Homer Modules (#75)

* feat(homer): Add initial makeTagDirectory

* feat(homer): Add initial findPeaks module

* feat(homer): Update with new options

See 1d30e2c21a

* fix(homer): Correct findpeaks process name

* fix(homer): Takes a bam file instead of bed

* feat(homer): Add initial makeTagDirectory test

* fix(homer): Hardcode genome and configureHomer

I'd like to modularize configureHomer, but I need to figure out how
exactly the genomes work.

* fix(homer): bam => bed

Bam requires samtools to be present, which it's not in this docker image

* feat(homer): Add initial configureHomer script

* ci(homer): Add initial test

* test(homer): Reproducible configuration workaround

- I can't run both tests(one file and two files) at the same time because it breaks
- I can't copy the genome stuff from the configurehomer module because it's read only
- So I can't make the makeTagDirectory module depend on configureHomer

* test(homer): Add placeholder annotatepeaks

The required inputs are necessarily required for all workflows from what
I've used, but I'll need to look at the actual docs

* test(homer): Add missing B.bed

* test(homer): Rename two => groseq

Then all of the various workflows that homer provides can be e2e tested

* feat(homer): Add initial makeUCSCfile module

* test(homer): Add start to makeUCSCfile testing

* chore(homer): Add various cleanups

* test(homer): Rewrite annotatepeaks

Not passing yet

* test(homer): Rewrite configurehomer

* test(homer): Rewrite findpeaks

Still failing

* test(homer): Rewrite makeucscfile

Not passing yet

* test(homer): Rewrite maketagdirectory

All homer modules now follow the new structure. Time to make them pass.

* test(homer): Fix typo for workflow name

* fix(homer): Use correct container

* fix(homer): Accept fasta in maketagdirectory

Apparently all of the homer stuff can just take any old fasta and you
don't need to configure the genome ahead of time with configureHomer

* test(homer): makeTagDirectory passes now

* fix(homer): Update containers in makeucscfile

* test(homer): Rewrite makeucscfile

Takes input from maketagdirectory which is how the module should be used

* fix(homer): Update makeUCSCFile bedgraph path

* test(homer): Update makeucscfile expected output

* fix(homer): Update containers in findpeaks

* fix(homer): Change findpeaks args

The user is just going to have to know what they're doing for now

* test(homer): findPeaks rewrite with tagDir input

* test(homer): Update expected files for findPeaks

And bump filters

* style: Appease editorconfig

* ci: Remove old workflow

* tests(homer): Add md5sums

* test(homer): Add meta test

* style(homer): Capitalize HOMER

* docs(homer): Add maketagdirectory meta.yml

* docs(homer): Add makeucscfile meta.yml

* docs(homer): Add findpeaks meta.yml

* test(homer): Update to new test data standards

* chore: Remove stuff that got revived in the rebase

* chore: software => modules

* test(homer): Update tags

* test(homer): Update annotatepeaks

* ci: Fix uploading of artifacts

GitHub actions doesn't like the / in the tags

* test(homer): Remove annotate md5sum

This is failing and breaking new tests

* test(homer): Use bams instead of beds

* test(homer): Fix meta maketagdirectory

* test(homer): Fix input in all tests

* test(homer): Move back to bed files

Forgot samtools isn't present

* chore(homer): Add TODOs for tests

* test(homer): Add bed format arg

* test(homer): Update md5sums

* test(homer): Fix tags tsvs

* style(homer): Appease nf-core linting

* docs(homer): Be in line with what is in the main.nf file

Co-authored-by: Kevin Menden <kevin.menden@live.com>

Co-authored-by: Kevin Menden <kevin.menden@live.com>

.github/workflows/pytest-workflow.yml

@@ -95,7 +95,7 @@ jobs:
         if: failure()
         uses: actions/upload-artifact@v2
         with:
-          name: logs-${{ matrix.tags }}-${{ matrix.profile }}-${{ matrix.nxf_version }}
+          name: logs-${{ matrix.profile }}-${{ matrix.nxf_version }}
           path: |
             /home/runner/pytest_workflow_*/*/.nextflow.log
             /home/runner/pytest_workflow_*/*/log.out

