resolve merge conflicts

.github/PULL_REQUEST_TEMPLATE.md

@@ -25,6 +25,6 @@ Learn more about contributing: [CONTRIBUTING.md](https://github.com/nf-core/modu
 - [ ] Add a resource `label`
 - [ ] Use BioConda and BioContainers if possible to fulfil software requirements.
 - Ensure that the test works with either Docker / Singularity. Conda CI tests can be quite flaky:
-    - [ ] `PROFILE=docker pytest --tag <MODULE> --symlink --wt 2 --keep-workflow-wd`
+    - [ ] `PROFILE=docker pytest --tag <MODULE> --symlink --keep-workflow-wd`
-    - [ ] `PROFILE=singularity pytest --tag <MODULE> --symlink --wt 2 --keep-workflow-wd`
+    - [ ] `PROFILE=singularity pytest --tag <MODULE> --symlink --keep-workflow-wd`
-    - [ ] `PROFILE=conda pytest --tag <MODULE> --symlink --wt 2 --keep-workflow-wd`
+    - [ ] `PROFILE=conda pytest --tag <MODULE> --symlink --keep-workflow-wd`

.github/filters.yml

@@ -18,6 +18,10 @@ bcftools_merge:
   - software/bcftools/merge/**
   - tests/software/bcftools/merge/**
 
+bcftools_mpileup:
+  - software/bcftools/mpileup/**
+  - tests/software/bcftools/mpileup/**
+
 bcftools_stats:
   - software/bcftools/stats/**
   - tests/software/bcftools/stats/**
@@ -54,6 +58,14 @@ bedtools_sort:
   - software/bedtools/sort/**
   - tests/software/bedtools/sort/**
 
+bismark_deduplicate:
+  - software/bismark/deduplicate/**
+  - tests/software/bismark/deduplicate/**
+
+bismark_genome_preparation:
+  - software/bismark/genome_preparation/**
+  - tests/software/bismark/genome_preparation/**
+
 blast_makeblastdb:
   - software/blast/makeblastdb/**
   - tests/software/blast/makeblastdb/**
@@ -96,6 +108,14 @@ bwamem2_mem:
   - software/bwamem2/mem/**
   - tests/software/bwamem2/mem/**
 
+bwameth_align:
+  - software/bwameth/align/**
+  - tests/software/bwameth/align/**
+
+bwameth_index:
+  - software/bwameth/index/**
+  - tests/software/bwameth/index/**
+
 cat_fastq:
   - software/cat/fastq/**
   - tests/software/cat/fastq/**
@@ -124,6 +144,26 @@ gatk_createsequencedictionary:
   - software/gatk/createsequencedictionary/**
   - tests/software/gatk/createsequencedictionary/**
 
+gatk4_mergevcfs:
+  - software/gatk4/mergevcfs/**
+  - tests/software/gatk4/mergevcfs/**
+
+gatk4_bedtointervallist:
+  - software/gatk4/bedtointervallist/**
+  - tests/software/gatk4/bedtointervallist/**
+
+gatk4_revertsam:
+  - software/gatk4/revertsam/**
+  - tests/software/gatk4/revertsam/**
+
+gatk4_samtofastq:
+  - software/gatk4/samtofastq/**
+  - tests/software/gatk4/samtofastq/**
+
+gatk4_splitncigarreads:
+  - software/gatk4/splitncigarreads/**
+  - tests/software/gatk4/splitncigarreads/**
+
 gffread:
   - software/gffread/**
   - tests/software/gffread/**
@@ -148,6 +188,14 @@ ivar_variants:
   - software/ivar/variants/**
   - tests/software/ivar/variants/**
 
+methyldackel_extract:
+  - software/methyldackel/extract/**
+  - tests/software/methyldackel/extract/**
+
+methyldackel_mbias:
+  - software/methyldackel/mbias/**
+  - tests/software/methyldackel/mbias/**
+
 minimap2_align:
   - software/minimap2/align/**
   - tests/software/minimap2/align/**
@@ -181,6 +229,10 @@ preseq_lcextrap:
   - software/preseq/lcextrap/**
   - tests/software/preseq/lcextrap/**
 
+qualimap_bamqc:
+  - software/qualimap/bamqc/**
+  - tests/software/qualimap/bamqc/**
+
 quast:
   - software/quast/**
   - tests/software/quast/**
@@ -193,6 +245,10 @@ salmon_quant:
   - software/salmon/quant/**
   - tests/software/salmon/quant/**
 
