Transition to patched nf-core modules

modules/local/fastqvalidator/environment.yml

@@ -0,0 +1,10 @@
+---
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
+channels:
+  - conda-forge
+  - bioconda
+dependencies:
+  # TODO nf-core: List required Conda package(s).
+  #               Software MUST be pinned to channel (i.e. "bioconda"), version (i.e. "1.10").
+  #               For Conda, the build (i.e. "h9402c20_2") must be EXCLUDED to support installation on different operating systems.
+  - "YOUR-TOOL-HERE"

modules/local/fastqvalidator/main.nf

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+process FASTQ_VALIDATOR {
+    tag "${sampleName}"
+    // tag "$meta.id"
+    label 'process_medium'
+
+    input:
+    tuple val(sampleName), path(sampleRead)
+    val ready
+
+
+    // tuple val(meta), path(sampleRead)
+
+
+
+    output:
+    path("*.fastq_report.csv")                                       , emit: fastq_report
+    tuple val(sampleName), path(sampleRead)                          , emit: reads
+
+    // 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}"
+
+    """
+    fastqvalidator \\
+        $args \\
+        -@ $task.cpus \\
+        -o ${prefix}.bam \\
+        $bam
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        fastqvalidator: \$(fastqvalidator --version)
+    END_VERSIONS
+    """
+
+    stub:
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+
+    """
+    touch ${sampleRead.simpleName}.check.csv
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        fastqvalidator: \$(fastqvalidator --version)
+    END_VERSIONS
+    """
+}

modules/local/fastqvalidator/meta.yml

@@ -0,0 +1,68 @@
+---
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json
+name: "fastqvalidator"
+## TODO nf-core: Add a description of the module and list keywords
+description: write your description here
+keywords:
+  - sort
+  - example
+  - genomics
+tools:
+  - "fastqvalidator":
+      ## TODO nf-core: Add a description and other details for the software below
+      description: ""
+      homepage: ""
+      documentation: ""
+      tool_dev_url: ""
+      doi: ""
+      licence:
+      identifier: biotools:fastqvalidator
+
+## TODO nf-core: Add a description of all of the variables used as input
+input:
+  # Only when we have meta
+  - - meta:
+        type: map
+        description: |
+          Groovy Map containing sample information
+          e.g. `[ id:'sample1' ]`
+
+    ## TODO nf-core: Delete / customise this example input
+    - bam:
+        type: file
+        description: Sorted BAM/CRAM/SAM file
+        pattern: "*.{bam,cram,sam}"
+        ontologies:
+          - edam: "http://edamontology.org/format_2572" # BAM
+          - edam: "http://edamontology.org/format_2573" # CRAM
+          - edam: "http://edamontology.org/format_3462" # SAM
+
+## TODO nf-core: Add a description of all of the variables used as output
+output:
+  - bam:
+      #Only when we have meta
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. `[ id:'sample1' ]`
+      ## TODO nf-core: Delete / customise this example output
+      - "*.bam":
+          type: file
+          description: Sorted BAM/CRAM/SAM file
+          pattern: "*.{bam,cram,sam}"
+          ontologies:
+            - edam: "http://edamontology.org/format_2572" # BAM
+            - edam: "http://edamontology.org/format_2573" # CRAM
+            - edam: "http://edamontology.org/format_3462" # SAM
+
+  - versions:
+      - "versions.yml":
+          type: file
+          description: File containing software versions
+          pattern: "versions.yml"
+
+authors:
+  - "@abhi18av"
+maintainers:
+  - "@abhi18av"

modules/local/fastqvalidator/tests/main.nf.test

@@ -0,0 +1,73 @@
+// TODO nf-core: Once you have added the required tests, please run the following command to build this file:
+// nf-core modules test fastqvalidator
+nextflow_process {
+
+    name "Test Process FASTQVALIDATOR"
+    script "../main.nf"
+    process "FASTQVALIDATOR"
+
+    tag "modules"
+    tag "modules_"
+    tag "fastqvalidator"
+
+    // TODO nf-core: Change the test name preferably indicating the test-data and file-format used
+    test("sarscov2 - bam") {
+
+        // TODO nf-core: If you are created a test for a chained module
+        // (the module requires running more than one process to generate the required output)
+        // add the 'setup' method here.
+        // You can find more information about how to use a 'setup' method in the docs (https://nf-co.re/docs/contributing/modules#steps-for-creating-nf-test-for-chained-modules).
+
+        when {
+            process {
+                """
+                // TODO nf-core: define inputs of the process here. Example:
+
+                input[0] = [
+                    [ id:'test', single_end:false ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true),
+                ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+                //TODO nf-core: Add all required assertions to verify the test output.
+                // See https://nf-co.re/docs/contributing/tutorials/nf-test_assertions for more information and examples.
+            )
+        }
+
+    }
+
+    // TODO nf-core: Change the test name preferably indicating the test-data and file-format used but keep the " - stub" suffix.
+    test("sarscov2 - bam - stub") {
+
+        options "-stub"
+
+        when {
+            process {
+                """
+                // TODO nf-core: define inputs of the process here. Example:
+
+                input[0] = [
+                    [ id:'test', single_end:false ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true),
+                ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+                //TODO nf-core: Add all required assertions to verify the test output.
+            )
+        }
+
+    }
+
+}

modules/nf-core/bcftools/merge/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::bcftools=1.21

