Ataqv mkarv (#1857)

* first draft

* fix test run

* Apply suggestions from code review

Co-authored-by: Jose Espinosa-Carrasco <kadomu@gmail.com>

* Update tests/modules/ataqv/mkarv/test.yml

* Update tests/modules/ataqv/mkarv/test.yml

* Update tests/modules/ataqv/mkarv/test.yml

* Update tests/modules/ataqv/mkarv/test.yml

* Update tests/modules/ataqv/mkarv/test.yml

* Update modules/ataqv/mkarv/nextflow.config

* Delete nextflow.config

* Update tests/modules/ataqv/mkarv/test.yml

* fix linting

* fix linting

Co-authored-by: bjlang <>
Co-authored-by: Jose Espinosa-Carrasco <kadomu@gmail.com>

modules/ataqv/mkarv/main.nf

@@ -0,0 +1,35 @@
+process ATAQV_MKARV {
+    label 'process_medium'
+
+    conda (params.enable_conda ? "bioconda::ataqv=1.3.0" : null)
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/ataqv:1.3.0--py39hccc85d7_2':
+        'quay.io/biocontainers/ataqv:1.3.0--py39hccc85d7_2' }"
+
+    input:
+    path json
+
+    output:
+    path "html"        , emit: html
+    path "versions.yml", emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args = task.ext.args ?: ''
+    """
+    mkarv \\
+        $args \\
+        --concurrency $task.cpus \\
+        --force \\
+        ./html/ \\
+        ${json.join(' ')}
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        # mkarv: \$( mkarv --version ) # Use this when version string has been fixed
+        ataqv: \$( ataqv --version )
+    END_VERSIONS
+    """
+}

modules/ataqv/mkarv/meta.yml

@@ -0,0 +1,31 @@
+name: "ataqv_mkarv"
+description: mkarv function of a corresponding ataqv tool
+keywords:
+  - mkarv
+tools:
+  - "ataqv":
+      description: "ataqv is a toolkit for measuring and comparing ATAC-seq results. It was written to help understand how well ATAC-seq assays have worked, and to make it easier to spot differences that might be caused by library prep or sequencing."
+      homepage: "https://github.com/ParkerLab/ataqv/blob/master/README.rst"
+      documentation: "https://github.com/ParkerLab/ataqv/blob/master/README.rst"
+      tool_dev_url: "https://github.com/ParkerLab/ataqv"
+      doi: ""
+      licence: "['GPL v3']"
+
+input:
+  - json:
+      type: file
+      description: The JSON file with ataqv metrics
+      pattern: "*.json"
+
+output:
+  - versions:
+      type: file
+      description: File containing software versions
+      pattern: "versions.yml"
+  - html:
+      type: directory
+      description: Web application to visualize results in HTML format
+      pattern: "*.html"
+
+authors:
+  - "@bjlang"

tests/config/pytest_modules.yml

@@ -86,6 +86,10 @@ ataqv/ataqv:
   - modules/ataqv/ataqv/**
   - tests/modules/ataqv/ataqv/**
 
+ataqv/mkarv:
+  - modules/ataqv/mkarv/**
+  - tests/modules/ataqv/mkarv/**
+
 atlas/call:
   - modules/atlas/call/**
   - tests/modules/atlas/call/**

tests/modules/ataqv/mkarv/main.nf

@@ -0,0 +1,19 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { ATAQV_ATAQV } from '../../../../modules/ataqv/ataqv/main.nf'
+include { ATAQV_MKARV } from '../../../../modules/ataqv/mkarv/main.nf'
+
+workflow test_ataqv_mkarv {
+
+    input = [
+        [ id:'test', single_end:false ],
+        file(params.test_data['sarscov2']['illumina']['test_paired_end_bam'], checkIfExists: true),
+        [],
+        []
+    ]
+
+    ATAQV_ATAQV ( input, 'human', [], [], [] )
+    ATAQV_MKARV ( ATAQV_ATAQV.out.json.collect{ it[1]} )
+}

