Module:ppflagfixer

modules/msk/ppflagfixer/environment.yml

@@ -0,0 +1,9 @@
+---
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
+name: "ppflagfixer"
+channels:
+  - conda-forge
+  - bioconda
+  - defaults
+dependencies:
+  - "YOUR-TOOL-HERE"

modules/msk/ppflagfixer/main.nf

@@ -0,0 +1,48 @@
+process PPFLAGFIXER {
+    tag "$meta.id"
+    label 'process_medium'
+
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'docker://mskcc/facets-suite:2.0.9':
+        'docker.io/mskcc/facets-suite:2.0.9' }"
+
+    input:
+    tuple val(meta), path(process_bam), path(process_bam_index)
+
+    output:
+    tuple val(meta), path("ppflag.*.bam")   , emit: ppflag_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}"
+
+    """
+    /usr/bin/ppflag-fixer \
+        ${args} \
+        ${process_bam} \
+        ppflag.${prefix}.bam
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        htslib: \$(bgzip --version | grep -oP '(?<=\\(htslib\\) ).*')
+        r: \$(R --version | grep -oP '(?<=R version ).*(?=\\()')
+    END_VERSIONS
+    """
+
+    stub:
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+
+    """
+    echo "stub test" >> ppflag.${prefix}.bam
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        htslib: \$(bgzip --version | grep -oP '(?<=\\(htslib\\) ).*')
+        r: \$(R --version | grep -oP '(?<=R version ).*(?=\\()')
+    END_VERSIONS
+    """
+}

modules/msk/ppflagfixer/meta.yml

@@ -0,0 +1,53 @@
+---
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json
+name: "ppflagfixer"
+## TODO nf-core: Add a description of the module and list keywords
+description: pplag-fixer for a single bam file
+keywords:
+  - ppflag
+  - fixer
+  - bams
+tools:
+  - "htstools":
+      description: "Contains tools to process bam files for downstream copy number analysis."
+      homepage: "https://github.com/mskcc/htstools"
+      documentation: "https://github.com/mskcc/htstools"
+
+input:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. `[ id:'sample_name' ]`
+
+  - process_bam:
+      type: file
+      description: Sorted BAM/CRAM/SAM file
+      pattern: "*.{bam,cram,sam}"
+
+  - process_bam_index:
+      type: file
+      description: "Index of the process bam file"
+      pattern: "*.bai"
+
+output:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. `[ id:'sample_name' ]`
+
+  - versions:
+      type: file
+      description: File containing software versions
+      pattern: "versions.yml"
+
+  - ppflag_bam:
+      type: file
+      description: Sorted BAM/CRAM/SAM file
+      pattern: "*.{bam,cram,sam}"
+
+authors:
+  - "@huyu335"
+maintainers:
+  - "@huyu335"

modules/msk/ppflagfixer/tests/main.nf.test

@@ -0,0 +1,87 @@
+nextflow_process {
+
+    name "Test PPFLAGFIXER"
+    script "../main.nf"
+    process "PPFLAGFIXER"
+    config "./nextflow.config"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "modules_msk"
+    tag "ppflagfixer"
+
+    test("ppflagfixer - normal bam") {
+
+        when {
+            process {
+                """
+                    meta = [ id:'test' ] // meta map
+                    input[0] = [
+                                    meta,
+                                    file(params.test_data_mskcc['bam_files']['test_argos_sample_1_normal_bam'], checkIfExists: true),
+                                    file(params.test_data_mskcc['bam_files']['test_argos_sample_1_normal_bam_bai'], checkIfExists: true)
+                                ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+
+    }
+
+    test("ppflagfixer - tumor bam") {
+
+        when {
+            process {
+                """
+                    meta = [ id:'test' ] // meta map
+                    input[0] = [
+                                    meta,
+                                    file(params.test_data_mskcc['bam_files']['test_argos_sample_1_tumor_bam'], checkIfExists: true),
+                                    file(params.test_data_mskcc['bam_files']['test_argos_sample_1_tumor_bam_bai'], checkIfExists: true)
+                                ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+
+    }
+
+    test("ppflagfixer - bam - stub") {
+
+        options "-stub"
+
+        when {
+            process {
+                """
+                    meta = [ id:'test' ] // meta map
+                    input[0] = [
+                                    meta,
+                                    file("stub_file"),
+                                    file("stub_file1")
+                                ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+
+    }
+
+}

modules/msk/ppflagfixer/tests/main.nf.test.snap

@@ -0,0 +1,101 @@
+{
+    "ppflagfixer - normal bam": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "ppflag.test.bam:md5,d25c13205b1d33c5c4b12999fc839d86"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,ed3820a8eb6f0db2010ddec9aefa7249"
+                ],
+                "ppflag_bam": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "ppflag.test.bam:md5,d25c13205b1d33c5c4b12999fc839d86"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,ed3820a8eb6f0db2010ddec9aefa7249"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.04.2"
+        },
+        "timestamp": "2024-02-26T23:05:23.642445"
+    },
+    "ppflagfixer - bam - stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "ppflag.test.bam:md5,3d77e3e110a219d3495d44e243450313"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,ed3820a8eb6f0db2010ddec9aefa7249"
+                ],
+                "ppflag_bam": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "ppflag.test.bam:md5,3d77e3e110a219d3495d44e243450313"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,ed3820a8eb6f0db2010ddec9aefa7249"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.04.2"
+        },
+        "timestamp": "2024-02-26T23:06:14.360871"
+    },
+    "ppflagfixer - tumor bam": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "ppflag.test.bam:md5,d05041f7678abb654e5d349ec430b131"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,ed3820a8eb6f0db2010ddec9aefa7249"
+                ],
+                "ppflag_bam": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "ppflag.test.bam:md5,d05041f7678abb654e5d349ec430b131"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,ed3820a8eb6f0db2010ddec9aefa7249"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.04.2"
+        },
+        "timestamp": "2024-02-26T23:06:08.243018"
+    }
+}

modules/msk/ppflagfixer/tests/nextflow.config

@@ -0,0 +1,10 @@
+params {
+    enable_conda = false
+}
+
+process {
+    publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+    withName: 'PPFLAGFIXER' {
+        ext.args = '-m 500'
+    }
+}

modules/msk/ppflagfixer/tests/tags.yml

@@ -0,0 +1,2 @@
+ppflagfixer:
+  - "modules/msk/ppflagfixer/**"