+samtools_faidx:
+  - software/samtools/faidx/**
+  - tests/software/samtools/faidx/**
+
 samtools_flagstat:
   - software/samtools/flagstat/**
   - tests/software/samtools/flagstat/**
@@ -228,6 +284,9 @@ seacr_callpeak:
 seqkit_split2:
   - software/seqkit/split2/**
   - tests/software/seqkit/split2/**
+seqwish_induce:
+  - software/seqwish/induce/**
+  - tests/software/seqwish/induce/**
 
 star_align:
   - software/star/align/**

.github/workflows/pytest-workflow.yml

@@ -80,7 +80,8 @@ jobs:
 
       # Test the module
       - name: Run pytest-workflow
-        run: TMPDIR=~ PROFILE=${{ matrix.profile }} pytest --tag ${{ matrix.tags }} --symlink --wt 2 --kwdof
+        # only use one thread for pytest-workflow to avoid race condition on conda cache. 
+        run: TMPDIR=~ PROFILE=${{ matrix.profile }} pytest --tag ${{ matrix.tags }} --symlink --kwdof
 
       - name: Upload logs on failure
         if: failure()

README.md

@@ -275,21 +275,21 @@ In order to test that each module added to `nf-core/modules` is actually working
 
         ```console
         cd /path/to/git/clone/of/nf-core/modules/
-        PROFILE=docker pytest --tag bowtie --symlink --wt 2 --keep-workflow-wd
+        PROFILE=docker pytest --tag bowtie --symlink --keep-workflow-wd
         ```
 
     - Typical command with Singularity:
 
         ```console
         cd /path/to/git/clone/of/nf-core/modules/
-        TMPDIR=~ PROFILE=singularity pytest --tag bowtie --symlink --wt 2 --keep-workflow-wd
+        TMPDIR=~ PROFILE=singularity pytest --tag bowtie --symlink --keep-workflow-wd
         ```
 
     - Typical command with Conda:
 
         ```console
         cd /path/to/git/clone/of/nf-core/modules/
-        PROFILE=conda pytest --tag bowtie --symlink --wt 2 --keep-workflow-wd
+        PROFILE=conda pytest --tag bowtie --symlink --keep-workflow-wd
         ```
 
     - See [docs on running pytest-workflow](https://pytest-workflow.readthedocs.io/en/stable/#running-pytest-workflow) for more info.

software/bcftools/mpileup/functions.nf

@@ -0,0 +1,61 @@
+
+/*
+ * -----------------------------------------------------
+ *  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/bcftools/mpileup/main.nf

@@ -0,0 +1,47 @@
+// Import generic module functions
+include { initOptions; saveFiles; getSoftwareName } from './functions'
+
+params.options = [:]
+def options    = initOptions(params.options)
+
+process BCFTOOLS_MPILEUP {
+    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::bcftools=1.11" : null)
+    if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
+        container "https://depot.galaxyproject.org/singularity/bcftools:1.11--h7c999a4_0"
+    } else {
+        container "quay.io/biocontainers/bcftools:1.11--h7c999a4_0"
+    }
+
+    input:
+    tuple val(meta), path(bam)
+    path  fasta
+
+    output:
+    tuple val(meta), path("*.gz")      , emit: vcf
+    tuple val(meta), path("*.tbi")     , emit: tbi
+    tuple val(meta), path("*stats.txt"), emit: stats
+    path  "*.version.txt"              , emit: version
+
+    script:
+    def software = getSoftwareName(task.process)
+    def prefix   = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
+    """
+    echo "${meta.id}" > sample_name.list
+    bcftools mpileup \\
+        --fasta-ref $fasta \\
+        $options.args \\
+        $bam \\
+        | bcftools call --output-type v $options.args2 \\
+        | bcftools reheader --samples sample_name.list \\
+        | bcftools view --output-file ${prefix}.vcf.gz --output-type z $options.args3
+    tabix -p vcf -f ${prefix}.vcf.gz
+    bcftools stats ${prefix}.vcf.gz > ${prefix}.bcftools_stats.txt
+    echo \$(bcftools --version 2>&1) | sed 's/^.*bcftools //; s/ .*\$//' > ${software}.version.txt
+    """
+}

