Added a draft for LAI

modules/nf-core/ltrretriever/lai/environment.yml

@@ -0,0 +1,9 @@
+---
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
+name: "ltrretriever_lai"
+channels:
+  - conda-forge
+  - bioconda
+  - defaults
+dependencies:
+  - "bioconda::LTR_retriever=2.9.9"

modules/nf-core/ltrretriever/lai/main.nf

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+process LTRRETRIEVER_LAI {
+    tag "$meta.id"
+    label 'process_medium'
+
+    conda "${moduleDir}/environment.yml"
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/ltr_retriever:2.9.9--hdfd78af_0':
+        'biocontainers/ltr_retriever:2.9.9--hdfd78af_0' }"
+
+    input:
+    tuple val(meta), path(fasta)
+    path pass_list
+    path annotation_out
+    path monoploid_seqs
+
+    output:
+    tuple val(meta), path("*.LAI.log")  , emit: log
+    tuple val(meta), path("*.LAI.out")  , emit: lai_out     , optional: true
+    path "versions.yml"                 , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args            = task.ext.args     ?: ''
+    def prefix          = task.ext.prefix   ?: "${meta.id}"
+    def monoploid_param = monoploid_seqs    ? "-mono $monoploid_seqs"                       : ''
+    def lai_output_name = monoploid_seqs    ? "${annotation_out}.${monoploid_seqs}.out.LAI" : "${annotation_out}.LAI"
+    def VERSION         = 'beta3.2' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions.
+    """
+    LAI \\
+        -genome $fasta \\
+        -intact $pass_list \\
+        -all $annotation_out \\
+        -t $task.cpus \\
+        $monoploid_param \\
+        $args \\
+        > >(tee "${prefix}.LAI.log") \\
+        || echo "LAI failed! See ${prefix}.LAI.log"
+
+    mv \\
+        $lai_output_name \\
+        "${prefix}.LAI.out" \\
+        || echo "LAI failed to estimate assembly index. See ${prefix}.LAI.log"
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        lai: $VERSION
+    END_VERSIONS
+    """
+
+    stub:
+    def args            = task.ext.args     ?: ''
+    def prefix          = task.ext.prefix   ?: "${meta.id}"
+    def monoploid_param = monoploid_seqs    ? "-mono $monoploid_seqs"                       : ''
+    def lai_output_name = monoploid_seqs    ? "${annotation_out}.${monoploid_seqs}.out.LAI" : "${annotation_out}.LAI"
+    def VERSION         = 'beta3.2' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions.
+    """
+    touch "${prefix}.LAI.log"
+    touch "$lai_output_name"
+
+    mv \\
+        $lai_output_name \\
+        "${prefix}.LAI.out"
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        lai: $VERSION
+    END_VERSIONS
+    """
+}

modules/nf-core/ltrretriever/lai/meta.yml

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+---
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json
+name: "ltrretriever_lai"
+description: |
+  Estimates the mean LTR sequence identity in the genome. The input genome fasta should
+  have short alphanumeric IDs without comments
+keywords:
+  - genomics
+  - annotation
+  - repeat
+  - long terminal retrotransposon
+  - retrotransposon
+  - stats
+  - qc
+tools:
+  - "lai":
+      description: Assessing genome assembly quality using the LTR Assembly Index (LAI)
+      homepage: "https://github.com/oushujun/LTR_retriever"
+      documentation: "https://github.com/oushujun/LTR_retriever"
+      tool_dev_url: "https://github.com/oushujun/LTR_retriever"
+      doi: "10.1093/nar/gky730"
+      licence: ["GPL v3"]
+input:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. `[ id:'sample1' ]`
+  - fasta:
+      type: file
+      description: The genome file that is used to generate everything
+      pattern: "*.{fsa,fa,fasta}"
+  - pass_list:
+      type: file
+      description: A list of intact LTR-RTs generated by LTR_retriever
+      pattern: "*.pass.list"
+  - annotation_out:
+      type: file
+      description: RepeatMasker annotation of all LTR sequences in the genome
+      pattern: "*.out"
+  - monoploid_seqs:
+      type: file
+      description: |
+        This parameter is mainly for ployploid genomes. User provides a list of
+        sequence names that represent a monoploid (1x). LAI will be calculated only
+        on these sequences if provided.
+      pattern: "*.txt"
+output:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. `[ id:'sample1', single_end:false ]`
+  - log:
+      type: file
+      description: Log from LAI
+      pattern: "*.LAI.log"
+  - lai_out:
+      type: file
+      description: |
+        Output file from LAI if LAI is able to estimate the index from the inputs
+      pattern: "*.LAI.out"
+  - versions:
+      type: file
+      description: File containing software versions
+      pattern: "versions.yml"
+authors:
+  - "@GallVp"
+maintainers:
+  - "@GallVp"

