Add IDR module

modules/idr/functions.nf

@@ -0,0 +1,78 @@
+//
+//  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()
+}
+
+//
+// Extract name of module from process name using $task.process
+//
+def getProcessName(task_process) {
+    return task_process.tokenize(':')[-1]
+}
+
+//
+// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
+//
+def initOptions(Map args) {
+    def Map options = [:]
+    options.args            = args.args ?: ''
+    options.args2           = args.args2 ?: ''
+    options.args3           = args.args3 ?: ''
+    options.publish_by_meta = args.publish_by_meta ?: []
+    options.publish_dir     = args.publish_dir ?: ''
+    options.publish_files   = args.publish_files
+    options.suffix          = args.suffix ?: ''
+    return options
+}
+
+//
+// Tidy up and join elements of a list to return a path string
+//
+def getPathFromList(path_list) {
+    def paths = path_list.findAll { item -> !item?.trim().isEmpty() }      // Remove empty entries
+    paths     = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
+    return paths.join('/')
+}
+
+//
+// Function to save/publish module results
+//
+def saveFiles(Map args) {
+    def ioptions  = initOptions(args.options)
+    def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
+
+    // Do not publish versions.yml unless running from pytest workflow
+    if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
+        return null
+    }
+    if (ioptions.publish_by_meta) {
+        def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
+        for (key in key_list) {
+            if (args.meta && key instanceof String) {
+                def path = key
+                if (args.meta.containsKey(key)) {
+                    path = args.meta[key] instanceof Boolean ? "${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/idr/main.nf

@@ -0,0 +1,56 @@
+// Import generic module functions
+include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
+
+params.options = [:]
+options        = initOptions(params.options)
+
+process IDR {
+    tag "$prefix"
+    label 'process_low'
+    publishDir "${params.outdir}",
+        mode: params.publish_dir_mode,
+        saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:[:], publish_by_meta:[]) }
+
+    conda (params.enable_conda ? "bioconda::idr=2.0.4.2" : null)
+    if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
+        container "https://depot.galaxyproject.org/singularity/idr:2.0.4.2--py39hcbe4a3b_5"
+    } else {
+        container "quay.io/biocontainers/idr:2.0.4.2--py38h9af456f_5"
+    }
+
+    input:
+    path peaks
+    val peak_type
+    val prefix
+
+    output:
+    path "*idrValues.txt", emit: idr
+    path "*log.txt"      , emit: log
+    path "*.png"         , emit: png
+    path "versions.yml"  , emit: versions
+
+    script:
+    if (peaks.toList().size < 2) {
+        log.error "[ERROR] idr needs at least two replicates only one provided."
+    }
+    def peak_types = ['narrowPeak', 'broadPeak', 'bed']
+    if (!peak_types.contains(peak_type)) {
+        log.error "[ERROR] Invalid option: '${peak_type}'. Valid options for 'peak_type': ${peak_types.join(', ')}."
+    }
+    def idr_vals = prefix ? "${prefix}.idrValues.txt" : "idrValues.txt"
+    def log_file = prefix ? "${prefix}.log.txt" : "log.txt"
+    """
+    idr \\
+        --samples $peaks \\
+        --input-file-type $peak_type \\
+        --output-file $idr_vals \\
+        --log-output-file $log_file \\
+        --plot \\
+        $options.args
+
+    cat <<-END_VERSIONS > versions.yml
+    ${getProcessName(task.process)}:
+        ${getSoftwareName(task.process)}: \$(echo \$(idr --version 2>&1) | sed 's/^.*IDR //; s/ .*\$//')
+    END_VERSIONS
+    """
+}

modules/idr/meta.yml

@@ -0,0 +1,53 @@
+name: idr
+description: |
+  Measures reproducibility of ChIP-seq, ATAC-seq peaks using IDR (Irreproducible
+  Discovery Rate)
+keywords:
+  - IDR
+  - peaks
+  - ChIP-seq
+  - ATAC-seq
+tools:
+  - idr:
+      description: |
+        The IDR (Irreproducible Discovery Rate) framework is a unified approach
+        to measure the reproducibility of findings identified from replicate
+        experiments and provide highly stable thresholds based on reproducibility.
+      homepage: None
+      documentation: None
+      tool_dev_url: https://github.com/kundajelab/idr
+      doi: ""
+      licence: ['GPL v2']
+input:
+  - peaks:
+      type: tuple of two files
+      description: BED, narrowPeak or broadPeak files of replicates
+      pattern: "*"
+  - peak_type:
+      type: value
+      description: Type of peak file
+      pattern: "{narrowPeak,broadPeak,bed}"
+  - prefix:
+      type: value
+      description: Prefix for output files
+output:
+  - versions:
+      type: file
+      description: File containing software versions
+      pattern: "versions.yml"
+  - idr:
+      type: file
+      description: Text file containing IDR values
+      pattern: "*.{txt}"
+  - log:
+      type: file
+      description: Log file
+      pattern: "*.{txt}"
+  - png:
+      type: file
+      description: Plot generated by idr
+      pattern: "*{.png}"
+
+authors:
+  - "@drpatelh"
+  - "@joseespinosa"

tests/config/pytest_modules.yml

@@ -581,6 +581,10 @@ homer/makeucscfile:
   - modules/homer/makeucscfile/**
   - tests/modules/homer/makeucscfile/**
 
+idr:
+  - modules/idr/**
+  - tests/modules/idr/**
+
 iqtree:
   - modules/iqtree/**
   - tests/modules/iqtree/**

tests/config/test_data.config

@@ -199,6 +199,13 @@ params {
                 test2_genome_vcf_gz_tbi                        = "${test_data_dir}/genomics/homo_sapiens/illumina/gvcf/test2.genome.vcf.gz.tbi"
                 test2_genome_vcf_idx                           = "${test_data_dir}/genomics/homo_sapiens/illumina/gvcf/test2.genome.vcf.idx"
 