modules/nf-core/bcftools/merge/main.nf

@@ -0,0 +1,74 @@
+process BCFTOOLS_MERGE {
+    tag "$meta.id"
+    label 'process_medium'
+
+    conda "${moduleDir}/environment.yml"
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/5a/5acacb55c52bec97c61fd34ffa8721fce82ce823005793592e2a80bf71632cd0/data':
+        'community.wave.seqera.io/library/bcftools:1.21--4335bec1d7b44d11' }"
+
+    input:
+    tuple val(meta), path(vcfs), path(tbis)
+    tuple val(meta2), path(fasta)
+    tuple val(meta3), path(fai)
+    tuple val(meta4), path(bed)
+
+    output:
+    tuple val(meta), path("*.{bcf,vcf}{,.gz}"), emit: vcf
+    tuple val(meta), path("*.{csi,tbi}")      , emit: index, optional: true
+    path "versions.yml"                       , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+
+    def input = (vcfs.collect().size() > 1) ? vcfs.sort{ it.name } : vcfs
+    def regions = bed ? "--regions-file $bed" : ""
+    def extension = args.contains("--output-type b") || args.contains("-Ob") ? "bcf.gz" :
+                    args.contains("--output-type u") || args.contains("-Ou") ? "bcf" :
+                    args.contains("--output-type z") || args.contains("-Oz") ? "vcf.gz" :
+                    args.contains("--output-type v") || args.contains("-Ov") ? "vcf" :
+                    "vcf"
+
+    """
+    bcftools merge \\
+        $args \\
+        $regions \\
+        --threads $task.cpus \\
+        --output ${prefix}.${extension} \\
+        $input
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        bcftools: \$(bcftools --version 2>&1 | head -n1 | sed 's/^.*bcftools //; s/ .*\$//')
+    END_VERSIONS
+    """
+
+    stub:
+    def args = task.ext.args   ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    def extension = args.contains("--output-type b") || args.contains("-Ob") ? "bcf.gz" :
+                    args.contains("--output-type u") || args.contains("-Ou") ? "bcf" :
+                    args.contains("--output-type z") || args.contains("-Oz") ? "vcf.gz" :
+                    args.contains("--output-type v") || args.contains("-Ov") ? "vcf" :
+                    "vcf"
+    def index = args.contains("--write-index=tbi") || args.contains("-W=tbi") ? "tbi" :
+                args.contains("--write-index=csi") || args.contains("-W=csi") ? "csi" :
+                args.contains("--write-index") || args.contains("-W") ? "csi" :
+                ""
+    def create_cmd = extension.endsWith(".gz") ? "echo '' | gzip >" : "touch"
+    def create_index = extension.endsWith(".gz") && index.matches("csi|tbi") ? "touch ${prefix}.${extension}.${index}" : ""
+
+    """
+    ${create_cmd} ${prefix}.${extension}
+    ${create_index}
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        bcftools: \$(bcftools --version 2>&1 | head -n1 | sed 's/^.*bcftools //; s/ .*\$//')
+    END_VERSIONS
+    """
+}

modules/nf-core/bcftools/merge/meta.yml

@@ -0,0 +1,96 @@
+name: bcftools_merge
+description: Merge VCF files
+keywords:
+  - variant calling
+  - merge
+  - VCF
+tools:
+  - merge:
+      description: |
+        Merge VCF files.
+      homepage: http://samtools.github.io/bcftools/bcftools.html
+      documentation: http://www.htslib.org/doc/bcftools.html
+      doi: 10.1093/bioinformatics/btp352
+      licence: ["MIT"]
+      identifier: biotools:bcftools
+input:
+  - - meta:
+        type: map
+        description: |
+          Groovy Map containing sample information
+          e.g. [ id:'test', single_end:false ]
+    - vcfs:
+        type: file
+        description: |
+          List containing 2 or more vcf files
+          e.g. [ 'file1.vcf', 'file2.vcf' ]
+    - tbis:
+        type: file
+        description: |
+          List containing the tbi index files corresponding to the vcfs input files
+          e.g. [ 'file1.vcf.tbi', 'file2.vcf.tbi' ]
+  - - meta2:
+        type: map
+        description: |
+          Groovy Map containing reference information
+          e.g. [ id:'genome' ]
+    - fasta:
+        type: file
+        description: "(Optional) The fasta reference file (only necessary for the `--gvcf
+          FILE` parameter)"
+        pattern: "*.{fasta,fa}"
+  - - meta3:
+        type: map
+        description: |
+          Groovy Map containing reference information
+          e.g. [ id:'genome' ]
+    - fai:
+        type: file
+        description: "(Optional) The fasta reference file index (only necessary for
+          the `--gvcf FILE` parameter)"
+        pattern: "*.fai"
+  - - meta4:
+        type: map
+        description: |
+          Groovy Map containing bed information
+          e.g. [ id:'genome' ]
+    - bed:
+        type: file
+        description: "(Optional) The bed regions to merge on"
+        pattern: "*.bed"
+output:
+  - vcf:
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test', single_end:false ]
+      - "*.{bcf,vcf}{,.gz}":
+          type: file
+          description: merged output file
+          pattern: "*.{vcf,vcf.gz,bcf,bcf.gz}"
+  - index:
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test', single_end:false ]
+      - "*.{csi,tbi}":
+          type: file
+          description: index of merged output
+          pattern: "*.{csi,tbi}"
+  - versions:
+      - versions.yml:
+          type: file
+          description: File containing software versions
+          pattern: "versions.yml"
+authors:
+  - "@joseespinosa"
+  - "@drpatelh"
+  - "@nvnieuwk"
+  - "@ramprasadn"
+maintainers:
+  - "@joseespinosa"
+  - "@drpatelh"
+  - "@nvnieuwk"
+  - "@ramprasadn"

modules/nf-core/bcftools/merge/tests/bcf.config

@@ -0,0 +1,3 @@
+process {
+    ext.args = '--output-type u --no-version'
+}

modules/nf-core/bcftools/merge/tests/bcf_gz.config

@@ -0,0 +1,3 @@
+process {
+    ext.args = '--output-type b --no-version'
+}