Add in OptiType (configbuilder, type) module(s) (#301)

* Adding in optitype prototype (To be worked on these days)

* I've tried my best 😆

* No idea

* Add in YML stuff

* Fix paths

* Ok, lets try this

* Adding proper options

* Replacec configbuilder thing

* Fix seq_type

* Adding human bam - sarscov doesnt work

* Fix a bunch of things

* -def

* Make this test run

* Fancy as fuck

* Update tests/software/optitype/test.yml

* Add proper tag

* Remove md5sums

Co-authored-by: Kevin Menden <kevin.menden@t-online.de>

software/optitype/functions.nf

@@ -0,0 +1,60 @@
+/*
+ * -----------------------------------------------------
+ *  Utility functions used in nf-core DSL2 module files
+ * -----------------------------------------------------
+ */
+
+/*
+ * Extract name of software tool from process name using $task.process
+ */
+def getSoftwareName(task_process) {
+    return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
+}
+
+/*
+ * Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
+ */
+def initOptions(Map args) {
+    def Map options = [:]
+    options.args          = args.args ?: ''
+    options.args2         = args.args2 ?: ''
+    options.args3         = args.args3 ?: ''
+    options.publish_by_id = args.publish_by_id ?: false
+    options.publish_dir   = args.publish_dir ?: ''
+    options.publish_files = args.publish_files
+    options.suffix        = args.suffix ?: ''
+    return options
+}
+
+/*
+ * Tidy up and join elements of a list to return a path string
+ */
+def getPathFromList(path_list) {
+    def paths = path_list.findAll { item -> !item?.trim().isEmpty() }  // Remove empty entries
+    paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
+    return paths.join('/')
+}
+
+/*
+ * Function to save/publish module results
+ */
+def saveFiles(Map args) {
+    if (!args.filename.endsWith('.version.txt')) {
+        def ioptions = initOptions(args.options)
+        def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
+        if (ioptions.publish_by_id) {
+            path_list.add(args.publish_id)
+        }
+        if (ioptions.publish_files instanceof Map) {
+            for (ext in ioptions.publish_files) {
+                if (args.filename.endsWith(ext.key)) {
+                    def ext_list = path_list.collect()
+                    ext_list.add(ext.value)
+                    return "${getPathFromList(ext_list)}/$args.filename"
+                }
+            }
+        } else if (ioptions.publish_files == null) {
+            return "${getPathFromList(path_list)}/$args.filename"
+        }
+    }
+}

software/optitype/main.nf

@@ -0,0 +1,53 @@
+// Import generic module functions
+include { initOptions; saveFiles; getSoftwareName } from './functions'
+
+params.options = [:]
+options        = initOptions(params.options)
+
+process OPTITYPE {
+    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), publish_id:meta.id) }
+
+    conda (params.enable_conda ? "bioconda::optitype=1.3.5" : null)
+    if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
+        container "https://depot.galaxyproject.org/singularity/optitype:1.3.5--0"
+    } else {
+        container "quay.io/biocontainers/optitype:1.3.5--0"
+    }
+
+    input:
+    tuple val(meta), path(bam)
+
+    output:
+    tuple val(meta), path("${prefix}"), emit: output
+    path "*.version.txt"              , emit: version
+
+    script:
+    def software = getSoftwareName(task.process)
+    prefix   = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
+
+    """
+    # Create a config for OptiType on a per sample basis with options.args2
+
+    #Doing it old school now
+    echo "[mapping]" > config.ini
+    echo "razers3=razers3" >> config.ini
+    echo "threads=$task.cpus" >> config.ini
+    echo "[ilp]" >> config.ini
+    echo "$options.args2" >> config.ini
+    echo "threads=1" >> config.ini
+    echo "[behavior]" >> config.ini
+    echo "deletebam=true" >> config.ini
+    echo "unpaired_weight=0" >> config.ini
+    echo "use_discordant=false" >> config.ini
+
+    # Run the actual OptiType typing with options.args
+    OptiTypePipeline.py -i ${bam} -c config.ini --${meta.seq_type} $options.args --prefix $prefix --outdir $prefix
+
+    #Couldn't find a nicer way of doing this
+    cat \$(which OptiTypePipeline.py) | grep -e "Version:" | sed -e "s/Version: //g" > ${software}.version.txt
+    """
+}

software/optitype/meta.yml

@@ -0,0 +1,46 @@
+name: optitype
+description: Perform HLA-I typing of sequencing data
+keywords:
+  - hla-typing
+  - ILP
+  - HLA-I
+tools:
+  - optitype:
+      description: Precision HLA typing from next-generation sequencing data
+      homepage: https://github.com/FRED-2/OptiType
+      documentation: https://github.com/FRED-2/OptiType
+      doi: "10.1093/bioinformatics/btu548"
+      licence: ['BSD']
+
+input:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  - bam:
+      type: file
+      description: BAM file
+      pattern: "*.{bam}"
+
+output:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', seq_type:'DNA' ]
+  - version:
+      type: file
+      description: File containing software version
+      pattern: "*.{version.txt}"
+  - output:
+      type: file
+      description: OptiType Results Folder
+      pattern: "${prefix}"
+  - pdf:
+      type: file
+      description: OptiType PDF Plots
+      pattern: "*.pdf"
+
+authors:
+  - "@apeltzer"

tests/config/pytest_software.yml

@@ -267,6 +267,10 @@ multiqc:
   - software/multiqc/**
   - tests/software/multiqc/**
 
+optitype:
+  - software/optitype/**
+  - tests/software/optitype/**
+
 pangolin:
   - software/pangolin/**
   - tests/software/pangolin/**
@@ -331,14 +335,14 @@ samtools_index:
   - software/samtools/index/**
   - tests/software/samtools/index/**
 
-samtools_mpileup:
-  - software/samtools/mpileup/**
-  - tests/software/samtools/mpileup/**
-
 samtools_merge:
   - software/samtools/merge/**
   - tests/software/samtools/merge/**
 
+samtools_mpileup:
+  - software/samtools/mpileup/**
+  - tests/software/samtools/mpileup/**
+
 samtools_sort:
   - software/samtools/sort/**
   - tests/software/samtools/sort/**

tests/software/optitype/main.nf

@@ -0,0 +1,14 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { OPTITYPE } from '../../../software/optitype/main.nf' addParams( options: ['args':'-e 1 -b 0.009', 'args2':'solver=glpk'] )
+
+workflow test_optitype {
+
+    def input = []
+    input = [ [ id:'test', seq_type:'dna' ], // meta map
+              file("${launchDir}/tests/data/genomics/human/bam/example_pe.bam", checkIfExists: true) ]
+
+    OPTITYPE ( input )
+}

tests/software/optitype/test.yml

@@ -0,0 +1,7 @@
+- name: optitype test_optitype
+  command: nextflow run tests/software/optitype -entry test_optitype -c tests/config/nextflow.config
+  tags:
+    - optitype
+  files:
+    - path: output/optitype/test/test_result.tsv
+    - path: output/optitype/test/test_coverage_plot.pdf