Reinstalled fasta_ltrretriever_lai

modules.json

@@ -40,6 +40,11 @@
                         "git_sha": "490f8ab54c632d84f99edd6f208305ac5e283ab3",
                         "installed_by": ["fasta_ltrretriever_lai"]
                     },
+                    "seqkit/seq": {
+                        "branch": "main",
+                        "git_sha": "8ec55a2c8e4ce3af070393768f6c2c57f5c34076",
+                        "installed_by": ["fasta_ltrretriever_lai"]
+                    },
                     "syri": {
                         "branch": "main",
                         "git_sha": "836bb223521eeaa08d65c1b7f4b82be1272a1964",

modules/gallvp/seqkit/seq/environment.yml

@@ -0,0 +1,9 @@
+---
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
+name: "seqkit_seq"
+channels:
+  - conda-forge
+  - bioconda
+  - defaults
+dependencies:
+  - "bioconda::seqkit=2.8.1"

modules/gallvp/seqkit/seq/main.nf

@@ -0,0 +1,63 @@
+process SEQKIT_SEQ {
+    tag "$meta.id"
+    label 'process_low'
+    // File IO can be a bottleneck. See: https://bioinf.shenwei.me/seqkit/usage/#parallelization-of-cpu-intensive-jobs
+
+    conda "${moduleDir}/environment.yml"
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/seqkit:2.8.1--h9ee0642_0':
+        'biocontainers/seqkit:2.8.1--h9ee0642_0' }"
+
+    input:
+    tuple val(meta), path(fastx)
+
+    output:
+    tuple val(meta), path("${prefix}.*")    , emit: fastx
+    path "versions.yml"                     , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args        = task.ext.args ?: ''
+    def args2       = task.ext.args2 ?: ''
+    prefix          = task.ext.prefix ?: "${meta.id}"
+    def extension   = "fastq"
+    if ("$fastx" ==~ /.+\.fasta|.+\.fasta.gz|.+\.fa|.+\.fa.gz|.+\.fas|.+\.fas.gz|.+\.fna|.+\.fna.gz|.+\.fsa|.+\.fsa.gz/ ) {
+        extension   = "fasta"
+    }
+    extension       = fastx.toString().endsWith('.gz') ? "${extension}.gz" : extension
+    def call_gzip   = extension.endsWith('.gz') ? "| gzip -c $args2" : ''
+    if("${prefix}.${extension}" == "$fastx") error "Input and output names are the same, use \"task.ext.prefix\" to disambiguate!"
+    """
+    seqkit \\
+        seq \\
+        --threads $task.cpus \\
+        $args \\
+        $fastx \\
+        $call_gzip \\
+        > ${prefix}.${extension}
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        seqkit: \$(seqkit version | cut -d' ' -f2)
+    END_VERSIONS
+    """
+
+    stub:
+    prefix          = task.ext.prefix ?: "${meta.id}"
+    def extension   = "fastq"
+    if ("$fastx" ==~ /.+\.fasta|.+\.fasta.gz|.+\.fa|.+\.fa.gz|.+\.fas|.+\.fas.gz|.+\.fna|.+\.fna.gz|.+\.fsa|.+\.fsa.gz/ ) {
+        extension   = "fasta"
+    }
+    extension = fastx.toString().endsWith('.gz') ? "${extension}.gz" : extension
+    if("${prefix}.${extension}" == "$fastx") error "Input and output names are the same, use \"task.ext.prefix\" to disambiguate!"
+    """
+    touch ${prefix}.${extension}
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        seqkit: \$(seqkit version | cut -d' ' -f2)
+    END_VERSIONS
+    """
+}

modules/gallvp/seqkit/seq/meta.yml

@@ -0,0 +1,48 @@
+---
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json
+name: "seqkit_seq"
+description: Transforms sequences (extract ID, filter by length, remove gaps, reverse complement...)
+keywords:
+  - genomics
+  - fasta
+  - fastq
+  - transform
+  - filter
+  - gaps
+  - complement
+tools:
+  - "seqkit":
+      description: "A cross-platform and ultrafast toolkit for FASTA/Q file manipulation"
+      homepage: "https://bioinf.shenwei.me/seqkit/"
+      documentation: "https://bioinf.shenwei.me/seqkit/usage/"
+      tool_dev_url: "https://github.com/shenwei356/seqkit"
+      doi: "10.1371/journal.pone.0163962"
+      licence: ["MIT"]
+input:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. `[ id:'sample1' ]`
+  - fastx:
+      type: file
+      description: Input fasta/fastq file
+      pattern: "*.{fsa,fas,fa,fasta,fastq,fq,fsa.gz,fas.gz,fa.gz,fasta.gz,fastq.gz,fq.gz}"
+output:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. `[ id:'sample1' ]`
+  - fastx:
+      type: file
+      description: Output fasta/fastq file
+      pattern: "*.{fasta,fasta.gz,fastq,fastq.gz}"
+  - versions:
+      type: file
+      description: File containing software versions
+      pattern: "versions.yml"
+authors:
+  - "@GallVp"
+maintainers:
+  - "@GallVp"

modules/gallvp/seqkit/seq/tests/main.nf.test

@@ -0,0 +1,145 @@
+nextflow_process {
+
+    name "Test Process SEQKIT_SEQ"
+    script "../main.nf"
+    process "SEQKIT_SEQ"
+    config './nextflow.config'
+
+    tag "modules"
+    tag "modules_gallvp"
+    tag "seqkit"
+    tag "seqkit/seq"
+
+    test("sarscov2-genome_fasta") {
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test' ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)
+                ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() },
+            )
+        }
+
+    }
+
+    test("sarscov2-genome_fasta_gz") {
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test' ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.gz', checkIfExists: true)
+                ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() },
+            )
+        }
+
+    }
+
+    test("sarscov2-test_1_fastq_gz") {
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test' ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true)
+                ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() },
+            )
+        }
+
+    }
+
+    test("file_name_conflict-fail_with_error") {
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test_1' ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true)
+                ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert !process.success },
+                { assert process.stdout.toString().contains("Input and output names are the same") }
+            )
+        }
+
+    }
+
+    test("sarscov2-genome_fasta-stub") {
+
+        options '-stub'
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test' ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)
+                ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() },
+            )
+        }
+
+    }
+
+    test("file_name_conflict-fail_with_error-stub") {
+
+        options '-stub'
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'genome' ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)
+                ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert !process.success },
+                { assert process.stdout.toString().contains("Input and output names are the same") }
+            )
+        }
+
+    }
+
+}