Merge remote-tracking branch 'origin/master' into gatk_filter

modules/gatk4/cnnscorevariants/main.nf

@@ -0,0 +1,57 @@
+process GATK4_CNNSCOREVARIANTS {
+    tag "$meta.id"
+    label 'process_low'
+
+    //Conda is not supported at the moment: https://github.com/broadinstitute/gatk/issues/7811
+    if (params.enable_conda) {
+        exit 1, "Conda environments cannot be used for GATK4/CNNScoreVariants at the moment. Please use docker or singularity containers."
+    }
+    container 'broadinstitute/gatk:4.2.6.1' //Biocontainers is missing a package
+
+    input:
+    tuple val(meta), path(vcf), path(aligned_input), path(intervals)
+    path fasta
+    path fai
+    path dict
+    path architecture
+    path weights
+
+    output:
+    tuple val(meta), path("*.vcf.gz"), emit: vcf
+    path "versions.yml"           , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    def aligned_input = aligned_input ? "--input $aligned_input" : ""
+    def interval_command = intervals ? "--intervals $intervals" : ""
+    def architecture = architecture ? "--architecture $architecture" : ""
+    def weights = weights ? "--weights $weights" : ""
+
+    def avail_mem = 3
+    if (!task.memory) {
+        log.info '[GATK CnnScoreVariants] Available memory not known - defaulting to 3GB. Specify process memory requirements to change this.'
+    } else {
+        avail_mem = task.memory.giga
+    }
+    """
+    gatk --java-options "-Xmx${avail_mem}g" CNNScoreVariants \\
+        --variant $vcf \\
+        --output ${prefix}.vcf.gz \\
+        --reference $fasta \\
+        $interval_command \\
+        $aligned_input \\
+        $architecture \\
+        $weights \\
+        --tmp-dir . \\
+        $args
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        gatk4: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//')
+    END_VERSIONS
+    """
+}

modules/gatk4/cnnscorevariants/meta.yml

@@ -0,0 +1,72 @@
+name: "gatk4_cnnscorevariants"
+description: Apply a Convolutional Neural Net to filter annotated variants
+keywords:
+  - gatk4_cnnscorevariants
+  - gatk4
+  - variants
+tools:
+  - gatk4:
+    description: |
+      Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools
+      with a primary focus on variant discovery and genotyping. Its powerful processing engine
+      and high-performance computing features make it capable of taking on projects of any size.
+    homepage: https://gatk.broadinstitute.org/hc/en-us
+    documentation: https://gatk.broadinstitute.org/hc/en-us/categories/360002369672s
+    doi: 10.1158/1538-7445.AM2017-3590
+    licence: ["Apache-2.0"]
+
+input:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  - vcf:
+      type: file
+      description: VCF file
+      pattern: "*.vcf.gz"
+  - aligned_input:
+      type: file
+      description: BAM/CRAM file from alignment (optional)
+      pattern: "*.{bam,cram}"
+  - intervals:
+      type: file
+      description: Bed file with the genomic regions included in the library (optional)
+  - fasta:
+      type: file
+      description: The reference fasta file
+      pattern: "*.fasta"
+  - fai:
+      type: file
+      description: Index of reference fasta file
+      pattern: "*.fasta.fai"
+  - dict:
+      type: file
+      description: GATK sequence dictionary
+      pattern: "*.dict"
+  - architecture:
+      type: file
+      description: Neural Net architecture configuration json file (optional)
+      pattern: "*.json"
+  - weights:
+      type: file
+      description: Keras model HD5 file with neural net weights. (optional)
+      pattern: "*.hd5"
+
+output:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  - versions:
+      type: file
+      description: File containing software versions
+      pattern: "versions.yml"
+  - vcf:
+      type: file
+      description: Annotated VCF file
+      pattern: "*.vcf"
+
+authors:
+  - "@FriederikeHanssen"

modules/motus/profile/main.nf

@@ -0,0 +1,54 @@
+process MOTUS_PROFILE {
+    tag "$meta.id"
+    label 'process_medium'
+
+    conda (params.enable_conda ? "bioconda::motus=3.0.1" : null)
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/motus:3.0.1--pyhdfd78af_0':
+        'quay.io/biocontainers/motus:3.0.1--pyhdfd78af_0' }"
+
+    input:
+    tuple val(meta), path(reads)
+    path db
+
+    output:
+    tuple val(meta), path("*.out"), emit: out
+    tuple val(meta), path("*.bam"), optional: true, emit: bam
+    tuple val(meta), path("*.mgc"), optional: true, emit: mgc
+    path "versions.yml"           , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    def inputs = reads[0].getExtension() == 'bam' ?
+                    "-i ${reads}" :
+                    reads[0].getExtension() == 'mgc' ? "-m $reads" :
+                        meta.single_end ?
+                            "-s $reads" : "-f ${reads[0]} -r ${reads[1]}"
+    def refdb = db ? "-db ${db}" : ""
+    """
+    motus profile \\
+        $args \\
+        $inputs \\
+        $refdb \\
+        -t $task.cpus \\
+        -n $prefix \\
+        -o ${prefix}.out
+
+    ## mOTUs version number is not available from command line.
+    ## mOTUs save the version number in index database folder.
+    ## mOTUs will check the database version is same version as exec version.
+    if [ "$db" == "" ]; then
+        VERSION=\$(echo \$(motus -h 2>&1) | sed 's/^.*Version: //; s/References.*\$//')
+    else
+        VERSION=\$(grep motus $db/db_mOTU_versions | sed 's/motus\\t//g')
+    fi
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        mOTUs: \$VERSION
+    END_VERSIONS
+    """
+}