software/bcftools/mpileup/meta.yml

@@ -0,0 +1,73 @@
+name: bcftools_mpileup
+description: Compresses VCF files
+keywords:
+    - variant calling
+    - mpileup
+    - VCF
+tools:
+    - consensus:
+        description: |
+          Generates genotype likelihoods at each genomic position with coverage.
+        homepage: http://samtools.github.io/bcftools/bcftools.html
+        documentation: http://www.htslib.org/doc/bcftools.html
+        doi: 10.1093/bioinformatics/btp352
+params:
+    - outdir:
+        type: string
+        description: |
+          The pipeline's output directory. By default, the module will
+          output files into `$params.outdir/<SOFTWARE>`
+    - publish_dir_mode:
+        type: string
+        description: |
+          Value for the Nextflow `publishDir` mode parameter.
+          Available: symlink, rellink, link, copy, copyNoFollow, move.
+    - enable_conda:
+        type: boolean
+        description: |
+          Run the module with Conda using the software specified
+          via the `conda` directive
+    - singularity_pull_docker_container:
+        type: boolean
+        description: |
+          Instead of directly downloading Singularity images for use with Singularity,
+          force the workflow to pull and convert Docker containers instead.
+input:
+    - meta:
+        type: map
+        description: |
+          Groovy Map containing sample information
+          e.g. [ id:'test', single_end:false ]
+    - bam:
+        type: file
+        description: Input BAM file
+        pattern: "*.{bam}"
+    - fasta:
+        type: file
+        description: FASTA reference file
+        pattern: "*.{fasta,fa}"
+output:
+    - meta:
+        type: map
+        description: |
+          Groovy Map containing sample information
+          e.g. [ id:'test', single_end:false ]
+    - vcf:
+        type: file
+        description: VCF gzipped output file
+        pattern: "*.{vcf.gz}"
+    - tbi:
+        type: file
+        description: tabix index file
+        pattern: "*.{tbi}"
+    - stats:
+        type: file
+        description: Text output file containing stats
+        pattern: "*{stats.txt}"
+    - version:
+        type: file
+        description: File containing software version
+        pattern: "*.{version.txt}"
+authors:
+    - "@joseespinosa"
+    - "@drpatelh"

software/bismark/deduplicate/functions.nf

@@ -0,0 +1,59 @@
+/*
+ * -----------------------------------------------------
+ *  Utility functions used in nf-core DSL2 module files
+ * -----------------------------------------------------
+ */
+
+/*
+ * Extract name of software tool from process name using $task.process
+ */
+def getSoftwareName(task_process) {
+    return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
+}
+
+/*
+ * Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
+ */
+def initOptions(Map args) {
+    def Map options = [:]
+    options.args          = args.args ?: ''
+    options.args2         = args.args2 ?: ''
+    options.publish_by_id = args.publish_by_id ?: false
+    options.publish_dir   = args.publish_dir ?: ''
+    options.publish_files = args.publish_files
+    options.suffix        = args.suffix ?: ''
+    return options
+}
+
+/*
+ * Tidy up and join elements of a list to return a path string
+ */
+def getPathFromList(path_list) {
+    def paths = path_list.findAll { item -> !item?.trim().isEmpty() }  // Remove empty entries
+    paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
+    return paths.join('/')
+}
+
+/*
+ * Function to save/publish module results
+ */
+def saveFiles(Map args) {
+    if (!args.filename.endsWith('.version.txt')) {
+        def ioptions = initOptions(args.options)
+        def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
+        if (ioptions.publish_by_id) {
+            path_list.add(args.publish_id)
+        }
+        if (ioptions.publish_files instanceof Map) {
+            for (ext in ioptions.publish_files) {
+                if (args.filename.endsWith(ext.key)) {
+                    def ext_list = path_list.collect()
+                    ext_list.add(ext.value)
+                    return "${getPathFromList(ext_list)}/$args.filename"
+                }
+            }
+        } else if (ioptions.publish_files == null) {
+            return "${getPathFromList(path_list)}/$args.filename"
+        }
+    }
+}