modules/homer/annotatepeaks/meta.yml

@@ -1,11 +1,11 @@
 name: homer_annotatepeaks
-description: Annotate peaks with homer
+description: Annotate peaks with HOMER suite
 keywords:
   - annotations
   - peaks
   - bed
 tools:
-  - cuatadapt:
+  - homer:
       description: |
         HOMER (Hypergeometric Optimization of Motif EnRichment) is a suite of tools for Motif Discovery and next-gen sequencing analysis.
       documentation: http://homer.ucsd.edu/homer/

modules/homer/findpeaks/functions.nf

@@ -0,0 +1,68 @@
+//
+//  Utility functions used in nf-core DSL2 module files
+//
+
+//
+// Extract name of software tool from process name using $task.process
+//
+def getSoftwareName(task_process) {
+    return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
+}
+
+//
+// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
+//
+def initOptions(Map args) {
+    def Map options = [:]
+    options.args            = args.args ?: ''
+    options.args2           = args.args2 ?: ''
+    options.args3           = args.args3 ?: ''
+    options.publish_by_meta = args.publish_by_meta ?: []
+    options.publish_dir     = args.publish_dir ?: ''
+    options.publish_files   = args.publish_files
+    options.suffix          = args.suffix ?: ''
+    return options
+}
+
+//
+// Tidy up and join elements of a list to return a path string
+//
+def getPathFromList(path_list) {
+    def paths = path_list.findAll { item -> !item?.trim().isEmpty() }      // Remove empty entries
+    paths     = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
+    return paths.join('/')
+}
+
+//
+// Function to save/publish module results
+//
+def saveFiles(Map args) {
+    if (!args.filename.endsWith('.version.txt')) {
+        def ioptions  = initOptions(args.options)
+        def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
+        if (ioptions.publish_by_meta) {
+            def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
+            for (key in key_list) {
+                if (args.meta && key instanceof String) {
+                    def path = key
+                    if (args.meta.containsKey(key)) {
+                        path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
+                    }
+                    path = path instanceof String ? path : ''
+                    path_list.add(path)
+                }
+            }
+        }
+        if (ioptions.publish_files instanceof Map) {
+            for (ext in ioptions.publish_files) {
+                if (args.filename.endsWith(ext.key)) {
+                    def ext_list = path_list.collect()
+                    ext_list.add(ext.value)
+                    return "${getPathFromList(ext_list)}/$args.filename"
+                }
+            }
+        } else if (ioptions.publish_files == null) {
+            return "${getPathFromList(path_list)}/$args.filename"
+        }
+    }
+}

modules/homer/findpeaks/main.nf

@@ -0,0 +1,42 @@
+// Import generic module functions
+include { initOptions; saveFiles; getSoftwareName } from './functions'
+
+params.options = [:]
+def options    = initOptions(params.options)
+
+def VERSION = '4.11'
+
+process HOMER_FINDPEAKS {
+    tag "$meta.id"
+    label 'process_medium'
+    publishDir "${params.outdir}",
+        mode: params.publish_dir_mode,
+        saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
+
+    conda (params.enable_conda ? "bioconda::homer=4.11=pl526hc9558a2_3" : null)
+    if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
+        container "https://depot.galaxyproject.org/singularity/homer:4.11--pl526hc9558a2_3"
+    } else {
+        container "quay.io/biocontainers/homer:4.11--pl526hc9558a2_3"
+    }
+
+    input:
+    tuple val(meta), path(tagDir)
+
+    output:
+    tuple val(meta), path("*peaks.txt"), emit: txt
+    path  "*.version.txt"              , emit: version
+
+    script:
+    def software = getSoftwareName(task.process)
+    def prefix   = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
+    """
+
+    findPeaks \\
+        $tagDir \\
+        $options.args \\
+        -o ${prefix}.peaks.txt
+
+    echo $VERSION > ${software}.version.txt
+    """
+}

