Added fastq_bwa_mem_samblaster

subworkflows/nf-core/fastq_bwa_mem_samblaster/main.nf

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+include { BWA_INDEX         } from '../../../modules/nf-core/bwa/index/main'
+include { BWA_MEM           } from '../../../modules/nf-core/bwa/mem/main'
+include { SAMBLASTER        } from '../../../modules/nf-core/samblaster/main'
+
+workflow FASTQ_BWA_MEM_SAMBLASTER {
+
+    take:
+    ch_fastq                // channel: [ val(meta), [ fq ] ]; meta ~ [ id: 'sample' ]
+    ch_reference            // channel: [ val(meta2), fasta, index ]; fasta | index; meta2 ~ [ id: 'genome' ]
+                            // Each item from ch_fastq is combined with each item from ch_reference
+
+    main:
+    ch_versions             = Channel.empty()
+
+    ch_has_index            = ch_reference
+                            | branch { meta2, fasta, index ->
+                                yes: index
+                                no: !index
+                            }
+
+    // MODULE: BWA_INDEX
+    BWA_INDEX ( ch_has_index.no.map { meta2, fasta, index -> [ meta2, fasta ] } )
+
+    ch_bwa_index            = BWA_INDEX.out.index
+                            | mix(
+                                ch_has_index.yes
+                                | map { meta2, fasta, index ->
+                                    [ meta2, index ]
+                                }
+                            )
+
+    ch_versions             = ch_versions.mix(BWA_INDEX.out.versions.first())
+
+    // MODULE: BWA_MEM
+    ch_mem_inputs           = ch_fastq
+                            | combine(
+                                ch_bwa_index
+                            )
+                            | map { meta, fq, meta2, index ->
+                                [ meta + [ ref_id: meta2.id ], fq, index ]
+                            }
+
+    def sort_bam            = false
+    BWA_MEM(
+        ch_mem_inputs.map { meta, fq, index -> [ meta, fq ] },
+        ch_mem_inputs.map { meta, fq, index -> [ [], index ] },
+        [ [], [] ],
+        sort_bam
+    )
+
+    ch_mem_bam              = BWA_MEM.out.bam
+    ch_versions             = ch_versions.mix(BWA_MEM.out.versions.first())
+
+    // MODULE: SAMBLASTER
+    SAMBLASTER ( ch_mem_bam )
+
+    ch_blasted_bam          = SAMBLASTER.out.bam
+    ch_versions             = ch_versions.mix(SAMBLASTER.out.versions.first())
+
+    emit:
+    bam                     = SAMBLASTER.out.bam    // channel: [ val(meta), bam ]; meta ~ [ id: 'sample', ref_id: 'genome' ]
+    versions                = ch_versions           // channel: [ versions.yml ]
+}

subworkflows/nf-core/fastq_bwa_mem_samblaster/meta.yml

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+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/subworkflows/yaml-schema.json
+name: "fastq_bwa_mem_samblaster"
+description: Index fasta if needed, map reads with BWA MEM and filter with samblaster
+keywords:
+  - sort
+  - bam
+  - duplicate marking
+components:
+  - bwa/index
+  - bwa/mem
+  - samblaster
+input:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  - reads:
+      type: file
+      description: |
+        List of input FastQ files of size 1 and 2 for single-end and paired-end data,
+        respectively.
+  - meta2:
+      type: map
+      description: |
+        Groovy Map containing reference information
+        e.g. [ id:'genome' ]
+  - fasta:
+      type: file
+      description: Input genome fasta file
+  - index:
+      type: file
+      description: BWA genome index files
+      pattern: "Directory containing BWA index *.{amb,ann,bwt,pac,sa}"
+output:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false, ref_id:'genome' ]
+  - bam:
+      type: file
+      description: Tagged or filtered BAM file
+      pattern: "*.bam"
+  - versions:
+      type: file
+      description: File containing software versions
+      pattern: "versions.yml"
+authors:
+  - "@GallVp"
+maintainers:
+  - "@GallVp"