software/bismark/deduplicate/main.nf

@@ -0,0 +1,41 @@
+// Import generic module functions
+include { initOptions; saveFiles; getSoftwareName } from './functions'
+
+params.options = [:]
+def options    = initOptions(params.options)
+
+process BISMARK_DEDUPLICATE {
+    tag "$meta.id"
+    label 'process_high'
+    publishDir "${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::bismark==0.23.0" : null)
+    if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
+        container "https://depot.galaxyproject.org/singularity/bismark:0.23.0--0"
+    } else {
+        container "quay.io/biocontainers/bismark:0.23.0--0"
+    }
+
+    input:
+    tuple val(meta), path(bam)
+
+    output:
+    tuple val(meta), path("*.deduplicated.bam")        , emit: bam
+    tuple val(meta), path("*.deduplication_report.txt"), emit: report
+    path  "*.version.txt"                              , emit: version
+
+    script:
+    def software   = getSoftwareName(task.process)
+    def prefix     = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
+    def seqtype    = meta.single_end ? '-s' : '-p'
+    """
+    deduplicate_bismark \\
+        $options.args \\
+        $seqtype \\
+        --bam $bam
+
+    echo \$(bismark -v 2>&1) | sed 's/^.*Bismark Version: v//; s/Copyright.*\$//' > ${software}.version.txt
+    """
+}

software/bismark/deduplicate/meta.yml

@@ -0,0 +1,72 @@
+name: bismark_deduplicate
+description: |
+    Removes alignments to the same position in the genome
+    from the Bismark mapping output.
+keywords:
+    - bismark
+    - 3-letter genome
+    - map
+    - methylation
+    - 5mC
+    - methylseq
+    - bisulphite
+    - bam
+tools:
+    - bismark:
+        description: |
+            Bismark is a tool to map bisulfite treated sequencing reads
+            and perform methylation calling in a quick and easy-to-use fashion.
+        homepage: https://github.com/FelixKrueger/Bismark
+        documentation: https://github.com/FelixKrueger/Bismark/tree/master/Docs
+        doi: 10.1093/bioinformatics/btr167
+params:
+    - outdir:
+        type: string
+        description: |
+            The pipeline's output directory. By default, the module will
+            output files into `$params.outdir/<SOFTWARE>`
+    - publish_dir_mode:
+        type: string
+        description: |
+            Value for the Nextflow `publishDir` mode parameter.
+            Available: symlink, rellink, link, copy, copyNoFollow, move.
+    - enable_conda:
+        type: boolean
+        description: |
+            Run the module with Conda using the software specified
+            via the `conda` directive
+    - singularity_pull_docker_container:
+        type: boolean
+        description: |
+            Instead of directly downloading Singularity images for use with Singularity,
+            force the workflow to pull and convert Docker containers instead.
+input:
+    - meta:
+        type: map
+        description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test', single_end:false ]
+    - bam:
+        type: file
+        description: BAM file containing read alignments
+        pattern: "*.{bam}"
+output:
+    - meta:
+        type: map
+        description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test', single_end:false ]
+    - bam:
+        type: file
+        description: Deduplicated output BAM file containing read alignments
+        pattern: "*.{deduplicated.bam}"
+    - report:
+        type: file
+        description: Bismark deduplication reports
+        pattern: "*.{deduplication_report.txt}"
+    - version:
+        type: file
+        description: File containing software version
+        pattern: "*.{version.txt}"
+authors:
+    - "@phue"

software/bismark/genome_preparation/functions.nf

@@ -0,0 +1,59 @@
+/*
+ * -----------------------------------------------------
+ *  Utility functions used in nf-core DSL2 module files
+ * -----------------------------------------------------
+ */
+
+/*
+ * Extract name of software tool from process name using $task.process
+ */
+def getSoftwareName(task_process) {
+    return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
+}
+
+/*
+ * Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
+ */
+def initOptions(Map args) {
+    def Map options = [:]
+    options.args          = args.args ?: ''
+    options.args2         = args.args2 ?: ''
+    options.publish_by_id = args.publish_by_id ?: false
+    options.publish_dir   = args.publish_dir ?: ''
+    options.publish_files = args.publish_files
+    options.suffix        = args.suffix ?: ''
+    return options
+}
+
+/*
+ * Tidy up and join elements of a list to return a path string
+ */
+def getPathFromList(path_list) {
+    def paths = path_list.findAll { item -> !item?.trim().isEmpty() }  // Remove empty entries
+    paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
+    return paths.join('/')
+}
+
+/*
+ * Function to save/publish module results
+ */
+def saveFiles(Map args) {
+    if (!args.filename.endsWith('.version.txt')) {
+        def ioptions = initOptions(args.options)
+        def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
+        if (ioptions.publish_by_id) {
+            path_list.add(args.publish_id)
+        }
+        if (ioptions.publish_files instanceof Map) {
+            for (ext in ioptions.publish_files) {
+                if (args.filename.endsWith(ext.key)) {
+                    def ext_list = path_list.collect()
+                    ext_list.add(ext.value)
+                    return "${getPathFromList(ext_list)}/$args.filename"
+                }
+            }
+        } else if (ioptions.publish_files == null) {
+            return "${getPathFromList(path_list)}/$args.filename"
+        }
+    }
+}

