Fastq screen

modules/nf-core/fastqscreen/buildfromindex/main.nf

@@ -0,0 +1,67 @@
+process FASTQSCREEN_BUILDFROMINDEX {
+    label 'process_single'
+
+    conda "fastq-screen"
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/fastq-screen%3A0.15.3--pl5321hdfd78af_0':
+        'quay.io/biocontainers/fastq-screen:0.15.3--pl5321hdfd78af_0'}"
+
+    input:
+    val(id)
+    path(index), stageAs: "dir*"
+
+    output:
+    path("FastQ_Screen_Genomes"), emit: database
+    path "versions.yml"         , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    dir = "FastQ_Screen_Genomes"
+    folder = index.collect { it.toString() }
+    database = [id, folder].transpose()
+    copy_index = folder.collect { "cp -r ${it} $dir/${it}"}.join(" && ")
+
+    // Folder name and index (within folder) name could be different - use bash to look for index name
+    config = database
+        .collect { "########## ${it[0]} \nDATABASE ${it[0]} $dir/${it[1]}/${it[1] + '_to_be_replaced'}" }
+        .join("\n\n")
+
+    """
+    mkdir $dir
+    $copy_index
+
+    echo "$config"  >> $dir/fastq_screen.conf
+    echo "Replace folder name real index name"
+
+    for f in ${folder.join(' ')}
+    do
+        TO_REPLACE=\${f}_to_be_replaced
+
+        REPLACE_WITH=(\$f"/*.rev.1.bt2")
+        REPLACE_WITH=\$(basename \$REPLACE_WITH)
+        REPLACE_WITH=\${REPLACE_WITH%%.rev.1.bt2}
+
+        sed "s/\$TO_REPLACE/\$REPLACE_WITH/g" $dir/fastq_screen.conf > new_conf.conf
+        mv new_conf.conf $dir/fastq_screen.conf
+    done
+
+    cat <<-END_VERSIONS > versions.yml
+
+    "${task.process}":
+        fastqscreen: \$(echo \$(fastq_screen --version 2>&1) | sed 's/^.*FastQ Screen v//; s/ .*\$//')
+    END_VERSIONS
+    """
+
+    stub:
+    """
+    mkdir $dir
+    touch $dir/fastq_screen.conf
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        fastqscreen: \$(echo \$(fastq_screen --version 2>&1) | sed 's/^.*FastQ Screen v//; s/ .*\$//')
+    END_VERSIONS
+    """
+}

modules/nf-core/fastqscreen/buildfromindex/meta.yml

@@ -0,0 +1,35 @@
+name: "fastqscreen_buildfromindex"
+description: Build fastq screen config file from bowtie index files
+keywords:
+  - build
+  - index
+  - genome
+  - reference
+tools:
+  - "fastqscreen":
+      description: "FastQ Screen allows you to screen a library of sequences in FastQ format against a set of sequence databases so you can see if the composition of the library matches with what you expect."
+      homepage: "https://www.bioinformatics.babraham.ac.uk/projects/fastq_screen/"
+      documentation: "https://stevenwingett.github.io/FastQ-Screen/"
+      tool_dev_url: "https://github.com/StevenWingett/FastQ-Screen/archive/refs/tags/v0.15.3.zip"
+      doi: "10.5281/zenodo.5838377"
+      licence: ["GPL-3.0-or-later"]
+input:
+  - id:
+      type: string
+      description: |
+        List of names for each index
+  - index:
+      type: directory
+      description: Bowtie2 genome directory with index files
+output:
+  - versions:
+      type: file
+      description: File containing software versions
+      pattern: "versions.yml"
+  - database:
+      type: directory
+      description: fastq screen database folder containing config file and index folders
+      pattern: "FastQ_Screen_Genomes"
+authors:
+  - "@snesic"
+  - "@JPejovicApis"

