Add coptr module

modules/nf-core/coptr/index/main.nf

@@ -4,8 +4,8 @@ process COPTR_INDEX {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/coptr:1.1.4--pyhdfd78af_1':
-        'biocontainers/coptr:1.1.4--pyhdfd78af_1' }"
+        'https://depot.galaxyproject.org/singularity/coptr:1.1.4--pyhdfd78af_3':
+        'biocontainers/coptr:1.1.4--pyhdfd78af_3' }"
 
     input:
     tuple val(meta), path(indexfasta, stageAs: "fastafolder/*")
@@ -29,6 +29,7 @@ process COPTR_INDEX {
         --bt2-threads $task.cpus \
         fastafolder \
         bowtie2/${prefix}
+
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
         coptr: \$(coptr |& sed -E '11!d ; s/CoPTR.*?\\(v(.*?)\\).*/\\1/')

modules/nf-core/coptr/index/tests/main.nf.test

@@ -32,29 +32,7 @@ nextflow_process {
 
     }
 
-    test("coptr index with multiple fastqs") {
-
-        when {
-            process {
-                """
-                input[0] = [
-                    [id:'indexNameExample'],
-                    [file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome2.fasta', checkIfExists: true),file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome3.fasta', checkIfExists: true)]
-                ]
-                """
-            }
-        }
-
-        then {
-            assertAll(
-                { assert process.success },
-                { assert snapshot(process.out).match() }
-            )
-        }
-
-    }
-
-    test("coptr index with multiple fastqs - stub") {
+    test("coptr index with single fastq - stub") {
 
         options "-stub"
 
@@ -63,7 +41,7 @@ nextflow_process {
                 """
                 input[0] = [
                     [id:'indexNameExample'],
-                    [file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome2.fasta', checkIfExists: true),file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome3.fasta', checkIfExists: true)]
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)
                 ]
                 """
             }
@@ -78,5 +56,4 @@ nextflow_process {
 
     }
 
-
 }

modules/nf-core/coptr/index/tests/main.nf.test.snap

@@ -43,12 +43,12 @@
             }
         ],
         "meta": {
-            "nf-test": "0.9.1",
+            "nf-test": "0.9.2",
             "nextflow": "24.10.0"
         },
-        "timestamp": "2024-11-01T15:20:08.028567181"
+        "timestamp": "2024-11-15T13:37:15.478846"
     },
-    "coptr index with multiple fastqs - stub": {
+    "coptr index with single fastq - stub": {
         "content": [
             {
                 "0": [
@@ -92,58 +92,9 @@
             }
         ],
         "meta": {
-            "nf-test": "0.9.1",
+            "nf-test": "0.9.2",
             "nextflow": "24.10.0"
         },
-        "timestamp": "2024-11-01T15:28:00.318435045"
-    },
-    "coptr index with multiple fastqs": {
-        "content": [
-            {
-                "0": [
-                    [
-                        {
-                            "id": "indexNameExample"
-                        },
-                        [
-                            "indexNameExample.1.bt2:md5,e88e383183a9dec8dd453b04dc89a903",
-                            "indexNameExample.2.bt2:md5,ae84a18d674ecc823c82188f5ca1ffc9",
-                            "indexNameExample.3.bt2:md5,702fe6c79ef7bc9b54b3661f2f4aaa0b",
-                            "indexNameExample.4.bt2:md5,a2234db869afc50b40f7e7d1289f5f0b",
-                            "indexNameExample.genomes:md5,d4ed161da3cf2ced8e7c66c0c90e8d3e",
-                            "indexNameExample.rev.1.bt2:md5,75d78b73949d636ec9750269a5ea1c8b",
-                            "indexNameExample.rev.2.bt2:md5,39a1186f6aad701a71d773074408b51e"
-                        ]
-                    ]
-                ],
-                "1": [
-                    "versions.yml:md5,6013eeb9d8ac97351260150f44091986"
-                ],
-                "index_dir": [
-                    [
-                        {
-                            "id": "indexNameExample"
-                        },
-                        [
-                            "indexNameExample.1.bt2:md5,e88e383183a9dec8dd453b04dc89a903",
-                            "indexNameExample.2.bt2:md5,ae84a18d674ecc823c82188f5ca1ffc9",
-                            "indexNameExample.3.bt2:md5,702fe6c79ef7bc9b54b3661f2f4aaa0b",
-                            "indexNameExample.4.bt2:md5,a2234db869afc50b40f7e7d1289f5f0b",
-                            "indexNameExample.genomes:md5,d4ed161da3cf2ced8e7c66c0c90e8d3e",
-                            "indexNameExample.rev.1.bt2:md5,75d78b73949d636ec9750269a5ea1c8b",
-                            "indexNameExample.rev.2.bt2:md5,39a1186f6aad701a71d773074408b51e"
-                        ]
-                    ]
-                ],
-                "versions": [
-                    "versions.yml:md5,6013eeb9d8ac97351260150f44091986"
-                ]
-            }
-        ],
-        "meta": {
-            "nf-test": "0.9.1",
-            "nextflow": "24.10.0"
-        },
-        "timestamp": "2024-11-01T15:24:04.847842182"
+        "timestamp": "2024-11-15T13:37:21.536745"
     }
 }

modules/nf-core/coptr/map/environment.yml

@@ -0,0 +1,7 @@
+---
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
+channels:
+  - conda-forge
+  - bioconda
+dependencies:
+  - "bioconda::coptr=1.1.4"

