Merge branch 'master' into boolean-parameter-to--log_skipped_fastqs

.pre-commit-config.yaml

@@ -18,7 +18,7 @@ repos:
         args: ["--schemafile", "subworkflows/yaml-schema.json"]
       - id: check-github-workflows
   - repo: https://github.com/renovatebot/pre-commit-hooks
-    rev: 37.368.10
+    rev: 37.371.1
     hooks:
       - id: renovate-config-validator
   # use ruff for python files

modules/nf-core/bamtofastq10x/environment.yml

@@ -0,0 +1,9 @@
+---
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
+name: "bamtofastq10x"
+channels:
+  - conda-forge
+  - bioconda
+  - defaults
+dependencies:
+  - "bioconda::10x_bamtofastq=1.4.1"

modules/nf-core/bamtofastq10x/main.nf

@@ -0,0 +1,45 @@
+process BAMTOFASTQ10X {
+    tag "$meta.id"
+    label 'process_low'
+
+    conda "${moduleDir}/environment.yml"
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/10x_bamtofastq:1.4.1--hdbdd923_2':
+        'biocontainers/10x_bamtofastq:1.4.1--hdbdd923_2' }"
+
+    input:
+    tuple val(meta), path(bam)
+
+    output:
+    tuple val(meta), path("*.fastq.gz"), emit: fastq
+    path "versions.yml"                , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    bamtofastq \\
+        $args \\
+        $bam \\
+        ${prefix}.fastq.gz
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        bamtofastq10x: \$(bamtofastq --version |& sed '1!d ; s/bamtofastq //')
+    END_VERSIONS
+    """
+
+    stub:
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    touch ${prefix}.fastq.gz
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        bamtofastq10x: \$(bamtofastq --version |& sed '1!d ; s/bamtofastq //')
+    END_VERSIONS
+    """
+}

modules/nf-core/bamtofastq10x/meta.yml

@@ -0,0 +1,48 @@
+name: bamtofastq10x
+
+description: Tool for converting 10x BAMs produced by Cell Ranger, Space Ranger, Cell Ranger ATAC, Cell Ranger DNA, and Long Ranger back to FASTQ files that can be used as inputs to re-run analysis
+
+keywords:
+  - bam
+  - convert
+  - fastq
+  - 10x
+
+tools:
+  - bamtofastq10x:
+      description: Tool for converting 10x BAMs produced by Cell Ranger, Space Ranger, Cell Ranger ATAC, Cell Ranger DNA, and Long Ranger back to FASTQ files that can be used as inputs to re-run analysis
+      homepage: https://github.com/10XGenomics/bamtofastq
+      documentation: https://github.com/10XGenomics/bamtofastq
+      tool_dev_url: https://github.com/10XGenomics/bamtofastq
+      licence: ["MIT"]
+input:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. `[ id:'sample1', single_end:false ]`
+  - bam:
+      type: file
+      description: BAM file
+      pattern: "*.bam"
+output:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. `[ id:'sample1', single_end:false ]`
+
+  - versions:
+      type: file
+      description: File containing software versions
+      pattern: "versions.yml"
+
+  - fastq:
+      type: file
+      description: fastq compressed file
+      pattern: "*.fastq.gz"
+
+authors:
+  - "@BlueBicycleBlog"
+maintainers:
+  - "@BlueBicycleBlog"

modules/nf-core/bamtofastq10x/tests/main.nf.test

@@ -0,0 +1,55 @@
+nextflow_process {
+
+    name "Test Process BAMTOFASTQ10X"
+    script "../main.nf"
+    process "BAMTOFASTQ10X"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "bamtofastq10x"
+
+    test("human - bam") {
+        when {
+            process {
+                """
+                input[0] = Channel.of([
+                    [ id:'test' ],
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/10xgenomics/10x_cr12.bam', checkIfExists: true)
+                ])
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+
+            )
+        }
+    }
+
+
+    test("human - bam - stub") {
+
+        options "-stub"
+
+        when {
+            process {
+                """
+                input[0] = Channel.of([
+                    [ id:'test' ],
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/10xgenomics/10x_cr12.bam', checkIfExists: true)
+                ])
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success }
+            )
+        }
+
+    }
+}