modules/nf-core/fastqscreen/fastqscreen/main.nf

@@ -0,0 +1,38 @@
+process FASTQSCREEN_FASTQSCREEN {
+    tag "$meta.id"
+    label 'process_medium'
+
+    conda "bioconda::fastq-screen=0.15.3"
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/fastq-screen%3A0.15.3--pl5321hdfd78af_0':
+        'quay.io/biocontainers/fastq-screen:0.15.3--pl5321hdfd78af_0'}"
+
+    input:
+    tuple val(meta), path(reads)  // .fastq files
+    path genome
+
+    output:
+    tuple val(meta), path ("*_fq_screen"), emit: fastq_screen
+    path "versions.yml"                  , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    def args = task.ext.args ?: ""
+
+    """
+    fastq_screen --threads ${task.cpus} \\
+        --aligner bowtie2 \\
+        --conf ${genome}/fastq_screen.conf \\
+        $reads \\
+        $args \\
+        --outdir ${prefix}_fq_screen
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        fastqscreen: \$(echo \$(fastq_screen --version 2>&1) | sed 's/^.*FastQ Screen v//; s/ .*\$//')
+    END_VERSIONS
+    """
+}

modules/nf-core/fastqscreen/fastqscreen/meta.yml

@@ -0,0 +1,49 @@
+name: fastqscreen_fastqscreen
+description: Align reads to multiple reference genomes using fastq-screen
+keywords:
+  - align
+  - map
+  - fasta
+  - fastq
+  - genome
+  - reference
+tools:
+  - "fastqscreen":
+      description: "FastQ Screen allows you to screen a library of sequences in FastQ format against a set of sequence databases so you can see if the composition of the library matches with what you expect."
+      homepage: "https://www.bioinformatics.babraham.ac.uk/projects/fastq_screen/"
+      documentation: "https://stevenwingett.github.io/FastQ-Screen/"
+      tool_dev_url: "https://github.com/StevenWingett/FastQ-Screen/archive/refs/tags/v0.15.3.zip"
+      doi: "10.5281/zenodo.5838377"
+      licence: ["GPL-3.0-or-later"]
+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 files of size 1 and 2 for single-end and paired-end data,
+        respectively.
+  - meta2:
+      type: map
+      description: |
+        Groovy Map containing reference information
+        e.g. [ id:'test', single_end:false ]
+  - database:
+      type: directory
+      description: fastq screen database folder containing config file and index folders
+      pattern: "FastQ_Screen_Genomes"
+output:
+  - fastq_screen:
+      type: directory
+      description: Output fastq_screen file containing alignment statistics
+      pattern: "*.{_fq_screen}"
+  - versions:
+      type: file
+      description: File containing software versions
+      pattern: "versions.yml"
+authors:
+  - "@snesic"
+  - "@JPejovicApis"

tests/config/pytest_modules.yml

@@ -1146,6 +1146,14 @@ fastqscan:
   - modules/nf-core/fastqscan/**
   - tests/modules/nf-core/fastqscan/**
 
+fastqscreen/buildfromindex:
+  - modules/nf-core/fastqscreen/buildfromindex/**
+  - tests/modules/nf-core/fastqscreen/buildfromindex/**
+
+fastqscreen/fastqscreen:
+  - modules/nf-core/fastqscreen/fastqscreen/**
+  - tests/modules/nf-core/fastqscreen/fastqscreen/**
+
 fasttree:
   - modules/nf-core/fasttree/**
   - tests/modules/nf-core/fasttree/**
@@ -3973,10 +3981,6 @@ whamg:
   - modules/nf-core/whamg/**
   - tests/modules/nf-core/whamg/**
 
-windowmasker/convert:
-  - modules/nf-core/windowmasker/convert/**
-  - tests/modules/nf-core/windowmasker/convert/**
-
 windowmasker/mk_counts:
   - modules/nf-core/windowmasker/mk_counts/**
   - tests/modules/windowmasker/mk_counts/**
@@ -3989,18 +3993,6 @@ wisecondorx/convert:
   - modules/nf-core/wisecondorx/convert/**
   - tests/modules/nf-core/wisecondorx/convert/**
 
