Checkm2 module

modules/ebi-metagenomics/checkm2/checkm2/main.nf

@@ -0,0 +1,80 @@
+process CHECKM2 {
+    tag "$meta.id"
+    label 'process_single'
+
+    conda "bioconda::checkm2=1.0.1"
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/checkm2:1.0.1--pyh7cba7a3_0':
+        'biocontainers/checkm2:1.0.1--pyh7cba7a3_0' }"
+
+    input:
+    tuple val(meta), path(bins)
+    path checkm_db
+
+    output:
+    tuple val(meta), path("${meta.id}_checkm_output/quality_report.tsv"), emit: checkm2_stats
+    path "versions.yml"           , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+
+    def bins_list = bins.collect()
+    if (bins_list.size() == 0) {
+        """
+        mkdir -p ${meta.id}_checkm_output
+        echo "genome\tcompleteness\tcontamination" > ${meta.id}_checkm_output/quality_report.tsv
+
+        cat <<-END_VERSIONS > versions.yml
+        "${task.process}":
+            CheckM2 : \$(checkm2 --version )
+        END_VERSIONS
+        """ }
+    else {
+        """
+        checkm2 predict --threads ${task.cpus} \
+                        --input ${bins} \
+                        --output-directory ${meta.id}_checkm_output \
+                        --database_path ${checkm_db} \
+                        ${args}
+
+        cat <<-END_VERSIONS > versions.yml
+        "${task.process}":
+            CheckM2 : \$(checkm2 --version )
+        END_VERSIONS
+        """
+    }
+
+    stub:
+    // create empty files for empty bins list
+    // create files with headers for not empty bins list
+
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+
+    def bins_list = bins.collect()
+    if (bins_list.size() == 0) {
+        """
+        mkdir -p ${meta.id}_checkm_output
+        touch ${meta.id}_checkm_output/quality_report.tsv
+
+        cat <<-END_VERSIONS > versions.yml
+        "${task.process}":
+            CheckM2 : \$(checkm2 --version )
+        END_VERSIONS
+        """ }
+    else {
+        """
+        mkdir -p ${meta.id}_checkm_output
+        echo "genome\tcompleteness\tcontamination" > ${meta.id}_checkm_output/quality_report.tsv
+
+        cat <<-END_VERSIONS > versions.yml
+        "${task.process}":
+            CheckM2 : \$(checkm2 --version )
+        END_VERSIONS
+        """
+    }
+}

modules/ebi-metagenomics/checkm2/checkm2/meta.yml

@@ -0,0 +1,47 @@
+---
+name: "checkm2"
+description: Rapid assessment of genome bin quality using machine learning
+keywords:
+  - completeness
+  - contamination
+  - quality
+tools:
+  - "checkm2":
+      description: "CheckM2 - Predicting the quality of metagenome-recovered bins"
+      tool_dev_url: "https://github.com/chklovski/CheckM2/tree/main"
+      doi: "10.1038/s41592-023-01940-w"
+      licence: "['GPL v3']"
+
+input:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. `[ id:'test', single_end:false ]`
+  - bins:
+      type: list
+      description: Bins list or folder with bins
+  - checkm_db:
+      type: file
+      description: Checkm2 database
+      pattern: "*.dmnd"
+
+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"
+
+  - checkm2_stats:
+      type: file
+      description: File with completeness and contamination of bins
+      pattern: "*.tsv"
+
+authors:
+  - "@KateSakharova"

modules/ebi-metagenomics/checkm2/download_db/main.nf

@@ -0,0 +1,46 @@
+process CHECKM2_DOWNLOAD_DB {
+    tag "$meta.id"
+    label 'process_single'
+
+    conda "bioconda::checkm2=1.0.1"
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/checkm2:1.0.1--pyh7cba7a3_0':
+        'biocontainers/checkm2:1.0.1--pyh7cba7a3_0' }"
+
+    input:
+    val(meta)
+
+    output:
+    tuple val(meta), path("out/CheckM2_database/*.dmnd"), emit: checkm2_db
+    path "versions.yml"           , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+
+    """
+    checkm2 database --download --path out
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        CheckM2 : \$(checkm2 --version )
+    END_VERSIONS
+    """
+
+    stub:
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+
+    """
+    mkdir -p out/CheckM2_database
+    touch out/CheckM2_database/fake.dmnd
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        CheckM2 : \$(checkm2 --version )
+    END_VERSIONS
+    """
+}

modules/ebi-metagenomics/checkm2/download_db/meta.yml

@@ -0,0 +1,40 @@
+---
+name: "checkm2_download_db"
+description: Download DB for checkm2
+keywords:
+  - completeness
+  - contamination
+  - database
+tools:
+  - "checkm2":
+      description: "CheckM2 - Predicting the quality of metagenome-recovered bins"
+      tool_dev_url: "https://github.com/chklovski/CheckM2/tree/main"
+      doi: "https://doi.org/10.1038/s41592-023-01940-w"
+      licence: "['GPL v3']"
+
+input:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. `[ id:'test', single_end:false ]`
+
+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"
+
+  - checkm2_db:
+      type: file
+      description: Diamond file with checkm2 database
+      pattern: "*.dmnd"
+
+authors:
+  - "@KateSakharova"

tests/config/pytest_modules.yml

@@ -6,6 +6,10 @@ bmtagger/bmtagger:
   - modules/ebi-metagenomics/bmtagger/bmtagger/**
   - tests/modules/ebi-metagenomics/bmtagger/bmtagger/**
 