software/bismark/genome_preparation/main.nf

@@ -0,0 +1,37 @@
+// Import generic module functions
+include { initOptions; saveFiles; getSoftwareName } from './functions'
+
+params.options = [:]
+def options    = initOptions(params.options)
+
+process BISMARK_GENOME_PREPARATION {
+    tag "$fasta"
+    label 'process_high'
+    publishDir "${params.outdir}",
+        mode: params.publish_dir_mode,
+        saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:'') }
+
+    conda (params.enable_conda ? "bioconda::bismark==0.23.0" : null)
+    if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
+        container "https://depot.galaxyproject.org/singularity/bismark:0.23.0--0"
+    } else {
+        container "quay.io/biocontainers/bismark:0.23.0--0"
+    }
+
+    input:
+    path fasta, stageAs: "BismarkIndex/*"
+
+    output:
+    path "BismarkIndex" , emit: index
+    path "*.version.txt", emit: version
+
+    script:
+    def software   = getSoftwareName(task.process)
+    """
+    bismark_genome_preparation \\
+        $options.args \\
+        BismarkIndex
+
+    echo \$(bismark -v 2>&1) | sed 's/^.*Bismark Version: v//; s/Copyright.*\$//' > ${software}.version.txt
+    """
+}

software/bismark/genome_preparation/meta.yml

@@ -0,0 +1,57 @@
+name: bismark_genome_preparation
+description: |
+    Converts a specified reference genome into two different bisulfite
+    converted versions and indexes them for alignments.
+keywords:
+    - bismark
+    - 3-letter genome
+    - index
+    - methylation
+    - 5mC
+    - methylseq
+    - bisulphite
+    - fasta
+tools:
+    - bismark:
+        description: |
+            Bismark is a tool to map bisulfite treated sequencing reads
+            and perform methylation calling in a quick and easy-to-use fashion.
+        homepage: https://github.com/FelixKrueger/Bismark
+        documentation: https://github.com/FelixKrueger/Bismark/tree/master/Docs
+        doi: 10.1093/bioinformatics/btr167
+params:
+    - outdir:
+        type: string
+        description: |
+            The pipeline's output directory. By default, the module will
+            output files into `$params.outdir/<SOFTWARE>`
+    - publish_dir_mode:
+        type: string
+        description: |
+            Value for the Nextflow `publishDir` mode parameter.
+            Available: symlink, rellink, link, copy, copyNoFollow, move.
+    - enable_conda:
+        type: boolean
+        description: |
+            Run the module with Conda using the software specified
+            via the `conda` directive
+    - singularity_pull_docker_container:
+        type: boolean
+        description: |
+            Instead of directly downloading Singularity images for use with Singularity,
+            force the workflow to pull and convert Docker containers instead.
+input:
+    - fasta:
+        type: file
+        description: Input genome fasta file
+output:
+    - index:
+        type: dir
+        description: Bismark genome index directory
+        pattern: "BismarkIndex"
+    - version:
+        type: file
+        description: File containing software version
+        pattern: "*.{version.txt}"
+authors:
+    - "@phue"