modules/nf-core/bamtofastq10x/tests/main.nf.test.snap

@@ -0,0 +1,47 @@
+{
+    "human - bam": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        [
+                            [
+                                "bamtofastq_S1_L000_I1_001.fastq.gz:md5,a33682ac881de7a7453d79721b7621a0",
+                                "bamtofastq_S1_L000_R1_001.fastq.gz:md5,5ccebf77d8636d7a7cdfc59737aea79f",
+                                "bamtofastq_S1_L000_R2_001.fastq.gz:md5,2ee7c90e4307deba74065cfd00a65002"
+                            ]
+                        ]
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,845cd1d09c8a3d0059da9d074a9e5436"
+                ],
+                "fastq": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        [
+                            [
+                                "bamtofastq_S1_L000_I1_001.fastq.gz:md5,a33682ac881de7a7453d79721b7621a0",
+                                "bamtofastq_S1_L000_R1_001.fastq.gz:md5,5ccebf77d8636d7a7cdfc59737aea79f",
+                                "bamtofastq_S1_L000_R2_001.fastq.gz:md5,2ee7c90e4307deba74065cfd00a65002"
+                            ]
+                        ]
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,845cd1d09c8a3d0059da9d074a9e5436"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.0"
+        },
+        "timestamp": "2024-05-22T16:43:24.999397"
+    }
+}

modules/nf-core/bamtofastq10x/tests/tags.yml

@@ -0,0 +1,2 @@
+bamtofastq10x:
+  - "modules/nf-core/bamtofastq10x/**"

modules/nf-core/bclconvert/main.nf

@@ -8,14 +8,14 @@ process BCLCONVERT {
     tuple val(meta), path(samplesheet), path(run_dir)
 
     output:
-    tuple val(meta), path("**_S[1-9]*_R?_00?.fastq.gz")          , emit: fastq
-    tuple val(meta), path("**_S[1-9]*_I?_00?.fastq.gz")          , optional:true, emit: fastq_idx
-    tuple val(meta), path("**Undetermined_S0*_R?_00?.fastq.gz")  , optional:true, emit: undetermined
-    tuple val(meta), path("**Undetermined_S0*_I?_00?.fastq.gz")  , optional:true, emit: undetermined_idx
-    tuple val(meta), path("Reports")                             , emit: reports
-    tuple val(meta), path("Logs")                                , emit: logs
-    tuple val(meta), path("InterOp/*.bin")                       , emit: interop
-    path("versions.yml")                                         , emit: versions
+    tuple val(meta), path("**_S[1-9]*_R?_00?.fastq.gz")           , emit: fastq
+    tuple val(meta), path("**_S[1-9]*_I?_00?.fastq.gz")           , optional:true, emit: fastq_idx
+    tuple val(meta), path("**Undetermined_S0*_R?_00?.fastq.gz")   , optional:true, emit: undetermined
+    tuple val(meta), path("**Undetermined_S0*_I?_00?.fastq.gz")   , optional:true, emit: undetermined_idx
+    tuple val(meta), path("Reports")                              , emit: reports
+    tuple val(meta), path("Logs")                                 , emit: logs
+    tuple val(meta), path("**/InterOp/*.bin", includeInputs: true), emit: interop
+    path("versions.yml")                                          , emit: versions
 
     when:
     task.ext.when == null || task.ext.when
@@ -62,8 +62,6 @@ process BCLCONVERT {
         --bcl-input-directory ${input_dir} \\
         --sample-sheet ${samplesheet}
 
