module: picard filtersamreads (#602)

* Start work filtersamreads

* Refactored to allow optional input

* Use proper readlist test data

* Remove typo

* Fix if else condition

* Remove debugging code

* Fix container URLs

* Add required input specification meta

* Cleanup

* Apply suggestions from code review

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>

* Fix suffixing

* Additional formatting tweaks

* Update modules/picard/filtersamreads/main.nf

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>

* Update modules/picard/filtersamreads/meta.yml

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>

modules/picard/filtersamreads/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/picard/filtersamreads/main.nf

@@ -0,0 +1,65 @@
+// Import generic module functions
+include { initOptions; saveFiles; getSoftwareName } from './functions'
+
+params.options = [:]
+options        = initOptions(params.options)
+
+process PICARD_FILTERSAMREADS {
+    tag "$meta.id"
+    label 'process_low'
+    publishDir "${params.outdir}",
+        mode: params.publish_dir_mode,
+        saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
+
+    conda (params.enable_conda ? "bioconda::picard=2.25.6" : null)
+    if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
+        container "https://depot.galaxyproject.org/singularity/picard:2.25.6--hdfd78af_0"
+    } else {
+        container "quay.io/biocontainers/picard:2.25.6--hdfd78af_0"
+    }
+
+    input:
+    tuple val(meta), path(bam)
+    val filter
+    path readlist
+
+    output:
+    tuple val(meta), path("*.bam"), emit: bam
+    path "*.version.txt"          , emit: version
+
+    script:
+    def software = getSoftwareName(task.process)
+    def prefix   = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
+    def avail_mem = 3
+    if (!task.memory) {
+        log.info '[Picard FilterSamReads] Available memory not known - defaulting to 3GB. Specify process memory requirements to change this.'
+    } else {
+        avail_mem = task.memory.giga
+    }
+    if ( filter == 'includeAligned' || filter == 'excludeAligned' ) {
+        """
+        picard \\
+            FilterSamReads \\
+            -Xmx${avail_mem}g \\
+            --INPUT $bam \\
+            --OUTPUT ${prefix}.bam \\
+            --FILTER $filter \\
+            $options.args
+
+        echo \$(picard FilterSamReads --version 2>&1) | grep -o 'Version:.*' | cut -f2- -d: > ${software}.version.txt
+        """
+    } else if ( filter == 'includeReadList' || filter == 'excludeReadList' ) {
+        """
+        picard \\
+            FilterSamReads \\
+            -Xmx${avail_mem}g \\
+            --INPUT $bam \\
+            --OUTPUT ${prefix}.bam \\
+            --FILTER $filter \\
+            --READ_LIST_FILE $readlist \\
+            $options.args
+
+        echo \$(picard FilterSamReads --version 2>&1) | grep -o 'Version:.*' | cut -f2- -d: > ${software}.version.txt
+        """
+    }
+}

modules/picard/filtersamreads/meta.yml

@@ -0,0 +1,51 @@
+name: picard_filtersamreads
+description: Filters SAM/BAM files to include/exclude either aligned/unaligned reads or based on a read list
+keywords:
+  - bam
+  - filter
+tools:
+  - picard:
+      description: |
+          A set of command line tools (in Java) for manipulating high-throughput sequencing (HTS)
+          data and formats such as SAM/BAM/CRAM and VCF.
+      homepage: https://broadinstitute.github.io/picard/
+      documentation: https://broadinstitute.github.io/picard/
+      tool_dev_url: https://github.com/broadinstitute/picard
+      doi: ""
+      licence: ['MIT']
+
+input:
+    - meta:
+        type: map
+        description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test', single_end:false ]
+    - bam:
+        type: file
+        description: List of BAM files. If filtering without read list must be sorted by queryname with picard sortsam
+        pattern: "*.{bam}"
+    - filter:
+        type: value
+        description: Picard filter type
+        pattern: "includeAligned|excludeAligned|includeReadList|excludeReadList"
+    - readlist:
+        type: file
+        description: Optional text file containing reads IDs to include or exclude
+
+output:
+    - meta:
+        type: map
+        description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test', single_end:false ]
+    - bam:
+        type: file
+        description: Filtered BAM file
+        pattern: "*.{bam}"
+    - version:
+        type: file
+        description: File containing software version
+        pattern: "*.{version.txt}"
+
+authors:
+  - "@jfy133"

tests/config/pytest_modules.yml

@@ -559,6 +559,10 @@ picard/collectwgsmetrics:
   - modules/picard/collectwgsmetrics/**
   - tests/modules/picard/collectwgsmetrics/**
 
+picard/filtersamreads:
+  - modules/picard/filtersamreads/**
+  - tests/modules/picard/filtersamreads/**
+
 picard/markduplicates:
   - modules/picard/markduplicates/**
   - tests/modules/picard/markduplicates/**

tests/config/test_data.config

@@ -74,6 +74,8 @@ params {
                 scaffolds_fasta                                = "${test_data_dir}/genomics/sarscov2/illumina/fasta/scaffolds.fasta"
 
                 assembly_gfa                                   = "${test_data_dir}/genomics/sarscov2/illumina/gfa/assembly.gfa"
+
+                test_single_end_bam_readlist_txt               = "${test_data_dir}/genomics/sarscov2/illumina/picard/test.single_end.bam.readlist.txt"
             }
             'nanopore' {
                 test_sorted_bam                                = "${test_data_dir}/genomics/sarscov2/nanopore/bam/test.sorted.bam"

tests/modules/picard/filtersamreads/main.nf

@@ -0,0 +1,27 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { PICARD_SORTSAM        } from '../../../../modules/picard/sortsam/main.nf'        addParams( options: [suffix:'.sorted']   )
+include { PICARD_FILTERSAMREADS } from '../../../../modules/picard/filtersamreads/main.nf' addParams( options: [suffix:'.filtered'] )
+
+workflow test_picard_filtersamreads {
+
+    input = [ [ id:'test', single_end:false ], // meta map
+              file(params.test_data['sarscov2']['illumina']['test_single_end_bam'], checkIfExists: true) ]
+    sort_order = 'queryname'
+    filter = 'includeAligned'
+
+    PICARD_SORTSAM ( input, sort_order )
+    PICARD_FILTERSAMREADS ( PICARD_SORTSAM.out.bam, filter, [] )
+}
+
+workflow test_picard_filtersamreads_readlist {
+
+    input = [ [ id:'test', single_end:false ], // meta map
+              file(params.test_data['sarscov2']['illumina']['test_single_end_bam'], checkIfExists: true) ]
+    filter = 'includeReadList'
+    readlist = file(params.test_data['sarscov2']['illumina']['test_single_end_bam_readlist_txt'], checkIfExists: true)
+
+    PICARD_FILTERSAMREADS ( input, filter, readlist )
+}

tests/modules/picard/filtersamreads/test.yml

@@ -0,0 +1,18 @@
+- name: picard filtersamreads
+  command: nextflow run ./tests/modules/picard/filtersamreads -entry test_picard_filtersamreads -c tests/config/nextflow.config
+  tags:
+    - picard
+    - picard/filtersamreads
+  files:
+    - path: output/picard/test.filtered.bam
+      md5sum: b44a6ca04811a9470c7813c3c9465fd5
+
+
+- name: picard filtersamreads_readlist
+  command: nextflow run ./tests/modules/picard/filtersamreads -entry test_picard_filtersamreads_readlist -c tests/config/nextflow.config
+  tags:
+    - picard
+    - picard/filtersamreads
+  files:
+    - path: output/picard/test.filtered.bam
+      md5sum: 1e86b738b56f2c2b09f4cab52baf05c7