-wisecondorx/gender:
-  - modules/nf-core/wisecondorx/gender/**
-  - tests/modules/nf-core/wisecondorx/gender/**
-
-wisecondorx/newref:
-  - modules/nf-core/wisecondorx/newref/**
-  - tests/modules/nf-core/wisecondorx/newref/**
-
-wisecondorx/predict:
-  - modules/nf-core/wisecondorx/predict/**
-  - tests/modules/nf-core/wisecondorx/predict/**
-
 yahs:
   - modules/nf-core/yahs/**
   - tests/modules/nf-core/yahs/**

tests/modules/nf-core/fastqscreen/buildfromindex/main.nf

@@ -0,0 +1,24 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { BOWTIE2_BUILD } from '../../../../../modules/nf-core/bowtie2/build/main.nf'
+include { FASTQSCREEN_BUILDFROMINDEX } from '../../../../../modules/nf-core/fastqscreen/buildfromindex/main.nf'
+
+workflow test_fastqscreen_buildfromindex {
+
+
+    ch_fasta = Channel.from([
+        [[id: 'sarscov2'], file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)],
+        [[id: 'homo_sapiens21'], file(params.test_data['homo_sapiens']['genome']['genome_21_fasta'], checkIfExists: true)]
+        ])
+
+
+    BOWTIE2_BUILD ( ch_fasta )
+
+    FASTQSCREEN_BUILDFROMINDEX (BOWTIE2_BUILD.out.index.map{it -> it[0].id}.collect(),
+                                BOWTIE2_BUILD.out.index.map{it -> it[1]}.collect())
+
+    FASTQSCREEN_BUILDFROMINDEX.out.database.view()
+    FASTQSCREEN_BUILDFROMINDEX.out.versions.view()
+}

tests/modules/nf-core/fastqscreen/buildfromindex/nextflow.config

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

tests/modules/nf-core/fastqscreen/buildfromindex/test.yml

@@ -0,0 +1,9 @@
+- name: "fastqscreen buildfromindex"
+  command: nextflow run ./tests/modules/nf-core/fastqscreen/buildfromindex -entry test_fastqscreen_buildfromindex -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/fastqscreen/buildfromindex/nextflow.config
+  tags:
+    - "fastqscreen"
+    - "fastqscreen/buildfromindex"
+  files:
+    - path: "output/fastqscreen/FastQ_Screen_Genomes"
+    # md5sum: e667c7caad0bc4b7ac383fd023c654fc
+    - path: "output/fastqscreen/versions.yml"

tests/modules/nf-core/fastqscreen/fastqscreen/main.nf

@@ -0,0 +1,35 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { BOWTIE2_BUILD } from '../../../../../modules/nf-core/bowtie2/build/main.nf'
+include { FASTQSCREEN_BUILDFROMINDEX } from '../../../../../modules/nf-core/fastqscreen/buildfromindex/main.nf'
+include { FASTQSCREEN_FASTQSCREEN } from '../../../../../modules/nf-core/fastqscreen/fastqscreen/main.nf'
+
+
+workflow test_fastqscreen_fastqscreen {
+
+
+    input = [
+        [ id:'test', single_end:true ], // meta map
+        [
+            file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true)
+        ]
+    ]
+
+    ch_fasta = Channel.from([
+        [[id: 'sarscov2'], file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)],
+        [[id: 'homo_sapiens21'], file(params.test_data['homo_sapiens']['genome']['genome_21_fasta'], checkIfExists: true)]
+        ])
+
+
+    BOWTIE2_BUILD ( ch_fasta )
+
+    FASTQSCREEN_BUILDFROMINDEX (BOWTIE2_BUILD.out.index.map{it -> it[0]}.collect(),
+                                BOWTIE2_BUILD.out.index.map{it -> it[1]}.collect())
+
+
+    FASTQSCREEN_FASTQSCREEN (input, 
+                             FASTQSCREEN_BUILDFROMINDEX.out.database)
+
+}

tests/modules/nf-core/fastqscreen/fastqscreen/nextflow.config

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

tests/modules/nf-core/fastqscreen/fastqscreen/test.yml

@@ -0,0 +1,10 @@
+- name: "fastqscreen fastqscreen"
+  command: nextflow run ./tests/modules/nf-core/fastqscreen/fastqscreen -entry test_fastqscreen_fastqscreen -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/fastqscreen/fastqscreen/nextflow.config
+  tags:
+    - "fastqscreen"
+    - "fastqscreen/fastqscreen"
+  files:
+    - path: "output/fastqscreen/test_fq_screen/test_1_screen.txt"
+      md5sum: 764fde5d19df5ce380148943699164b5
+    - path: "output/fastqscreen/versions.yml"
+      md5sum: 3ad3f89a04d88fec5932d0887c462467