modules/homer/findpeaks/meta.yml

@@ -0,0 +1,37 @@
+name: homer_findpeaks
+description: Find peaks with HOMER suite
+keywords:
+  - annotations
+  - peaks
+tools:
+  - homer:
+      description: |
+        HOMER (Hypergeometric Optimization of Motif EnRichment) is a suite of tools for Motif Discovery and next-gen sequencing analysis.
+      documentation: http://homer.ucsd.edu/homer/
+      doi: 10.1016/j.molcel.2010.05.004.
+input:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  - tagDir:
+      type: directory
+      description: "The 'Tag Directory'"
+      pattern: "tagDir"
+output:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  - peaks:
+      type: file
+      description: The found peaks
+      pattern: "*peaks.txt"
+  - version:
+      type: file
+      description: File containing software version
+      pattern: "*.{version.txt}"
+authors:
+  - "@EMiller88"

modules/homer/maketagdirectory/functions.nf

@@ -0,0 +1,68 @@
+//
+//  Utility functions used in nf-core DSL2 module files
+//
+
+//
+// Extract name of software tool from process name using $task.process
+//
+def getSoftwareName(task_process) {
+    return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
+}
+
+//
+// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
+//
+def initOptions(Map args) {
+    def Map options = [:]
+    options.args            = args.args ?: ''
+    options.args2           = args.args2 ?: ''
+    options.args3           = args.args3 ?: ''
+    options.publish_by_meta = args.publish_by_meta ?: []
+    options.publish_dir     = args.publish_dir ?: ''
+    options.publish_files   = args.publish_files
+    options.suffix          = args.suffix ?: ''
+    return options
+}
+
+//
+// Tidy up and join elements of a list to return a path string
+//
+def getPathFromList(path_list) {
+    def paths = path_list.findAll { item -> !item?.trim().isEmpty() }      // Remove empty entries
+    paths     = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
+    return paths.join('/')
+}
+
+//
+// Function to save/publish module results
+//
+def saveFiles(Map args) {
+    if (!args.filename.endsWith('.version.txt')) {
+        def ioptions  = initOptions(args.options)
+        def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
+        if (ioptions.publish_by_meta) {
+            def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
+            for (key in key_list) {
+                if (args.meta && key instanceof String) {
+                    def path = key
+                    if (args.meta.containsKey(key)) {
+                        path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
+                    }
+                    path = path instanceof String ? path : ''
+                    path_list.add(path)
+                }
+            }
+        }
+        if (ioptions.publish_files instanceof Map) {
+            for (ext in ioptions.publish_files) {
+                if (args.filename.endsWith(ext.key)) {
+                    def ext_list = path_list.collect()
+                    ext_list.add(ext.value)
+                    return "${getPathFromList(ext_list)}/$args.filename"
+                }
+            }
+        } else if (ioptions.publish_files == null) {
+            return "${getPathFromList(path_list)}/$args.filename"
+        }
+    }
+}

modules/homer/maketagdirectory/main.nf

@@ -0,0 +1,43 @@
+// Import generic module functions
+include { initOptions; saveFiles; getSoftwareName } from './functions'
+
+params.options = [:]
+def options    = initOptions(params.options)
+
+def VERSION = '4.11'
+
+process HOMER_MAKETAGDIRECTORY {
+    tag "$meta.id"
+    label 'process_medium'
+    publishDir "${params.outdir}",
+        mode: params.publish_dir_mode,
+        saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
+
+    conda (params.enable_conda ? "bioconda::homer=4.11=pl526hc9558a2_3" : null)
+    if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
+        container "https://depot.galaxyproject.org/singularity/homer:4.11--pl526hc9558a2_3"
+    } else {
+        container "quay.io/biocontainers/homer:4.11--pl526hc9558a2_3"
+    }
+
+    input:
+    tuple val(meta), path(bed)
+    path fasta
+
+    output:
+    tuple val(meta), path("tag_dir"), emit: tagdir
+    path  "*.version.txt"            , emit: version
+
+    script:
+    def software = getSoftwareName(task.process)
+    def prefix   = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
+    """
+    makeTagDirectory \\
+        tag_dir \\
+        $options.args \\
+        $bed \\
+        -genome $fasta
+
+    echo $VERSION > ${software}.version.txt
+    """
+}

