Merge branch 'master' into meryl/histogram

modules/meryl/count/main.nf

@@ -0,0 +1,37 @@
+process MERYL_COUNT {
+    tag "$meta.id"
+    label 'process_medium'
+
+    conda (params.enable_conda ? "bioconda::meryl=1.3" : null)
+    container "${ 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(reads)
+
+    output:
+    tuple val(meta), path("*.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}"
+    """
+    for READ in $reads; do
+        meryl count \\
+            threads=$task.cpus \\
+            $args \\
+            $reads \\
+            output read.\${READ%.f*}.meryldb
+    done
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        meryl: \$( meryl --version |& sed 's/meryl //' )
+    END_VERSIONS
+    """
+}

modules/meryl/count/meta.yml

@@ -0,0 +1,43 @@
+name: "meryl_count"
+description: A genomic k-mer counter (and sequence utility) with nice features.
+keywords:
+  - k-mer
+  - count
+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 ]
+  - reads:
+      type: file
+      description: |
+        List of input FastQ files of size 1 and 2 for single-end and paired-end data,
+        respectively.
+
+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
+      pattern: "*.meryldb"
+
+authors:
+  - "@mahesh-panchal"

tests/config/pytest_modules.yml

@@ -1214,6 +1214,10 @@ meningotype:
   - modules/meningotype/**
   - tests/modules/meningotype/**
 
+meryl/count:
+  - modules/meryl/count/**
+  - tests/modules/meryl/count/**
+
 meryl/histogram:
   - modules/meryl/histogram/**
   - tests/modules/meryl/histogram/**

tests/config/test_data.config

@@ -345,6 +345,7 @@ params {
                 genome_gbff_gz                  = "${test_data_dir}/genomics/prokaryotes/bacteroides_fragilis/genome/genome.gbff.gz"
                 genome_paf                      = "${test_data_dir}/genomics/prokaryotes/bacteroides_fragilis/genome/genome.paf"
                 genome_mapping_potential_arg    = "${test_data_dir}/genomics/prokaryotes/bacteroides_fragilis/genome/genome.mapping.potential.ARG"
+                genome_gff_gz                  = "${test_data_dir}/genomics/prokaryotes/bacteroides_fragilis/genome/genome.gff.gz"
 
             }
             'illumina' {

tests/modules/meryl/count/main.nf

@@ -0,0 +1,28 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { MERYL_COUNT } from '../../../../modules/meryl/count/main.nf'
+
+workflow test_meryl_count_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 )
+}
+
+workflow test_meryl_count_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 )
+}

tests/modules/meryl/count/nextflow.config

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

tests/modules/meryl/count/test.yml

@@ -0,0 +1,17 @@
+- name: meryl count test_meryl_count_single_end
+  command: nextflow run tests/modules/meryl/count -entry test_meryl_count_single_end -c tests/config/nextflow.config
+  tags:
+    - meryl/count
+    - meryl
+  files:
+    - path: output/meryl/versions.yml
+      md5sum: 5fe537d873925ccbcc4edf0983e9eda0
+
+- name: meryl count test_meryl_count_paired_end
+  command: nextflow run tests/modules/meryl/count -entry test_meryl_count_paired_end -c tests/config/nextflow.config
+  tags:
+    - meryl/count
+    - meryl
+  files:
+    - path: output/meryl/versions.yml
+      md5sum: 4961f13cfb60ba8764ed666e70dbf12c