subworkflows/nf-core/fastq_bwa_mem_samblaster/tests/main.nf.test

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+nextflow_workflow {
+
+    name "Test Subworkflow FASTQ_BWA_MEM_SAMBLASTER"
+    script "../main.nf"
+    workflow "FASTQ_BWA_MEM_SAMBLASTER"
+    config './nextflow.config'
+
+    tag "subworkflows"
+    tag "subworkflows_nfcore"
+    tag "subworkflows/fastq_bwa_mem_samblaster"
+    tag "samblaster"
+    tag "bwa/index"
+    tag "bwa/mem"
+
+
+    test("sarscov2-fq-gz") {
+
+        when {
+            workflow {
+                """
+                input[0] = Channel.of(
+                    [
+                        [ id:'test' ],
+                        [
+                            file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
+                            file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true)
+                        ]
+                    ]
+                )
+                input[1] = Channel.of(
+                    [ [ id: 'genome' ], file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true), [] ]
+                )
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert workflow.success },
+                { assert snapshot(
+                    bam(workflow.out.bam[0][1]).getReadsMD5(),
+                    workflow.out.versions
+                    ).match()
+                }
+            )
+        }
+    }
+
+    test("sarscov2-fq-gz-stub") {
+
+        options '-stub'
+
+        when {
+            workflow {
+                """
+                input[0] = Channel.of(
+                    [
+                        [ id:'test' ],
+                        [
+                            file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
+                            file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true)
+                        ]
+                    ]
+                )
+                input[1] = Channel.of(
+                    [ [ id: 'genome' ], file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true), [] ]
+                )
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert workflow.success },
+                { assert snapshot(workflow.out).match() }
+            )
+        }
+    }
+}

subworkflows/nf-core/fastq_bwa_mem_samblaster/tests/main.nf.test.snap

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+{
+    "sarscov2-fq-gz": {
+        "content": [
+            "7cf71131809f63c5c05c767742ed70ff",
+            [
+                "versions.yml:md5,3b59736950270bca59c29afeb5289b4f",
+                "versions.yml:md5,80949a94ee1be8238b1c79d89ed9fa83",
+                "versions.yml:md5,ddd810edeee1008ec55b628e3a9d6204"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-08-28T09:36:34.757275"
+    },
+    "sarscov2-fq-gz-stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "ref_id": "genome"
+                        },
+                        "test.on.genome.samblaster.bam:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,3b59736950270bca59c29afeb5289b4f",
+                    "versions.yml:md5,80949a94ee1be8238b1c79d89ed9fa83",
+                    "versions.yml:md5,ddd810edeee1008ec55b628e3a9d6204"
+                ],
+                "bam": [
+                    [
+                        {
+                            "id": "test",
+                            "ref_id": "genome"
+                        },
+                        "test.on.genome.samblaster.bam:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,3b59736950270bca59c29afeb5289b4f",
+                    "versions.yml:md5,80949a94ee1be8238b1c79d89ed9fa83",
+                    "versions.yml:md5,ddd810edeee1008ec55b628e3a9d6204"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-08-28T09:36:42.43377"
+    }
+}

subworkflows/nf-core/fastq_bwa_mem_samblaster/tests/nextflow.config

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+process {
+    withName: BWA_MEM {
+        ext.prefix = { "${meta.id}.on.${meta.ref_id}.bwa.mem" }
+        ext.args = '-5SP'
+    }
+
+    withName: SAMBLASTER {
+        ext.prefix = { "${meta.id}.on.${meta.ref_id}.samblaster" }
+        ext.args3 = '-h -F 2316'
+    }
+}

subworkflows/nf-core/fastq_bwa_mem_samblaster/tests/tags.yml

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+subworkflows/fastq_bwa_mem_samblaster:
+  - subworkflows/nf-core/fastq_bwa_mem_samblaster/**