-    cp -r ${input_dir}/InterOp .
-
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
         bclconvert: \$(bcl-convert -V 2>&1 | head -n 1 | sed 's/^.*Version //')

modules/nf-core/biscuit/align/tests/main.nf.test

@@ -0,0 +1,72 @@
+nextflow_process {
+
+    name "Test Process BISCUIT_ALIGN"
+    script "../main.nf"
+    process "BISCUIT_ALIGN"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "biscuit"
+    tag "biscuit/align"
+    tag "biscuit/index"
+
+    setup {
+        run("BISCUIT_INDEX") {
+            script "../../index/main.nf"
+            process {
+            """
+            input[0] = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
+            """
+        }
+        }
+    }
+
+    test("Single-End sarscov2 test_methylated_1 [fastq_gz]") {
+
+        when {
+            process {
+                """
+                input[0] = [
+                            [ id:'test' ], // meta map
+                            [ file(params.test_data['sarscov2']['illumina']['test_methylated_1_fastq_gz'], checkIfExists: true) ]
+                ]
+                input[1] = BISCUIT_INDEX.out.index
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert file(process.out.bam[0][1]).name == "test.bam" },
+                { assert file(process.out.bai[0][1]).name == "test.bam.bai" },
+                { assert snapshot(process.out.versions).match("single-end-versions") }
+          )
+        }
+    }
+
+    test("Paired-End sarscov2 test_methylated_1 [fastq_gz]") {
+
+        when {
+            process {
+                """
+                input[0] = [
+                            [ id:'test' ], // meta map
+                            [ file(params.test_data['sarscov2']['illumina']['test_methylated_1_fastq_gz'], checkIfExists: true),
+                              file(params.test_data['sarscov2']['illumina']['test_methylated_2_fastq_gz'], checkIfExists: true) ]
+                ]
+                input[1] = BISCUIT_INDEX.out.index
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert file(process.out.bam[0][1]).name == "test.bam" },
+                { assert file(process.out.bai[0][1]).name == "test.bam.bai" },
+                { assert snapshot(process.out.versions).match("paired-end-versions") }
+          )
+        }
+    }
+}

modules/nf-core/biscuit/align/tests/main.nf.test.snap

@@ -0,0 +1,26 @@
+{
+    "single-end-versions": {
+        "content": [
+            [
+                "versions.yml:md5,0b2a8c4c438a785a890110a458399bfd"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.1"
+        },
+        "timestamp": "2024-05-22T20:06:02.295706212"
+    },
+    "paired-end-versions": {
+        "content": [
+            [
+                "versions.yml:md5,0b2a8c4c438a785a890110a458399bfd"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.1"
+        },
+        "timestamp": "2024-05-22T20:06:17.879689395"
+    }
+}

modules/nf-core/biscuit/align/tests/tags.yml

@@ -0,0 +1,3 @@
+biscuit/align:
+  - modules/nf-core/biscuit/index/**
+  - modules/nf-core/biscuit/align/**

modules/nf-core/checkm/lineagewf/tests/main.nf.test

@@ -0,0 +1,38 @@
+nextflow_process {
+
+    name "Test Process CHECKM_LINEAGEWF"
+    script "../main.nf"
+    process "CHECKM_LINEAGEWF"
+    tag "modules"
+    tag "modules_nfcore"
+    tag "checkm"
+    tag "checkm/lineagewf"
+
+    test("Should run without failures") {
+
+        when {
+            process {
+                """
+                input[0] = [
+                                [ id:'test', single_end:false ], // meta map
+                                file(params.test_data['sarscov2']['illumina']['contigs_fasta'], checkIfExists: true)
+                            ]
+                input[1] = 'fasta'
+                input[2] = [] // Download CheckM database
+                """
+            }
+        }
+
+        then {
+            assert process.success
+            assert file(process.out.checkm_output[0][1]).list().find { file(it).name == "checkm.log" }
+            assert snapshot(
+                path(process.out.marker_file[0][1]).readLines().any{it.contains("PF00312.17")},
+                process.out.checkm_tsv,
+                process.out.versions
+                ).match()
+        }
+
+    }
+
+}