tests/modules/ataqv/mkarv/nextflow.config

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

tests/modules/ataqv/mkarv/test.yml

@@ -0,0 +1,55 @@
+- name: ataqv mkarv test_ataqv_mkarv
+  command: nextflow run ./tests/modules/ataqv/mkarv -entry test_ataqv_mkarv -c ./tests/config/nextflow.config  -c ./tests/modules/ataqv/mkarv/nextflow.config
+  tags:
+    - ataqv/mkarv
+    - ataqv
+
+  files:
+    - path: output/ataqv/html/css/ataqv.css
+      md5sum: 7bb9e18974018dd29bdc12a46a6d6d65
+    - path: output/ataqv/html/css/datatables.buttons.min.css
+      md5sum: 675306abc9d3239314f2c66c0e22ef7a
+    - path: output/ataqv/html/css/datatables.fontawesome.css
+      md5sum: 716d7a3edd2c75e712b1ffe26f12a861
+    - path: output/ataqv/html/css/datatables.min.css
+      md5sum: 00ef3e39d9302618395ab189ec8bcd9f
+    - path: output/ataqv/html/css/font-awesome.min.css
+      md5sum: 89916fa773ce96569604016ef25cab50
+    - path: output/ataqv/html/css/normalize.css
+      md5sum: 40d20cc85100840580df4346bb99d7ed
+    - path: output/ataqv/html/data/1.json.gz
+    - path: output/ataqv/html/fonts/FontAwesome.otf
+      md5sum: 9ccfa32dd4cd1b8e83f68899d85bd5e6
+    - path: output/ataqv/html/fonts/fontawesome-webfont.eot
+      md5sum: 404a525502f8e5ba7e93b9f02d9e83a9
+    - path: output/ataqv/html/fonts/fontawesome-webfont.svg
+      md5sum: bae4a87c1e5dff40baa3f49d52f5347a
+    - path: output/ataqv/html/fonts/fontawesome-webfont.ttf
+      md5sum: fb650aaf10736ffb9c4173079616bf01
+    - path: output/ataqv/html/fonts/fontawesome-webfont.woff
+      md5sum: 891e3f340c1126b4c7c142e5f6e86816
+    - path: output/ataqv/html/fonts/fontawesome-webfont.woff2
+      md5sum: 926c93d201fe51c8f351e858468980c3
+    - path: output/ataqv/html/fonts/sourcesanspro-regular.woff
+      md5sum: f7bd788f18b8c4bb93dd37d140348e1e
+    - path: output/ataqv/html/fonts/sourcesanspro-regularit.woff
+      md5sum: c3638b17f4fd76dae12fe2ae14571e57
+    - path: output/ataqv/html/fonts/sourcesanspro-semibold.woff
+      md5sum: e7fc8925d9364e9d177d9e1d08bb1855
+    - path: output/ataqv/html/fonts/sourcesanspro-semiboldit.woff
+      md5sum: f1d255aa459786dfc6aa2e488ac01245
+    - path: output/ataqv/html/index.html
+      md5sum: bf7747be761e56ad7c54c842ac88461a
+    - path: output/ataqv/html/js/ataqv.js
+      md5sum: feb291b7839e9e43ed304565e3a605d9
+    - path: output/ataqv/html/js/configuration.js
+      md5sum: 073bc07f1371e28a97098f8b10469ae4
+    - path: output/ataqv/html/js/d3.min.js
+      md5sum: db69fb2626a71a286ee772d673138aca
+    - path: output/ataqv/html/js/datatables.min.js
+      md5sum: e369b872620dadb05e4eb555b81f9112
+    - path: output/ataqv/html/js/jszip.min.js
+      md5sum: 09e492cb492ffa75484bbe10f1f721d1
+    - path: output/ataqv/test.ataqv.json
+      contains:
+        - '"properly_paired_and_mapped_reads": 192,'