add alignmentSieve (#6693)

* add alignmentSieve * longer keywords * add three keywords * possible solution with size * using logs instead of bam files * fix meta * Update modules/nf-core/deeptools/alignmentsieve/tests/main.nf.test Co-authored-by: Simon Pearce <[email protected]> * update snapshot * fix keywords Co-authored-by: Jose Espinosa-Carrasco <[email protected]> * fix authors Co-authored-by: Jose Espinosa-Carrasco <[email protected]> * fix authors names Co-authored-by: Jose Espinosa-Carrasco <[email protected]> * add to maintainers Co-authored-by: Jose Espinosa-Carrasco <[email protected]> --------- Co-authored-by: Alexander Peltzer <[email protected]> Co-authored-by: Simon Pearce <[email protected]> Co-authored-by: Jose Espinosa-Carrasco <[email protected]>
nf-core · Sep 27, 2024 · 5c2ab5d · 5c2ab5d
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diff --git a/modules/nf-core/deeptools/alignmentsieve/environment.yml b/modules/nf-core/deeptools/alignmentsieve/environment.yml
@@ -0,0 +1,6 @@
+channels:
+  - conda-forge
+  - bioconda
+dependencies:
+  - bioconda::deeptools=3.5.5
+  - bioconda::samtools=1.20
diff --git a/modules/nf-core/deeptools/alignmentsieve/main.nf b/modules/nf-core/deeptools/alignmentsieve/main.nf
@@ -0,0 +1,49 @@
+process DEEPTOOLS_ALIGNMENTSIEVE {
+    tag "$meta.id"
+    label 'process_low'
+
+    conda "${moduleDir}/environment.yml"
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/mulled-v2-eb9e7907c7a753917c1e4d7a64384c047429618a:41defd13a6f2ce014549fcc05d0b051f655777f9-0':
+        'biocontainers/mulled-v2-eb9e7907c7a753917c1e4d7a64384c047429618a:41defd13a6f2ce014549fcc05d0b051f655777f9-0' }"
+
+    input:
+    tuple val(meta), path(input), path(input_index)
+
+    output:
+    tuple val(meta), path("*_as.bam") , emit: bam
+    path  "versions.yml"              , emit: versions
+    path  "*_log.txt"                 , emit: logs
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args      = task.ext.args ?: ''
+    def prefix    = task.ext.prefix ?: "${meta.id}"
+    """
+    alignmentSieve \\
+        $args \\
+        -b $input \\
+        -o ${prefix}_as.bam \\
+        --filterMetrics ${prefix}_log.txt \\
+        --numberOfProcessors $task.cpus
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        deeptools: \$(alignmentSieve --version | sed -e "s/alignmentSieve //g")
+    END_VERSIONS
+    """
+
+    stub:
+    def prefix    = task.ext.prefix ?: "${meta.id}"
+    """
+    touch ${prefix}_as.bam
+    touch ${prefix}_log.txt
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        deeptools: \$(alignmentSieve --version | sed -e "s/alignmentSieve //g")
+    END_VERSIONS
+    """
+}
diff --git a/modules/nf-core/deeptools/alignmentsieve/meta.yml b/modules/nf-core/deeptools/alignmentsieve/meta.yml
@@ -0,0 +1,56 @@
+name: deeptools_alignmentSieve
+description: This tool filters alignments in a BAM/CRAM file according the the specified parameters.
+keywords:
+  - ATACseq
+  - filter
+  - shift
+  - ATACshift
+tools:
+  - deeptools:
+      description: A set of user-friendly tools for normalization and visualzation of
+        deep-sequencing data
+      homepage: https://deeptools.readthedocs.io/en/develop/content/tools/alignmentSieve.html
+      documentation: https://deeptools.readthedocs.io/en/develop/content/tools/alignmentSieve.html
+      tool_dev_url: https://github.com/deeptools/deepTools/
+      doi: "10.1093/nar/gkw257"
+      licence: ["GPL v3"]
+      identifier: biotools:deeptools
+input:
+  - - meta:
+        type: map
+        description: |
+          Groovy Map containing sample information
+          e.g. [ id:'test', single_end:false ]
+    - input:
+        type: file
+        description: BAM file
+        pattern: "*.{bam}"
+    - input_index:
+        type: file
+        description: BAM index file
+        pattern: "*.{bai}"
+output:
+  - bam:
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test', single_end:false ]
+      - "*_as.bam":
+          type: file
+          description: BAM file
+          pattern: "*.bam"
+  - logs:
+      - "*_log.txt":
+          type: file
+          description: TXT file
+          pattern: "*.txt"
+  - versions:
+      - versions.yml:
+          type: file
+          description: File containing software versions
+          pattern: "versions.yml"
+authors:
+  - "@lpantano"
+maintainers:
+  - "@lpantano"
diff --git a/modules/nf-core/deeptools/alignmentsieve/tests/main.nf.test b/modules/nf-core/deeptools/alignmentsieve/tests/main.nf.test
@@ -0,0 +1,60 @@
+nextflow_process {
+
+    name "Test Process DEEPTOOLS_ALIGNMENTSIEVE"
+    script "../main.nf"
+    process "DEEPTOOLS_ALIGNMENTSIEVE"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "deeptools"
+    tag "deeptools/alignmentsieve"
+
+    test("homo_sampiens - bam") {
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test', single_end:false ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true)
+                ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out.logs,
+                                  bam(process.out.bam[0][1]).getReadsMD5(),
+                                  process.out.versions)
+                                  .match()
+                }
+            )
+        }
+    }
+    test("homo_sampiens - bam - stub") {
+
+        options "-stub"
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test', single_end:false ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true)
+                ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+}
diff --git a/modules/nf-core/deeptools/alignmentsieve/tests/main.nf.test.snap b/modules/nf-core/deeptools/alignmentsieve/tests/main.nf.test.snap
@@ -0,0 +1,59 @@
+{
+    "homo_sampiens - bam": {
+        "content": [
+            [
+                "test_log.txt:md5,39f97a6a2ff83330d5c93411113df63a"
+            ],
+            "463ac3b905fbf4ddf113a94dbfa8d69f",
+            [
+                "versions.yml:md5,baf8080ab016b89a27483809252bc803"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-09-26T12:59:06.183167"
+    },
+    "homo_sampiens - bam - stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test_as.bam:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,baf8080ab016b89a27483809252bc803"
+                ],
+                "2": [
+                    "test_log.txt:md5,d41d8cd98f00b204e9800998ecf8427e"
+                ],
+                "bam": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test_as.bam:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "logs": [
+                    "test_log.txt:md5,d41d8cd98f00b204e9800998ecf8427e"
+                ],
+                "versions": [
+                    "versions.yml:md5,baf8080ab016b89a27483809252bc803"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-09-26T12:59:10.273315"
+    }
+}
diff --git a/modules/nf-core/deeptools/alignmentsieve/tests/tags.yml b/modules/nf-core/deeptools/alignmentsieve/tests/tags.yml
@@ -0,0 +1,2 @@
+deeptools/bamcoverage:
+  - "modules/nf-core/deeptools/alignmentsieve/**"