+checkm2/checkm2:
+  - modules/ebi-metagenomics/checkm2/checkm2/**
+  - tests/modules/ebi-metagenomics/checkm2/checkm2/**
+
 cmsearchtbloutdeoverlap:
   - modules/ebi-metagenomics/cmsearchtbloutdeoverlap/**
   - tests/modules/ebi-metagenomics/cmsearchtbloutdeoverlap/**

tests/modules/ebi-metagenomics/checkm2/checkm2/data/bins/bin1.fa

@@ -0,0 +1,2 @@
+>NODE-1
+AAA

tests/modules/ebi-metagenomics/checkm2/checkm2/main.nf

@@ -0,0 +1,34 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { CHECKM2               } from '../../../../../modules/ebi-metagenomics/checkm2/checkm2/main.nf'
+include { CHECKM2_DOWNLOAD_DB   } from '../../../../../modules/ebi-metagenomics/checkm2/download_db/main.nf'
+
+workflow test_checkm2 {
+    meta = [ id:'test', single_end:false ]
+
+    CHECKM2_DOWNLOAD_DB(meta)
+
+    input = [
+        meta,
+        file("./tests/modules/ebi-metagenomics/checkm2/checkm2/data/bins", checkIfExists: true)
+    ]
+
+    checkm_db = CHECKM2_DOWNLOAD_DB.out.checkm2_db.map{it -> it[1]}
+
+    CHECKM2 ( input, checkm_db)
+}
+
+workflow test_checkm2_empty_directory {
+    meta = [ id:'test', single_end:false ]
+
+    input = [
+        meta,
+        file("./tests/modules/ebi-metagenomics/checkm2/checkm2/data/empty_bins/*")
+    ]
+
+    checkm_db = file("./tests/modules/ebi-metagenomics/checkm2/checkm2/data/NO_FILE")
+
+    CHECKM2 (input, checkm_db)
+}

tests/modules/ebi-metagenomics/checkm2/checkm2/nextflow.config

@@ -0,0 +1,5 @@
+process {
+
+    publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+}

tests/modules/ebi-metagenomics/checkm2/checkm2/test.yml

@@ -0,0 +1,35 @@
+# TODO: fix test_checkm2 test
+# Doesn't work because of download db issue
+# OSError: [Errno 30] Read-only file system: '/usr/local/lib/python3.8/site-packages/checkm2/version/diamond_path.json'
+
+- name: "checkm2_stub"
+  command: nextflow run ./tests/modules/ebi-metagenomics/checkm2/checkm2 -stub -entry test_checkm2 -c ./tests/config/nextflow.config -c ./tests/modules/ebi-metagenomics/checkm2/checkm2/nextflow.config
+  tags:
+    - "checkm2"
+    - "checkm2/checkm2"
+  files:
+    - path: "output/checkm2/test_checkm_output/quality_report.tsv"
+      md5sum: 32e53028a395debce647fa88da2261e5
+    - path: "output/checkm2/versions.yml"
+      md5sum: fcebefe734201aedddd0037fb274d572
+
+- name: "checkm2_empty_directory"
+  command: nextflow run ./tests/modules/ebi-metagenomics/checkm2/checkm2 -entry test_checkm2_empty_directory -c ./tests/config/nextflow.config -c ./tests/modules/ebi-metagenomics/checkm2/checkm2/nextflow.config
+  tags:
+    - "checkm2"
+    - "checkm2/checkm2"
+  files:
+    - path: "output/checkm2/test_checkm_output/quality_report.tsv"
+      md5sum: 32e53028a395debce647fa88da2261e5
+    - path: "output/checkm2/versions.yml"
+      md5sum: c1ac7bf61a1f5a47711141ca1d34fd8d
+
+- name: "checkm2_empty_directory_stub"
+  command: nextflow run ./tests/modules/ebi-metagenomics/checkm2/checkm2 -stub -entry test_checkm2_empty_directory -c ./tests/config/nextflow.config -c ./tests/modules/ebi-metagenomics/checkm2/checkm2/nextflow.config
+  tags:
+    - "checkm2"
+    - "checkm2/checkm2"
+  files:
+    - path: "output/checkm2/test_checkm_output/quality_report.tsv"
+    - path: "output/checkm2/versions.yml"
+      md5sum: c1ac7bf61a1f5a47711141ca1d34fd8d