+                test_broad_peaks                               = "${test_data_dir}/genomics/homo_sapiens/illumina/broadpeak/test.broadPeak"
+                test2_broad_peaks                              = "${test_data_dir}/genomics/homo_sapiens/illumina/broadpeak/test2.broadPeak"
+
+                test_narrow_peaks                              = "${test_data_dir}/genomics/homo_sapiens/illumina/narrowpeak/test.narrowPeak"
+                test2_narrow_peaks                             = "${test_data_dir}/genomics/homo_sapiens/illumina/narrowpeak/test2.narrowPeak"
+
+
                 test_10x_1_fastq_gz                           = "${test_data_dir}/genomics/homo_sapiens/illumina/10xgenomics/test.10x_1.fastq.gz"
                 test_10x_2_fastq_gz                           = "${test_data_dir}/genomics/homo_sapiens/illumina/10xgenomics/test.10x_2.fastq.gz"
 

tests/modules/idr/main.nf

@@ -0,0 +1,57 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { IDR } from '../../../modules/idr/main.nf' addParams( options: [:] )
+
+myFile = file('http://jordan.biology.gatech.edu/page/software/broadpeak/downloads/H3K27me3.bed', checkIfExists: true)
+myFile.copyTo('peak_test')
+
+workflow test_idr_narrowpeak {
+
+    input = [
+                file(params.test_data['homo_sapiens']['illumina']['test_narrow_peaks'], checkIfExists: true),
+                file(params.test_data['homo_sapiens']['illumina']['test2_narrow_peaks'], checkIfExists: true)
+            ]
+
+    IDR ( input, 'narrowPeak', 'test' )
+}
+
+workflow test_idr_broadpeak {
+
+    input = [
+                file(params.test_data['homo_sapiens']['illumina']['test_broad_peaks'], checkIfExists: true),
+                file(params.test_data['homo_sapiens']['illumina']['test2_broad_peaks'], checkIfExists: true)
+            ]
+
+    IDR ( input, 'broadPeak', 'test' )
+}
+
+workflow test_idr_noprefix {
+
+    input = [
+                file(params.test_data['homo_sapiens']['illumina']['test_narrow_peaks'], checkIfExists: true),
+                file(params.test_data['homo_sapiens']['illumina']['test2_narrow_peaks'], checkIfExists: true)
+    ]
+
+    IDR ( input, 'narrowPeak', '' )
+}
+
+// workflow test_idr_bed {
+
+//     // Also tried with these two replicates in bed format from this course
+//     // (http://jvanheld.github.io/cisreg_course/chip-seq/practical/annotation.html) and did not work
+//     // http://pedagogix-tagc.univ-mrs.fr/courses/data/ngs/td_chip_seq/all/siGATA_ER_E2_r1_SRX176857_peaks.bed
+//     // http://pedagogix-tagc.univ-mrs.fr/courses/data/ngs/td_chip_seq/all/siGATA_ER_E2_r2_SRX176859_peaks.bed
+
+//     input = [
+//         //Does not work with the data in test-datasets
+//         // file(params.test_data['sarscov2']['genome']['test_bed'], checkIfExists: true),
+//         // file(params.test_data['sarscov2']['genome']['test2_bed'], checkIfExists: true)
+//         // Also tried to see weather it swallow the same file as narrow and broad mode, but it does not
+//         // file('https://raw.githubusercontent.com/kundajelab/idr/master/tests/data/peak1', checkIfExists: true),
+//         // file('https://raw.githubusercontent.com/kundajelab/idr/master/tests/data/peak2', checkIfExists: true)
+//     ]
+
+//     IDR ( input, 'bed', 'test' )
+// }

tests/modules/idr/test.yml

@@ -0,0 +1,35 @@
+- name: idr test_idr_narrowpeak
+  command: nextflow run tests/modules/idr -entry test_idr_narrowpeak -c tests/config/nextflow.config
+  tags:
+    - idr
+  files:
+    - path: output/idr/test.idrValues.txt
+      md5sum: 09be837cc6abbc3eb5958b74802eea55
+    - path: output/idr/test.idrValues.txt.png
+      md5sum: 4a7143ccc0ccadb37c2317bf626e6d96
+    - path: output/idr/test.log.txt
+      md5sum: 6443507ac66b9d3b64bc56b78328083e
+
+- name: idr test_idr_broadpeak
+  command: nextflow run tests/modules/idr -entry test_idr_broadpeak -c tests/config/nextflow.config
+  tags:
+    - idr
+  files:
+    - path: output/idr/test.idrValues.txt
+      md5sum: 387441c716815e4caec3e70a2cc11a4a
+    - path: output/idr/test.idrValues.txt.png
+      md5sum: 7204083ca5b920b4215a5991c12cb4e7
+    - path: output/idr/test.log.txt
+      md5sum: e6917133112b5cec135c182ffac19237
+
+- name: idr test_idr_noprefix
+  command: nextflow run tests/modules/idr -entry test_idr_noprefix -c tests/config/nextflow.config
+  tags:
+    - idr
+  files:
+    - path: output/idr/idrValues.txt
+      md5sum: 09be837cc6abbc3eb5958b74802eea55
+    - path: output/idr/idrValues.txt.png
+      md5sum: 4a7143ccc0ccadb37c2317bf626e6d96
+    - path: output/idr/log.txt
+      md5sum: 6443507ac66b9d3b64bc56b78328083e