Start Meryl count

modules/meryl/count/main.nf

@@ -0,0 +1,45 @@
+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("*.meryl"), emit: meryl
+    path "versions.yml"             , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args = task.ext.args ?: ''
+    def args2 = task.ext.args2 ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    for READ in $reads; do
+        meryl count \\
+            threads=$task.cpus \\
+            $args \\
+            $reads \\
+            output read.\${READ%.f*}.meryl
+    done
+    meryl union-sum \\
+        threads=$task.cpus \\
+        $args2 \\
+        output ${prefix}.meryl
+
+    # clean up
+    rm -rf read.*.meryl
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        meryl: \$( meryl --version |& sed 's/meryl //' )
+    END_VERSIONS
+    """
+}

modules/meryl/count/meta.yml

@@ -0,0 +1,51 @@
+name: "meryl_count"
+## TODO nf-core: Add a description of the module and list keywords
+description: write your description here
+keywords:
+  - sort
+tools:
+  - "meryl":
+      ## TODO nf-core: Add a description and other details for the software below
+      description: ""
+      homepage: "{}"
+      documentation: "{}"
+      tool_dev_url: "{}"
+      doi: ""
+      licence: "['GPL']"
+
+## 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:'test', single_end:false ]
+  # 
+  ## TODO nf-core: Delete / customise this example input
+  - bam:
+      type: file
+      description: BAM/CRAM/SAM file
+      pattern: "*.{bam,cram,sam}"
+
+## TODO nf-core: Add a description of all of the variables used as output
+output:
+  #Only when we have meta
+  - 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"
+  ## TODO nf-core: Delete / customise this example output
+  - bam:
+      type: file
+      description: Sorted BAM/CRAM/SAM file
+      pattern: "*.{bam,cram,sam}"
+
+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/**
+
 metabat2/jgisummarizebamcontigdepths:
   - modules/metabat2/jgisummarizebamcontigdepths/**
   - tests/modules/metabat2/jgisummarizebamcontigdepths/**

tests/modules/meryl/count/main.nf

@@ -0,0 +1,15 @@
+#!/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' ], // meta map
+        file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true)
+    ]
+
+    MERYL_COUNT ( input )
+}

tests/modules/meryl/count/nextflow.config

@@ -0,0 +1,7 @@
+process {
+
+    publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+    ext.args = 'k=21'
+    ext.args2 = 'k=21'
+
+}

tests/modules/meryl/count/test.yml

@@ -0,0 +1,8 @@
+- 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