modules/homer/maketagdirectory/meta.yml

@@ -0,0 +1,41 @@
+name: homer_maketagdirectory
+description: Create a tag directory with the HOMER suite
+keywords:
+  - peaks
+  - bed
+tools:
+  - homer:
+      description: |
+        HOMER (Hypergeometric Optimization of Motif EnRichment) is a suite of tools for Motif Discovery and next-gen sequencing analysis.
+      documentation: http://homer.ucsd.edu/homer/
+      doi: 10.1016/j.molcel.2010.05.004.
+input:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  - bed:
+      type: file
+      description: The peak files in bed format
+      pattern: "*.bed"
+  - fasta:
+      type: file
+      description: Fasta file of reference genome
+      pattern: "*.fasta"
+output:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  - tag_dir:
+      type: directory
+      description: The "Tag Directory"
+      pattern: "tag_dir"
+  - version:
+      type: file
+      description: File containing software version
+      pattern: "*.{version.txt}"
+authors:
+  - "@EMiller88"

modules/homer/makeucscfile/functions.nf

@@ -0,0 +1,68 @@
+//
+//  Utility functions used in nf-core DSL2 module files
+//
+
+//
+// Extract name of software tool from process name using $task.process
+//
+def getSoftwareName(task_process) {
+    return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
+}
+
+//
+// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
+//
+def initOptions(Map args) {
+    def Map options = [:]
+    options.args            = args.args ?: ''
+    options.args2           = args.args2 ?: ''
+    options.args3           = args.args3 ?: ''
+    options.publish_by_meta = args.publish_by_meta ?: []
+    options.publish_dir     = args.publish_dir ?: ''
+    options.publish_files   = args.publish_files
+    options.suffix          = args.suffix ?: ''
+    return options
+}
+
+//
+// Tidy up and join elements of a list to return a path string
+//
+def getPathFromList(path_list) {
+    def paths = path_list.findAll { item -> !item?.trim().isEmpty() }      // Remove empty entries
+    paths     = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
+    return paths.join('/')
+}
+
+//
+// Function to save/publish module results
+//
+def saveFiles(Map args) {
+    if (!args.filename.endsWith('.version.txt')) {
+        def ioptions  = initOptions(args.options)
+        def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
+        if (ioptions.publish_by_meta) {
+            def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
+            for (key in key_list) {
+                if (args.meta && key instanceof String) {
+                    def path = key
+                    if (args.meta.containsKey(key)) {
+                        path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
+                    }
+                    path = path instanceof String ? path : ''
+                    path_list.add(path)
+                }
+            }
+        }
+        if (ioptions.publish_files instanceof Map) {
+            for (ext in ioptions.publish_files) {
+                if (args.filename.endsWith(ext.key)) {
+                    def ext_list = path_list.collect()
+                    ext_list.add(ext.value)
+                    return "${getPathFromList(ext_list)}/$args.filename"
+                }
+            }
+        } else if (ioptions.publish_files == null) {
+            return "${getPathFromList(path_list)}/$args.filename"
+        }
+    }
+}

modules/homer/makeucscfile/main.nf

@@ -0,0 +1,41 @@
+// Import generic module functions
+include { initOptions; saveFiles; getSoftwareName } from './functions'
+
+params.options = [:]
+def options    = initOptions(params.options)
+
+def VERSION = '4.11'
+
+process HOMER_MAKEUCSCFILE {
+    tag "$meta.id"
+    label 'process_medium'
+    publishDir "${params.outdir}",
+        mode: params.publish_dir_mode,
+        saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
+
+    conda (params.enable_conda ? "bioconda::homer=4.11=pl526hc9558a2_3" : null)
+    if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
+        container "https://depot.galaxyproject.org/singularity/homer:4.11--pl526hc9558a2_3"
+    } else {
+        container "quay.io/biocontainers/homer:4.11--pl526hc9558a2_3"
+    }
+
+    input:
+    tuple val(meta), path(tagDir)
+
+    output:
+    tuple val(meta), path("tag_dir/*ucsc.bedGraph.gz"), emit: bedGraph
+    path  "*.version.txt"                             , emit: version
+
+    script:
+    def software = getSoftwareName(task.process)
+    def prefix   = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
+    """
+    makeUCSCfile \\
+        $tagDir \\
+        -o auto
+        $options.args
+
+    echo $VERSION > ${software}.version.txt
+    """
+}

