Merge branch 'master' into nanofilt

.github/workflows/test.yml

@@ -487,6 +487,8 @@ jobs:
         profile: [conda, docker, singularity]
         exclude:
           - tags: nf-test
+          - profile: conda
+            tags: angsd/gl
           - profile: conda
             tags: annotsv
           - profile: conda
@@ -559,6 +561,8 @@ jobs:
             tags: merquryfk/merquryfk
           - profile: conda
             tags: merquryfk/ploidyplot
+          - profile: conda
+            tags: molkartgarage/clahe
           - profile: conda
             tags: quartonotebook
           - profile: conda
@@ -583,6 +587,8 @@ jobs:
             tags: subworkflows/vcf_annotate_ensemblvep
           - profile: singularity
             tags: bases2fastq
+          - profile: conda
+            tags: wittyer
     env:
       NXF_ANSI_LOG: false
       SENTIEON_LICENSE_BASE64: ${{ secrets.SENTIEON_LICENSE_BASE64 }}

modules/nf-core/ale/environment.yml

@@ -0,0 +1,10 @@
+---
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
+name: "ale"
+channels:
+  - conda-forge
+  - bioconda
+  - defaults
+  - tanghaibao
+dependencies:
+  - "bioconda::ale=20180904"

modules/nf-core/ale/main.nf

@@ -0,0 +1,50 @@
+process ALE {
+    tag "$meta.id"
+    label 'process_single'
+
+    // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions.
+    conda "${moduleDir}/environment.yml"
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/ale:20180904--py27ha92aebf_0':
+        'biocontainers/ale:20180904--py27ha92aebf_0' }"
+
+    input:
+    tuple val(meta), path(asm), path(bam)
+
+    output:
+    tuple val(meta), path("*_ALEoutput.txt"), emit: ale
+    path "versions.yml"                     , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args    = task.ext.args ?: ''
+    def prefix  = task.ext.prefix ?: "${meta.id}"
+    def VERSION = '20180904' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions.
+    """
+    ALE \\
+        $args \\
+        $bam \\
+        $asm \\
+        ${prefix}_ALEoutput.txt
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        ale: $VERSION
+    END_VERSIONS
+    """
+
+    stub:
+    def args    = task.ext.args ?: ''
+    def prefix  = task.ext.prefix ?: "${meta.id}"
+    def VERSION = '20180904' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions.
+    """
+    touch ${prefix}_ALEoutput.txt
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        ale: $VERSION
+    END_VERSIONS
+    """
+}

modules/nf-core/ale/meta.yml

@@ -0,0 +1,51 @@
+---
+name: "ale"
+description: "ALE: assembly likelihood estimator."
+keywords:
+  - reference-independent
+  - assembly
+  - evaluation
+tools:
+  - "ale":
+      description: "ALE is a generic assembly likelihood evaluation framework for assessing the accuracy of genome and metagenome assemblies."
+      documentation: "https://portal.nersc.gov/dna/RD/Adv-Seq/ALE-doc/index.html#document-install"
+      tool_dev_url: "https://github.com/sc932/ALE"
+      doi: "10.1093/bioinformatics/bts723"
+      licence: ["NCSA"]
+
+input:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. `[ id:'sample1', single_end:false ]`
+
+  - asm:
+      type: file
+      description: Assembly in FASTA format
+      pattern: "*.{fasta,fa}"
+
+  - bam:
+      type: file
+      description: BAM file containing sorted read mappings
+      pattern: "*.{bam}"
+
+output:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. `[ id:'sample1', single_end:false ]`
+  - ale:
+      type: file
+      description: Output TXT file containing ALE results
+      pattern: "*_ALEoutput.{txt}"
+  - versions:
+      type: file
+      description: File containing software versions
+      pattern: "versions.yml"
+
+authors:
+  - "@rodtheo"
+maintainers:
+  - "@rodtheo"

modules/nf-core/ale/tests/main.nf.test

@@ -0,0 +1,108 @@
+// nf-core modules test ale
+nextflow_process {
+
+    name "Test Process ALE"
+    script "../main.nf"
+    process "ALE"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "ale"
+
+    test("sarscov2 [fasta] - paired-end sorted bam") {
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test', single_end:false ], // meta map
+                    file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true),
+                    file(params.test_data['sarscov2']['illumina']['test_paired_end_bam'], checkIfExists: true)
+                    ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() },
+                { assert path(process.out.ale[0][1]).readLines().first().contains("ALE_score") }
+            )
+        }
+
+    }
+
+    test("sarscov2 [fasta_gz] - paired-end sorted bam") {
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test', single_end:false ], // meta map
+                    file(params.test_data['sarscov2']['genome']['genome_fasta_gz'], checkIfExists: true),
+                    file(params.test_data['sarscov2']['illumina']['test_paired_end_bam'], checkIfExists: true)
+                    ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() },
+                { assert path(process.out.ale[0][1]).readLines().first().contains("ALE_score") }
+            )
+        }
+
+    }
+
+    test("sarscov2 [fasta] - single-end sorted bam") {
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test', single_end:true ], // meta map
+                    file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true),
+                    file(params.test_data['sarscov2']['illumina']['test_single_end_bam'], checkIfExists: true)
+                    ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() },
+                { assert path(process.out.ale[0][1]).readLines().first().contains("ALE_score") }
+                )
+        }
+
+    }
+
+    test("sarscov2 [fasta_gz] - single-end sorted bam") {
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test', single_end:true ], // meta map
+                    file(params.test_data['sarscov2']['genome']['genome_fasta_gz'], checkIfExists: true),
+                    file(params.test_data['sarscov2']['illumina']['test_single_end_bam'], checkIfExists: true)
+                    ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() },
+                { assert path(process.out.ale[0][1]).readLines().first().contains("ALE_score") }
+                )
+        }
+
+    }
+
+}

modules/nf-core/ale/tests/tags.yml

@@ -0,0 +1,2 @@
+ale:
+  - "modules/nf-core/ale/**"