Merge pull request #1636 from mahesh-panchal/meryl/histogram

Add meryl histogram

modules/meryl/histogram/main.nf

@@ -0,0 +1,34 @@
+process MERYL_HISTOGRAM {
+    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_db)
+
+    output:
+    tuple val(meta), path("*.hist"), emit: hist
+    path "versions.yml"            , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    meryl histogram \\
+        threads=$task.cpus \\
+        $args \\
+        $meryl_db > ${prefix}.hist
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        meryl: \$( meryl --version |& sed 's/meryl //' )
+    END_VERSIONS
+    """
+}

modules/meryl/histogram/meta.yml

@@ -0,0 +1,41 @@
+name: "meryl_histogram"
+description: A genomic k-mer counter (and sequence utility) with nice features.
+keywords:
+  - k-mer
+  - histogram
+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 database
+
+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"
+  - hist:
+      type: file
+      description: Histogram of k-mers
+      pattern: "*.hist"
+
+authors:
+  - "@mahesh-panchal"

tests/config/pytest_modules.yml

@@ -1218,6 +1218,10 @@ meryl/count:
   - modules/meryl/count/**
   - tests/modules/meryl/count/**
 
+meryl/histogram:
+  - modules/meryl/histogram/**
+  - tests/modules/meryl/histogram/**
+
 metabat2/jgisummarizebamcontigdepths:
   - modules/metabat2/jgisummarizebamcontigdepths/**
   - tests/modules/metabat2/jgisummarizebamcontigdepths/**
@@ -1767,14 +1771,14 @@ slimfastq:
   - modules/slimfastq/**
   - tests/modules/slimfastq/**
 
-snapaligner/index:
-  - modules/snapaligner/index/**
-  - tests/modules/snapaligner/index/**
-
 snapaligner/align:
   - modules/snapaligner/align/**
   - tests/modules/snapaligner/align/**
 
+snapaligner/index:
+  - modules/snapaligner/index/**
+  - tests/modules/snapaligner/index/**
+
 snpdists:
   - modules/snpdists/**
   - tests/modules/snpdists/**

tests/modules/meryl/histogram/main.nf

@@ -0,0 +1,17 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { MERYL_COUNT     } from '../../../../modules/meryl/count/main.nf'
+include { MERYL_HISTOGRAM } from '../../../../modules/meryl/histogram/main.nf'
+
+workflow test_meryl_histogram {
+
+    input = [
+        [ id:'test' ], // meta map
+        file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true)
+    ]
+
+    MERYL_COUNT ( input )
+    MERYL_HISTOGRAM ( MERYL_COUNT.out.meryl_db )
+}

tests/modules/meryl/histogram/nextflow.config

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

tests/modules/meryl/histogram/test.yml

@@ -0,0 +1,10 @@
+- name: meryl histogram test_meryl_histogram
+  command: nextflow run tests/modules/meryl/histogram -entry test_meryl_histogram -c tests/config/nextflow.config
+  tags:
+    - meryl/histogram
+    - meryl
+  files:
+    - path: output/meryl/test.hist
+      md5sum: 4bfdc8b287ee0cfd9922bbfa8cd64650
+    - path: output/meryl/versions.yml
+      md5sum: 050038f1b1df79977a393cce1b4b2ddb