+    touch okayset/${prefix}.pubids
+    touch okayset/${prefix}.pubids.old
+    touch okayset/${prefix}.pubids.realt.log
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        tr2aacds: \$(cat \$EVIGENEHOME/scripts/prot/tr2aacds.pl | sed -n 's/use constant VERSION =>  \\([^;]*\\);.*/\\1/p')
+    END_VERSIONS
+    """
+}

modules/nf-core/evigene/tr2aacds/meta.yml

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+---
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json
+name: "evigene_tr2aacds"
+description: Uses evigene/scripts/prot/tr2aacds.pl to filter a transcript assembly
+keywords:
+  - genomics
+  - transcript
+  - assembly
+  - clean
+  - polish
+  - filter
+  - redundant
+  - duplicate
+tools:
+  - "evigene":
+      description: |
+        EvidentialGene is a genome informatics project for "Evidence Directed Gene Construction
+        for Eukaryotes", for constructing high quality, accurate gene sets for animals and
+        plants (any eukaryotes), being developed by Don Gilbert at Indiana University, gilbertd at indiana edu.
+      homepage: "http://arthropods.eugenes.org/EvidentialGene/evigene/"
+      documentation: "http://arthropods.eugenes.org/EvidentialGene/evigene/"
+      tool_dev_url: "http://arthropods.eugenes.org/EvidentialGene/evigene/"
+      doi: "10.7490/f1000research.1112594.1 "
+      licence: ["Don Gilbert, gilbertd At indiana edu, 2018"]
+input:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. `[ id:'sample1' ]`
+  - fasta:
+      type: file
+      description: Transcript assembly in fasta format
+      pattern: "*.{fsa,fa,fasta,fsa.gz,fa.gz,fasta.gz}"
+output:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. `[ id:'sample1' ]`
+  - dropset:
+      type: directory
+      description: Directory containing dropped transcripts and associated files
+      pattern: "dropset"
+  - okayset:
+      type: directory
+      description: Directory containing included transcripts and associated files
+      pattern: "okayset"
+  - versions:
+      type: file
+      description: File containing software versions
+      pattern: "versions.yml"
+authors:
+  - "@GallVp"
+maintainers:
+  - "@GallVp"

modules/nf-core/evigene/tr2aacds/tests/main.nf.test

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+nextflow_process {
+
+    name "Test Process EVIGENE_TR2AACDS"
+    script "../main.nf"
+    process "EVIGENE_TR2AACDS"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "evigene"
+    tag "evigene/tr2aacds"
+
+    test("homo_sapiens - transcriptome_fasta") {
+        when {
+            process {
+                """
+
+                input[0] = [
+                    [ id:'test', single_end:false ], // meta map
+                    file(params.test_data['homo_sapiens']['genome']['transcriptome_fasta'], checkIfExists: true)
+                ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(
+                    process.out.dropset[0][1],
+                    file(process.out.okayset[0][1]).listFiles().collect { it.name }.toSorted(),
+                    process.out.versions,
+                    ).match()
+                }
+            )
+        }
+
+    }
+
+    test("stub") {
+
+        options '-stub'
+
+        when {
+            process {
+                """
+
+                input[0] = [
+                    [ id:'test', single_end:false ], // meta map
+                    file(params.test_data['homo_sapiens']['genome']['transcriptome_fasta'], checkIfExists: true)
+                ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+
+    }
+
+}

modules/nf-core/evigene/tr2aacds/tests/main.nf.test.snap

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+{
+    "stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        [
+                            "test.drop.aa:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "test.drop.cds:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "test.drop.tr:md5,d41d8cd98f00b204e9800998ecf8427e"
+                        ]
+                    ]
+                ],
+                "1": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        [
+                            "test.ann.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "test.cull.aa:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "test.cull.cds:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "test.cull.mrna:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "test.genesum.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "test.mainalt.tab:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "test.okay.aa:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "test.okay.cds:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "test.okay.mrna:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "test.pubids:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "test.pubids.old:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "test.pubids.realt.log:md5,d41d8cd98f00b204e9800998ecf8427e"
+                        ]
+                    ]
+                ],
+                "2": [
+                    "versions.yml:md5,57e8000ce92f5f8d590e7baffa762e84"
+                ],
+                "dropset": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        [
+                            "test.drop.aa:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "test.drop.cds:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "test.drop.tr:md5,d41d8cd98f00b204e9800998ecf8427e"
+                        ]
+                    ]
+                ],
+                "okayset": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        [
+                            "test.ann.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "test.cull.aa:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "test.cull.cds:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "test.cull.mrna:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "test.genesum.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "test.mainalt.tab:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "test.okay.aa:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "test.okay.cds:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "test.okay.mrna:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "test.pubids:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "test.pubids.old:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "test.pubids.realt.log:md5,d41d8cd98f00b204e9800998ecf8427e"
+                        ]
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,57e8000ce92f5f8d590e7baffa762e84"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.2"
+        },
+        "timestamp": "2024-06-30T13:24:57.680066"
+    },
+    "homo_sapiens - transcriptome_fasta": {
+        "content": [
+            [
+                "test.drop.aa:md5,b43c660c34a419ec35090c163a4e4a54",
+                "test.drop.cds:md5,5adb810e379fde7d2057a34ead7eaa58",
+                "test.drop.tr:md5,5f38aa1a7e7adb09ce34c0bd74727d67"
+            ],
+            [
+                "test.ann.txt",
+                "test.cull.aa",
+                "test.cull.cds",
+                "test.cull.mrna",
+                "test.genesum.txt",
+                "test.mainalt.tab",
+                "test.okay.aa",
+                "test.okay.cds",
+                "test.okay.mrna",
+                "test.pubids",
+                "test.pubids.old",
+                "test.pubids.realt.log"
+            ],
+            [
+                "versions.yml:md5,57e8000ce92f5f8d590e7baffa762e84"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.2"
+        },
+        "timestamp": "2024-06-30T13:46:54.373144"
+    }
+}