modules/nf-core/ltrretriever/lai/tests/main.nf.test

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+nextflow_process {
+
+    name "Test Process LTRRETRIEVER_LAI"
+    script "../main.nf"
+    process "LTRRETRIEVER_LAI"
+    config "./nextflow.config"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "gunzip"
+    tag "ltrretriever"
+    tag "ltrretriever/ltrretriever"
+    tag "ltrretriever/lai"
+    tag "ltrharvest"
+    tag "ltrfinder"
+    tag "cat/cat"
+
+    test("actinidia_chinensis-genome_21_fasta_gz-success") {
+
+        setup {
+
+            run("GUNZIP") {
+                script "../../../gunzip"
+
+                process {
+                    """
+                    input[0] = [
+                        [ id:'test' ],
+                        file(params.test_data['actinidia_chinensis']['genome']['genome_21_fasta_gz'], checkIfExists: true)
+                    ]
+                    """
+                }
+            }
+
+            run("LTRHARVEST") {
+                script "../../../ltrharvest"
+
+                process {
+                    """
+                    input[0] = GUNZIP.out.gunzip
+                    """
+                }
+            }
+
+            run("LTRFINDER") {
+                script "../../../ltrfinder"
+
+                process {
+                    """
+                    input[0] = GUNZIP.out.gunzip
+                    """
+                }
+            }
+
+            run("CAT_CAT") {
+                script "../../../cat/cat"
+
+                process {
+                    """
+                    input[0] = LTRHARVEST.out.scn.mix(LTRFINDER.out.scn).groupTuple()
+                    """
+                }
+            }
+
+            run("LTRRETRIEVER_LTRRETRIEVER") {
+                script "../../ltrretriever"
+
+                process {
+                    """
+                    input[0] = GUNZIP.out.gunzip
+                    input[1] = CAT_CAT.out.file_out.map { meta, tabout -> tabout }
+                    input[2] = []
+                    input[3] = []
+                    input[4] = []
+                    """
+                }
+            }
+        }
+
+        when {
+            process {
+                """
+                input[0] = GUNZIP.out.gunzip
+                input[1] = LTRRETRIEVER_LTRRETRIEVER.out.pass_list.map { meta, pass_list -> pass_list }
+                input[2] = LTRRETRIEVER_LTRRETRIEVER.out.annotation_out.map { meta, annotation_out -> annotation_out }
+                input[3] = []
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert path(process.out.log[0][1]).text.contains("Dependency checking: Passed!") },
+                { assert path(process.out.log[0][1]).text.contains("Calculate LAI:") },
+                { assert path(process.out.log[0][1]).text.contains("Done!") },
+                { assert path(process.out.log[0][1]).text.contains("Result file:") },
+                { assert Math.abs(Float.parseFloat(path(process.out.lai_out[0][1]).text.split("\n")[1].split("\t")[6]) - 31.29) <= 1.0 }
+            )
+        }
+
+    }
+
+    test("stub") {
+
+        options '-stub'
+
+        when {
+            process {
+                """
+                def pass_list       = new File('test.pass.list')
+                def out_file        = new File('test.out')
+                def monoploid_seqs  = new File('some_seqs.list.txt')
+
+                input[0] = [
+                    [ id:'test' ],
+                    file(params.test_data['actinidia_chinensis']['genome']['genome_21_fasta_gz'], checkIfExists: true)
+                ]
+                input[1] = pass_list.toPath()
+                input[2] = out_file.toPath()
+                input[3] = []
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+
+    }
+
+    test("stub_with_monoploid_seqs") {
+
+        options '-stub'
+
+        when {
+            process {
+                """
+                def pass_list       = new File('test.pass.list')
+                def out_file        = new File('test.out')
+                def monoploid_seqs  = new File('some_seqs.list.txt')
+
+                input[0] = [
+                    [ id:'test' ],
+                    file(params.test_data['actinidia_chinensis']['genome']['genome_21_fasta_gz'], checkIfExists: true)
+                ]
+                input[1] = pass_list.toPath()
+                input[2] = out_file.toPath()
+                input[3] = monoploid_seqs.toPath()
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+
+    }
+
+}