Merge branch 'master' into new-module-rtg/vcfeval

modules/meryl/unionsum/main.nf

@@ -0,0 +1,35 @@
+process MERYL_UNIONSUM {
+    tag "$meta.id"
+    label 'process_low'
+
+    conda (params.enable_conda ? "bioconda::meryl=1.3" : null)
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/meryl:1.3--h87f3376_1':
+        'quay.io/biocontainers/meryl:1.3--h87f3376_1' }"
+
+    input:
+    tuple val(meta), path(meryl_dbs)
+
+    output:
+    tuple val(meta), path("*.unionsum.meryldb"), emit: meryl_db
+    path "versions.yml"                        , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    meryl union-sum \\
+        threads=$task.cpus \\
+        $args \\
+        output ${prefix}.unionsum.meryldb \\
+        $meryl_dbs
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        meryl: \$( meryl --version |& sed 's/meryl //' )
+    END_VERSIONS
+    """
+}

modules/meryl/unionsum/meta.yml

@@ -0,0 +1,41 @@
+name: "meryl_unionsum"
+description: A genomic k-mer counter (and sequence utility) with nice features.
+keywords:
+  - k-mer
+  - unionsum
+tools:
+  - "meryl":
+      description: "A genomic k-mer counter (and sequence utility) with nice features. "
+      homepage: "https://github.com/marbl/meryl"
+      documentation: "https://meryl.readthedocs.io/en/latest/quick-start.html"
+      tool_dev_url: "https://github.com/marbl/meryl"
+      doi: ""
+      licence: "['GPL']"
+
+input:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  - meryl_dbs:
+      type: directory
+      description: Meryl k-mer databases
+
+output:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  - versions:
+      type: file
+      description: File containing software versions
+      pattern: "versions.yml"
+  - meryl_db:
+      type: directory
+      description: A Meryl k-mer database that is the union sum of the input databases
+      pattern: "*.unionsum.meryldb"
+
+authors:
+  - "@mahesh-panchal"

tests/config/pytest_modules.yml

@@ -1222,6 +1222,10 @@ meryl/histogram:
   - modules/meryl/histogram/**
   - tests/modules/meryl/histogram/**
 
+meryl/unionsum:
+  - modules/meryl/unionsum/**
+  - tests/modules/meryl/unionsum/**
+
 metabat2/jgisummarizebamcontigdepths:
   - modules/metabat2/jgisummarizebamcontigdepths/**
   - tests/modules/metabat2/jgisummarizebamcontigdepths/**

tests/modules/meryl/unionsum/main.nf

@@ -0,0 +1,31 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { MERYL_COUNT    } from '../../../../modules/meryl/count/main.nf'
+include { MERYL_UNIONSUM } from '../../../../modules/meryl/unionsum/main.nf'
+
+workflow test_meryl_unionsum_single_end {
+
+    input = [
+        [ id:'test', single_end: true ], // meta map
+        file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true)
+    ]
+
+    MERYL_COUNT ( input )
+    MERYL_UNIONSUM ( MERYL_COUNT.out.meryl_db )
+}
+
+workflow test_meryl_unionsum_paired_end {
+
+    input = [
+        [ id:'test', single_end: false ], // meta map
+        [
+            file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
+            file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true)
+        ]
+    ]
+
+    MERYL_COUNT ( input )
+    MERYL_UNIONSUM ( MERYL_COUNT.out.meryl_db )
+}

tests/modules/meryl/unionsum/nextflow.config

@@ -0,0 +1,6 @@
+process {
+
+    publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+    ext.args = 'k=21'
+
+}

tests/modules/meryl/unionsum/test.yml

@@ -0,0 +1,17 @@
+- name: meryl unionsum test_meryl_unionsum_single_end
+  command: nextflow run tests/modules/meryl/unionsum -entry test_meryl_unionsum_single_end -c tests/config/nextflow.config
+  tags:
+    - meryl
+    - meryl/unionsum
+  files:
+    - path: output/meryl/versions.yml
+      md5sum: 7de859c6d3a29d72f6c9c976609d0913
+
+- name: meryl unionsum test_meryl_unionsum_paired_end
+  command: nextflow run tests/modules/meryl/unionsum -entry test_meryl_unionsum_paired_end -c tests/config/nextflow.config
+  tags:
+    - meryl
+    - meryl/unionsum
+  files:
+    - path: output/meryl/versions.yml
+      md5sum: a16decdec014ccb9bdab69a4a1d30818