modules/homer/makeucscfile/meta.yml

@@ -0,0 +1,38 @@
+name: homer_makeucscfile
+description: Create a UCSC bed graph with the HOMER suite
+keywords:
+  - peaks
+  - bed
+  - bedGraph
+tools:
+  - homer:
+      description: |
+        HOMER (Hypergeometric Optimization of Motif EnRichment) is a suite of tools for Motif Discovery and next-gen sequencing analysis.
+      documentation: http://homer.ucsd.edu/homer/
+      doi: 10.1016/j.molcel.2010.05.004.
+input:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  - tagDir:
+      type: directory
+      description: "The 'Tag Directory'"
+      pattern: "tagDir"
+output:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  - bedGraph:
+      type: file
+      description: The UCSC bed graph
+      pattern: "tag_dir/*ucsc.bedGraph.gz"
+  - version:
+      type: file
+      description: File containing software version
+      pattern: "*.{version.txt}"
+authors:
+  - "@EMiller88"

tests/config/pytest_modules.yml

@@ -421,6 +421,18 @@ homer/annotatepeaks:
   - modules/homer/annotatepeaks/**
   - tests/modules/homer/annotatepeaks/**
 
+homer/findpeaks:
+  - modules/homer/findpeaks/**
+  - tests/modules/homer/findpeaks/**
+
+homer/maketagdirectory:
+  - modules/homer/maketagdirectory/**
+  - tests/modules/homer/maketagdirectory/**
+
+homer/makeucscfile:
+  - modules/homer/makeucscfile/**
+  - tests/modules/homer/makeucscfile/**
+
 iqtree:
   - modules/iqtree/**
   - tests/modules/iqtree/**

tests/modules/homer/findpeaks/main.nf

@@ -0,0 +1,17 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { HOMER_MAKETAGDIRECTORY } from '../../../../modules/homer/maketagdirectory/main.nf' addParams( options: [args: '-format bed'] )
+include { HOMER_FINDPEAKS } from '../../../../modules/homer/findpeaks/main.nf' addParams( options: [args: '-style factor'] )
+
+workflow test_homer_findpeaks {
+    input = [[id:'test'],
+             [file(params.test_data['sarscov2']['genome']['test_bed'], checkIfExists: true),
+              file(params.test_data['sarscov2']['genome']['test2_bed'], checkIfExists: true)]]
+    fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
+
+    HOMER_MAKETAGDIRECTORY (input, fasta)
+    HOMER_FINDPEAKS ( HOMER_MAKETAGDIRECTORY.out.tagdir )
+}
+

tests/modules/homer/findpeaks/test.yml

@@ -0,0 +1,8 @@
+- name: homer findpeaks
+  command: nextflow run ./tests/modules/homer/findpeaks -entry test_homer_findpeaks -c tests/config/nextflow.config
+  tags:
+    - homer
+    - homer/findpeaks
+  files:
+    - path: output/homer/test.peaks.txt
+      md5sum: f75ac1fea67f1e307a1ad4d059a9b6cc

