hmmcopy/mapCounter (#1175)

* hmmcopy/mapCounter

* update test

* Remove bam tag

* Remove /tmp/ path from test.yml

* Update modules/hmmcopy/mapcounter/meta.yml

Incorporate formatting changes

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>

* Update modules/hmmcopy/mapcounter/meta.yml

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>

* Update tests/modules/hmmcopy/mapcounter/main.nf

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>

Co-authored-by: Simon Pearce <simon.pearce@cruk.manchester.ac.uk>
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>

modules/hmmcopy/mapcounter/main.nf

@@ -0,0 +1,31 @@
+def VERSION = '0.1.1' // Version information not provided by tool on CLI
+
+process HMMCOPY_MAPCOUNTER {
+    label 'process_medium'
+
+    conda (params.enable_conda ? "bioconda::hmmcopy=0.1.1" : null)
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/hmmcopy:0.1.1--h2e03b76_7':
+        'quay.io/biocontainers/hmmcopy:0.1.1--h2e03b76_7' }"
+
+    input:
+    path bigwig
+
+    output:
+    path "*.map.wig"              , emit: wig
+    path "versions.yml"           , emit: versions
+
+    script:
+    def args = task.ext.args ?: ''
+
+    """
+    mapCounter \\
+        $args \\
+        $bigwig > ${bigwig.baseName}.map.wig
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        hmmcopy: \$(echo $VERSION)
+    END_VERSIONS
+    """
+}

modules/hmmcopy/mapcounter/meta.yml

@@ -0,0 +1,34 @@
+name: hmmcopy_mapcounter
+description: mapCounter function from HMMcopy utilities, used to generate mappability in non-overlapping windows from a bigwig file
+keywords:
+  - hmmcopy
+  - mapcounter
+  - cnv
+tools:
+  - hmmcopy:
+      description: C++ based programs for analyzing BAM files and preparing read counts -- used with bioconductor-hmmcopy
+      homepage: https://github.com/shahcompbio/hmmcopy_utils
+      documentation: https://github.com/shahcompbio/hmmcopy_utils
+      tool_dev_url: https://github.com/shahcompbio/hmmcopy_utils
+      doi: ""
+      licence: ['GPL v3']
+
+input:
+  - bigwig:
+      type: file
+      description: BigWig file with the mappability score of the genome, for instance made with generateMap function.
+      pattern: "*.wig"
+
+output:
+  - versions:
+      type: file
+      description: File containing software versions
+      pattern: "versions.yml"
+
+  - wig:
+      type: file
+      description: wig file containing mappability of each window of the genome
+      pattern: "*.map.wig"
+
+authors:
+  - "@sppearce"

tests/config/pytest_modules.yml

@@ -695,6 +695,10 @@ hmmcopy/generatemap:
   - modules/hmmcopy/generatemap/**
   - tests/modules/hmmcopy/generatemap/**
 
+hmmcopy/mapcounter:
+  - modules/hmmcopy/mapcounter/**
+  - tests/modules/hmmcopy/mapcounter/**
+
 hmmcopy/readcounter:
   - modules/hmmcopy/readcounter/**
   - tests/modules/hmmcopy/readcounter/**

tests/modules/hmmcopy/mapcounter/main.nf

@@ -0,0 +1,14 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { HMMCOPY_MAPCOUNTER } from '../../../../modules/hmmcopy/mapcounter/main.nf'
+include { HMMCOPY_GENERATEMAP } from '../../../../modules/hmmcopy/generatemap/main.nf'
+workflow test_hmmcopy_mapcounter {
+
+    fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
+
+    HMMCOPY_GENERATEMAP( fasta )
+
+    HMMCOPY_MAPCOUNTER ( HMMCOPY_GENERATEMAP.out.bigwig )
+}

tests/modules/hmmcopy/mapcounter/nextflow.config

@@ -0,0 +1,5 @@
+process {
+
+    publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+    
+}

tests/modules/hmmcopy/mapcounter/test.yml

@@ -0,0 +1,12 @@
+- name: hmmcopy mapcounter test_hmmcopy_mapcounter
+  command: nextflow run tests/modules/hmmcopy/mapcounter -entry test_hmmcopy_mapcounter -c tests/config/nextflow.config
+  tags:
+    - hmmcopy/mapcounter
+    - hmmcopy
+  files:
+    - path: output/hmmcopy/genome.fasta.map.bw
+      md5sum: 7ad68224a1e40287978284c387e8eb70
+    - path: output/hmmcopy/genome.fasta.map.map.wig
+      md5sum: e2d39dc204ed31c1ce372d633a42560f
+    - path: output/hmmcopy/versions.yml
+      md5sum: 8361e3c0f8b96cf84834678cf988a209