modules/motus/profile/meta.yml

@@ -0,0 +1,61 @@
+name: "motus_profile"
+description: Taxonomic meta-omics profiling using universal marker genes
+keywords:
+  - classify
+  - metagenomics
+  - fastq
+  - taxonomic profiling
+tools:
+  - "motus":
+      description: "Marker gene-based OTU (mOTU) profiling"
+      homepage: "https://motu-tool.org/"
+      documentation: "https://github.com/motu-tool/mOTUs/wiki"
+      tool_dev_url: "https://github.com/motu-tool/mOTUs"
+      doi: "10.1038/s41467-019-08844-4"
+      licence: "['GPL v3']"
+
+input:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  - reads:
+      type: file
+      description: |
+        List of input fastq/fasta files of size 1 and 2 for single-end and paired-end data,
+        respectively.
+        Or the intermediate bam file mapped by bwa to the mOTUs database or
+        the output bam file from motus profile.
+        Or the intermediate mgc read counts table.
+      pattern: "*.{fastq,fq,fasta,fa,fastq.gz,fq.gz,fasta.gz,fa.gz,.bam,.mgc}"
+  - db:
+      type: directory
+      description: |
+        mOTUs database downloaded by `motus downloadDB`
+
+output:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  - versions:
+      type: file
+      description: File containing software versions
+      pattern: "versions.yml"
+  - out:
+      type: file
+      description: Results with taxonomic classification of each read
+      pattern: "*.out"
+  - bam:
+      type: file
+      description: Optional intermediate sorted BAM file from BWA
+      pattern: "*.{bam}"
+  - mgc:
+      type: file
+      description: Optional intermediate mgc read count table file saved with `-M`.
+      pattern: "*.{mgc}"
+
+authors:
+  - "@jianhong"

tests/config/pytest_modules.yml

@@ -731,6 +731,10 @@ gatk4/calculatecontamination:
   - modules/gatk4/calculatecontamination/**
   - tests/modules/gatk4/calculatecontamination/**
 
+gatk4/cnnscorevariants:
+  - modules/gatk4/cnnscorevariants/**
+  - tests/modules/gatk4/cnnscorevariants/**
+
 gatk4/combinegvcfs:
   - modules/gatk4/combinegvcfs/**
   - tests/modules/gatk4/combinegvcfs/**
@@ -1314,6 +1318,10 @@ motus/downloaddb:
   - modules/motus/downloaddb/**
   - tests/modules/motus/downloaddb/**
 
+motus/profile:
+  - modules/motus/profile/**
+  - tests/modules/motus/profile/**
+
 msisensor/msi:
   - modules/msisensor/msi/**
   - tests/modules/msisensor/msi/**

tests/modules/gatk4/cnnscorevariants/main.nf

@@ -0,0 +1,18 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { GATK4_CNNSCOREVARIANTS } from '../../../../modules/gatk4/cnnscorevariants/main.nf'
+
+workflow test_gatk4_cnnscorevariants {
+
+    input     = [ [ id:'test' ], // meta map
+                    file(params.test_data['homo_sapiens']['illumina']['test_genome_vcf'], checkIfExists: true),
+                    [],
+                    []
+                ]
+    fasta  = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
+    fai    = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)
+    dict   = file(params.test_data['homo_sapiens']['genome']['genome_dict'], checkIfExists: true)
+    GATK4_CNNSCOREVARIANTS ( input, fasta, fai, dict, [], [] )
+}

tests/modules/gatk4/cnnscorevariants/nextflow.config

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

tests/modules/gatk4/cnnscorevariants/test.yml

@@ -0,0 +1,9 @@
+- name: gatk4 cnnscorevariants test_gatk4_cnnscorevariants
+  command: nextflow run ./tests/modules/gatk4/cnnscorevariants -entry test_gatk4_cnnscorevariants -c ./tests/config/nextflow.config  -c ./tests/modules/gatk4/cnnscorevariants/nextflow.config
+  tags:
+    - gatk4
+    - gatk4/cnnscorevariants
+  files:
+    - path: output/gatk4/test.vcf.gz
+      contains:
+        - "##ALT=<ID=NON_REF,Description="

tests/modules/motus/profile/main.nf

@@ -0,0 +1,19 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { MOTUS_DOWNLOADDB } from '../../../../modules/motus/downloaddb/main.nf'
+include { MOTUS_PROFILE    } from '../../../../modules/motus/profile/main.nf'
+
+workflow test_motus_profile_single_end {
+
+    input = [
+        [ id:'test', single_end:true ], // meta map
+        file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true)
+    ]
+
+    MOTUS_DOWNLOADDB(file('https://raw.githubusercontent.com/motu-tool/mOTUs/master/motus/downloadDB.py'))
+
+    MOTUS_PROFILE ( input,  MOTUS_DOWNLOADDB.out.db )
+}
+

tests/modules/motus/profile/nextflow.config

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

tests/modules/motus/profile/test.yml

@@ -0,0 +1,8 @@
+- name: motus profile test_motus_profile_single_end
+  command: nextflow run tests/modules/motus/profile -entry test_motus_profile_single_end -c tests/config/nextflow.config
+  tags:
+    - motus
+    - motus/profile
+  files:
+    - path: output/motus/test.out
+      contains: ["#consensus_taxonomy\ttest"]