tests/modules/homer/maketagdirectory/main.nf

@@ -0,0 +1,32 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { HOMER_MAKETAGDIRECTORY } from '../../../../modules/homer/maketagdirectory/main.nf' addParams( options: [args: '-format bed'] )
+
+workflow test_homer_maketagdirectory {
+    input = [[id:'test'],
+             [file(params.test_data['sarscov2']['genome']['test_bed'], checkIfExists: true),
+              file(params.test_data['sarscov2']['genome']['test2_bed'], checkIfExists: true)]]
+    fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
+
+    HOMER_MAKETAGDIRECTORY (input, fasta)
+}
+
+
+workflow test_homer_meta_maketagdirectory {
+    input =
+        [[[ id:'test1'],
+          [file(params.test_data['sarscov2']['genome']['test_bed'], checkIfExists: true)]],
+         [[ id:'test2'],
+          [file(params.test_data['sarscov2']['genome']['test2_bed'], checkIfExists: true)]]]
+
+    fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
+
+    meta_input = [[id: 'meta_test']] + [ input.collect{it[1]}.flatten() ]
+
+    HOMER_MAKETAGDIRECTORY (meta_input, fasta)
+}
+
+// TODO Make a failing bam test
+// TODO Make a pass bam test that feeds the bam through samtools first

tests/modules/homer/maketagdirectory/test.yml

@@ -0,0 +1,33 @@
+- name: homer maketagdirectory
+  command: nextflow run ./tests/modules/homer/maketagdirectory -entry test_homer_maketagdirectory -c tests/config/nextflow.config
+  tags:
+    - homer
+    - homer/maketagdirectory
+  files:
+    - path: output/homer/tag_dir/MT192765.1.tags.tsv
+      md5sum: e29522171ca2169b57396495f8b97485
+    - path: output/homer/tag_dir/tagAutocorrelation.txt
+      md5sum: 62b107c4971b94126fb89a0bc2800455
+    - path: output/homer/tag_dir/tagCountDistribution.txt
+      md5sum: fd4ee7ce7c5dfd7c9d739534b8180578
+    - path: output/homer/tag_dir/tagInfo.txt
+      md5sum: 816baa642c946f8284eaa465638e9abb
+    - path: output/homer/tag_dir/tagLengthDistribution.txt
+      md5sum: e5aa2b9843ca9c04ace297280aed6af4
+
+- name: homer meta maketagdirectory
+  command: nextflow run ./tests/modules/homer/maketagdirectory -entry test_homer_meta_maketagdirectory -c tests/config/nextflow.config
+  tags:
+    - homer
+    - homer/maketagdirectory
+  files:
+    - path: output/homer/tag_dir/MT192765.1.tags.tsv
+      md5sum: e29522171ca2169b57396495f8b97485
+    - path: output/homer/tag_dir/tagAutocorrelation.txt
+      md5sum: 62b107c4971b94126fb89a0bc2800455
+    - path: output/homer/tag_dir/tagCountDistribution.txt
+      md5sum: fd4ee7ce7c5dfd7c9d739534b8180578
+    - path: output/homer/tag_dir/tagInfo.txt
+      md5sum: 816baa642c946f8284eaa465638e9abb
+    - path: output/homer/tag_dir/tagLengthDistribution.txt
+      md5sum: e5aa2b9843ca9c04ace297280aed6af4

tests/modules/homer/makeucscfile/main.nf

@@ -0,0 +1,17 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { HOMER_MAKETAGDIRECTORY } from '../../../../modules/homer/maketagdirectory/main.nf' addParams( options: [args: '-format bed'] )
+include { HOMER_MAKEUCSCFILE } from '../../../../modules/homer/makeucscfile/main.nf' addParams( options: [:] )
+
+workflow test_homer_makeucscfile {
+    input = [[id:'test'],
+             [file(params.test_data['sarscov2']['genome']['test_bed'], checkIfExists: true),
+              file(params.test_data['sarscov2']['genome']['test2_bed'], checkIfExists: true)]]
+    fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
+
+    HOMER_MAKETAGDIRECTORY (input, fasta)
+    HOMER_MAKEUCSCFILE ( HOMER_MAKETAGDIRECTORY.out.tagdir )
+}
+

tests/modules/homer/makeucscfile/test.yml

@@ -0,0 +1,7 @@
+- name: homer makeucscfile
+  command: nextflow run ./tests/modules/homer/makeucscfile -entry test_homer_makeucscfile -c tests/config/nextflow.config
+  tags:
+    - homer
+    - homer/makeucscfile
+  files:
+    - path: output/homer/tag_dir/tag_dir.ucsc.bedGraph.gz