modules/nf-core/coptr/map/main.nf

@@ -0,0 +1,61 @@
+process COPTR_MAP {
+    tag "$meta.id"
+    label 'process_low'
+
+    conda "${moduleDir}/environment.yml"
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/coptr:1.1.4--pyhdfd78af_3':
+        'biocontainers/coptr:1.1.4--pyhdfd78af_3' }"
+
+    input:
+    tuple val(meta), path(fasta, stageAs: "fastafolder/*")
+    tuple val(meta2), path(index)
+
+    output:
+    tuple val(meta), path("*.bam"), emit: bam
+    path "versions.yml"           , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args   = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    def prefix2 = task.ext.prefix ?: "${meta2.id}"
+
+    def paired_end = ""
+    if ( ! meta.single_end ) {
+        paired_end = "--paired"
+    }
+    """
+    INDEX=`find -L ./ -name "*.rev.1.bt2" | sed "s/\\.rev.1.bt2\$//"`
+    [ -z "\$INDEX" ] && INDEX=`find -L ./ -name "*.rev.1.bt2l" | sed "s/\\.rev.1.bt2l\$//"`
+    [ -z "\$INDEX" ] && echo "Bowtie2 index files not found" 1>&2 && exit 1
+
+    coptr \
+        map \
+        $args $paired_end \
+        --threads $task.cpus \
+        \$INDEX \
+        fastafolder \
+        .
+
+    mv ${prefix}.bam ${prefix}_${prefix2}.bam
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        coptr: \$(coptr |& sed -E '11!d ; s/CoPTR.*?\\(v(.*?)\\).*/\\1/')
+    END_VERSIONS
+    """
+
+    stub:
+    def args   = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    touch ${prefix}.bam
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        coptr: \$(coptr |& sed -E '11!d ; s/CoPTR.*?\\(v(.*?)\\).*/\\1/')
+    END_VERSIONS
+    """
+}

modules/nf-core/coptr/map/meta.yml

@@ -0,0 +1,63 @@
+---
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json
+name: "coptr_map"
+description: Maps the reads to the reference database
+keywords:
+  - coptr
+  - mapping
+  - ptr
+tools:
+  - "coptr":
+      description: "Accurate and robust inference of microbial growth dynamics from
+        metagenomic sequencing reads."
+      homepage: "https://github.com/tyjo/coptr"
+      documentation: "https://coptr.readthedocs.io/"
+      tool_dev_url: "https://github.com/tyjo/coptr"
+      doi: "10.1101/gr.275533.121"
+      licence: ["GPL v3"]
+      identifier: biotools:coptr
+
+input:
+  - - meta:
+        type: map
+        description: |
+          Groovy Map containing sample information
+          e.g. `[ id:'sample1', single_end:false ]`
+    - fasta:
+        type: file
+        description: fastq file with reads
+        pattern: "*.{.fastq,.fq,.fastq.gz,fq.gz}"
+        ontologies:
+          - edam: "http://edamontology.org/format_1929"
+  - - meta2:
+        type: map
+        description: |
+          Groovy Map containing index genome id and path
+          e.g. [ id:'test', 'bowtie2' ]
+    - index:
+        type: file
+        description: Directory with Bowtie2 genome index files
+        pattern: "*.ebwt"
+
+output:
+  - bam:
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. `[ id:'sample1', single_end:false ]`
+      - "*.bam":
+          type: file
+          description: Alignment (BAM) file of reads mapped to the reference database
+          pattern: "*.{bam}"
+          ontologies:
+            - edam: "http://edamontology.org/format_2572"
+  - versions:
+      - "versions.yml":
+          type: file
+          description: File containing software versions
+          pattern: "versions.yml"
+authors:
+  - "@ramirobarrantes"
+maintainers:
+  - "@ramirobarrantes"

modules/nf-core/coptr/map/tests/main.nf.test

@@ -0,0 +1,106 @@
+nextflow_process {
+
+    name "Test Process COPTR_MAP"
+    script "../main.nf"
+    process "COPTR_MAP"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "coptr"
+    tag "coptr/index"
+    tag "coptr/map"
+
+    setup {
+        run("COPTR_INDEX") {
+            script "../../index/main.nf"
+            process {
+                """
+                input[0] = [
+                    [id:'test_0'],
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)
+                ]
+                """
+            }
+        }
+    }
+
+    test("sarscov2 - single end test") {
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test_1', single_end: true ],
+                    file(params.modules_testdata_base_path + "genomics/sarscov2/illumina/fastq/test_1.fastq.gz", checkIfExists: true)
+                ]
+                input[1] = COPTR_INDEX.out.index_dir
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(
+                    process.out.bam.collect{bam(it[1]).getReads(10)},
+                    process.out.bam.collect{bam(it[1]).getStatistics(include:["readCount"])},
+                    process.out.versions
+                    ).match() }
+            )
+        }
+    }
+
+    test("sarscov2 - paired end") {
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test', single_end: false ],
+                    [
+                        file(params.modules_testdata_base_path + "genomics/sarscov2/illumina/fastq/test_1.fastq.gz", checkIfExists: true),
+                        file(params.modules_testdata_base_path + "genomics/sarscov2/illumina/fastq/test_2.fastq.gz", checkIfExists: true)
+                    ]
+                ]
+                input[1] = COPTR_INDEX.out.index_dir
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(
+                    process.out.bam.collect{bam(it[1]).getStatistics(include:["readCount"])},
+                    process.out.versions
+                    ).match() }
+            )
+        }
+    }
+
+
+    test("sarscov2 - single end - stub") {
+
+        options "-stub"
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test', single_end: true ],
+                    file(params.modules_testdata_base_path + "genomics/sarscov2/illumina/fastq/test_1.fastq.gz", checkIfExists: true)
+                ]
+                input[1] = COPTR_INDEX.out.index_dir
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+
+}