Busco

modules/busco/main.nf

@@ -0,0 +1,41 @@
+process BUSCO {
+    tag "$meta.id"
+    label 'process_medium'
+    conda (params.enable_conda ? "bioconda::busco=5.2.2" : null)
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/busco:5.2.2--pyhdfd78af_0' :
+        'quay.io/biocontainers/busco:5.2.2--pyhdfd78af_0' }"
+
+    input:
+    tuple val(meta), path(fasta)
+    path(augustus_config)
+    val(lineage)
+
+    output:
+    tuple val(meta), path("${meta.id}/run_*/full_table.tsv"), emit: tsv
+    tuple val(meta), path("${meta.id}/run_*/short_summary.txt"), emit: txt
+    path "versions.yml", emit: versions
+
+    script:
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    if (lineage) args += " --lineage_dataset $lineage"
+    """
+    # Ensure the input is uncompressed
+    gzip -cdf $fasta > __UNCOMPRESSED_FASTA_FILE__
+    # Copy the image's AUGUSTUS config directory if it was not provided to the module
+    [ ! -e augustus_config ] && cp -a /usr/local/config augustus_config
+    AUGUSTUS_CONFIG_PATH=augustus_config \\
+    busco \\
+        $args \\
+        --augustus \\
+        --cpu $task.cpus \\
+        --in __UNCOMPRESSED_FASTA_FILE__ \\
+        --out $meta.id
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        busco: \$( busco --version 2>&1 | sed 's/^BUSCO //' )
+    END_VERSIONS
+    """
+}

modules/busco/meta.yml

@@ -0,0 +1,52 @@
+name: busco
+description: Benchmarking Universal Single Copy Orthologs
+keywords:
+  - quality control
+  - genome
+  - transcriptome
+  - proteome
+tools:
+  - busco:
+      description: BUSCO provides measures for quantitative assessment of genome assembly, gene set, and transcriptome completeness based on evolutionarily informed expectations of gene content from near-universal single-copy orthologs selected from OrthoDB.
+      homepage: https://busco.ezlab.org/
+      documentation: ttps://busco.ezlab.org/busco_userguide.html
+      tool_dev_url: https://gitlab.com/ezlab/busco
+      doi: "10.1007/978-1-4939-9173-0_14"
+      licence: ['MIT']
+
+input:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  - fasta:
+      type: file
+      description: Nucleic or amino acid sequence file in FASTA format
+      pattern: "*.{fasta}"
+  - augustus_config:
+      type: directory
+      description: AUGUSTUS config directory
+
+output:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  - versions:
+      type: file
+      description: File containing software versions
+      pattern: "versions.yml"
+  - tsv:
+      type: file
+      description: Full summary table
+      pattern: "*.{tsv}"
+  - txt:
+      type: file
+      description: Short summary text
+      pattern: "*.{txt}"
+
+authors:
+  - "@charles-plessy"
+  - "@priyanka-surana"

tests/config/test_data.config

@@ -114,8 +114,8 @@ params {
                 genome_bed_gz_tbi                              = "${test_data_dir}/genomics/homo_sapiens/genome/genome.bed.gz.tbi"
                 transcriptome_fasta                            = "${test_data_dir}/genomics/homo_sapiens/genome/transcriptome.fasta"
                 genome2_fasta                                  = "${test_data_dir}/genomics/homo_sapiens/genome/genome2.fasta"
-		        genome_chain_gz                                = "${test_data_dir}/genomics/homo_sapiens/genome/genome.chain.gz"
-
+		genome_chain_gz                                = "${test_data_dir}/genomics/homo_sapiens/genome/genome.chain.gz"
+                chr22_odb10_tar_gz                             = "${test_data_dir}/genomics/homo_sapiens/genome/BUSCO/chr22_odb10.tar.gz"
                 dbsnp_146_hg38_vcf_gz                          = "${test_data_dir}/genomics/homo_sapiens/genome/vcf/dbsnp_146.hg38.vcf.gz"
                 dbsnp_146_hg38_vcf_gz_tbi                      = "${test_data_dir}/genomics/homo_sapiens/genome/vcf/dbsnp_146.hg38.vcf.gz.tbi"
                 gnomad_r2_1_1_vcf_gz                           = "${test_data_dir}/genomics/homo_sapiens/genome/vcf/gnomAD.r2.1.1.vcf.gz"

tests/modules/busco/main.nf

@@ -0,0 +1,26 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { BUSCO as BUSCO_BACTE } from '../../../modules/busco/main.nf'
+include { BUSCO as BUSCO_CHR22 } from '../../../modules/busco/main.nf'
+include { UNTAR                } from '../../../modules/untar/main.nf'
+
+// This tests genome decompression, empty input channels and data download
+workflow test_busco_bacteroidales {
+   input = [ [ id:'test' ], file(params.test_data['bacteroides_fragilis']['genome']['genome_fna_gz'], checkIfExists: true) ]    
+   BUSCO_BACTE ( input,
+                 [],
+                 [] )
+}
+
+// This tests uncompressed genome, BUSCO lineage file provided via input channel, and offline mode
+workflow test_busco_chr22 {
+    input = [ [ id:'test' ],  file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true) ]
+    lineage_dataset = [ file(params.test_data['homo_sapiens']['genome']['chr22_odb10_tar_gz'], checkIfExists: true) ]
+    UNTAR(lineage_dataset)
+    BUSCO_CHR22 ( input,
+                  [],
+                  UNTAR.out.untar )
+}
+

tests/modules/busco/nextflow.config

@@ -0,0 +1,14 @@
+process {
+
+    publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+    withName: BUSCO_BACTE {
+        ext.args = '--mode genome --lineage_dataset bacteroidales_odb10'
+    }
+
+    withName: BUSCO_CHR22 {
+        ext.args = '--mode genome --offline'
+    }
+
+}
+

tests/modules/busco/test.yml

@@ -0,0 +1,20 @@
+- name: busco test_busco_bacteroidales
+  command: nextflow run tests/modules/busco -entry test_busco_bacteroidales -c tests/config/nextflow.config
+  tags:
+    - busco
+  files:
+    - path: output/busco/test/run_bacteroidales_odb10/full_table.tsv
+      md5sum: 8d7b401d875ecd9291b01bf4485bf080
+    - path: output/busco/test/run_bacteroidales_odb10/short_summary.txt
+      contains: ['Complete BUSCOs (C)']
+
+- name: busco test_busco_chr22
+  command: nextflow run tests/modules/busco -entry test_busco_chr22 -c tests/config/nextflow.config
+  tags:
+    - busco
+  files:
+    - path: output/busco/test/run_chr22_odb10/full_table.tsv
+      md5sum: 83f20e8996c591338ada73b6ab0eb269
+    - path: output/busco/test/run_chr22_odb10/short_summary.txt
+      contains: ['Complete BUSCOs (C)']
+