software/bwameth/align/functions.nf

@@ -0,0 +1,59 @@
+/*
+ * -----------------------------------------------------
+ *  Utility functions used in nf-core DSL2 module files
+ * -----------------------------------------------------
+ */
+
+/*
+ * Extract name of software tool from process name using $task.process
+ */
+def getSoftwareName(task_process) {
+    return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
+}
+
+/*
+ * Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
+ */
+def initOptions(Map args) {
+    def Map options = [:]
+    options.args          = args.args ?: ''
+    options.args2         = args.args2 ?: ''
+    options.publish_by_id = args.publish_by_id ?: false
+    options.publish_dir   = args.publish_dir ?: ''
+    options.publish_files = args.publish_files
+    options.suffix        = args.suffix ?: ''
+    return options
+}
+
+/*
+ * Tidy up and join elements of a list to return a path string
+ */
+def getPathFromList(path_list) {
+    def paths = path_list.findAll { item -> !item?.trim().isEmpty() }  // Remove empty entries
+    paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
+    return paths.join('/')
+}
+
+/*
+ * Function to save/publish module results
+ */
+def saveFiles(Map args) {
+    if (!args.filename.endsWith('.version.txt')) {
+        def ioptions = initOptions(args.options)
+        def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
+        if (ioptions.publish_by_id) {
+            path_list.add(args.publish_id)
+        }
+        if (ioptions.publish_files instanceof Map) {
+            for (ext in ioptions.publish_files) {
+                if (args.filename.endsWith(ext.key)) {
+                    def ext_list = path_list.collect()
+                    ext_list.add(ext.value)
+                    return "${getPathFromList(ext_list)}/$args.filename"
+                }
+            }
+        } else if (ioptions.publish_files == null) {
+            return "${getPathFromList(path_list)}/$args.filename"
+        }
+    }
+}

software/bwameth/align/main.nf

@@ -0,0 +1,46 @@
+// Import generic module functions
+include { initOptions; saveFiles; getSoftwareName } from './functions'
+
+params.options = [:]
+def options    = initOptions(params.options)
+
+process BWAMETH_ALIGN {
+    tag "$meta.id"
+    label 'process_high'
+    publishDir "${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::bwameth=0.2.2" : null)
+    if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
+        container "https://depot.galaxyproject.org/singularity/bwameth:0.20--py35_0"
+    } else {
+        container "quay.io/biocontainers/bwameth:0.20--py35_0"
+    }
+
+    input:
+    tuple val(meta), path(reads)
+    path index
+
+    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 read_group = meta.read_group ? "-R ${meta.read_group}" : ""
+    """
+    INDEX=`find -L ${index} -name "*.bwameth.c2t" | sed 's/.bwameth.c2t//'`
+
+    bwameth.py \\
+        $options.args \\
+        $read_group \\
+        -t $task.cpus \\
+        --reference \$INDEX \\
+        $reads \\
+        | samtools view $options.args2 -@ $task.cpus -bhS -o ${prefix}.bam -
+
+    echo \$(bwameth.py --version 2>&1) | cut -f2 -d" " > ${software}.version.txt
+    """
+}

software/bwameth/align/meta.yml

@@ -0,0 +1,72 @@
+name: bwameth_align
+description: Performs alignment of BS-Seq reads using bwameth
+keywords:
+    - bwameth
+    - alignment
+    - 3-letter genome
+    - map
+    - methylation
+    - 5mC
+    - methylseq
+    - bisulphite
+    - fastq
+    - bam
+tools:
+    - bwameth:
+        description: |
+            Fast and accurate alignment of BS-Seq reads
+            using bwa-mem and a 3-letter genome.
+        homepage: https://github.com/brentp/bwa-meth
+        documentation: https://github.com/brentp/bwa-meth
+        arxiv: arXiv:1401.1129
+params:
+    - outdir:
+        type: string
+        description: |
+            The pipeline's output directory. By default, the module will
+            output files into `$params.outdir/<SOFTWARE>`
+    - publish_dir_mode:
+        type: string
+        description: |
+            Value for the Nextflow `publishDir` mode parameter.
+            Available: symlink, rellink, link, copy, copyNoFollow, move.
+    - enable_conda:
+        type: boolean
+        description: |
+            Run the module with Conda using the software specified
+            via the `conda` directive
+    - singularity_pull_docker_container:
+        type: boolean
+        description: |
+            Instead of directly downloading Singularity images for use with Singularity,
+            force the workflow to pull and convert Docker containers instead.
+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.
+    - index:
+        type: dir
+        description: Directory containing bwameth genome index
+output:
+    - meta:
+        type: map
+        description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test', single_end:false ]
+    - bam:
+        type: file
+        description: Output BAM file containing read alignments
+        pattern: "*.{bam}"
+    - version:
+        type: file
+        description: File containing software version
+        pattern: "*.{version.txt}"
+authors:
+    - "@phue"

software/bwameth/index/functions.nf

@@ -0,0 +1,59 @@
+/*
+ * -----------------------------------------------------
+ *  Utility functions used in nf-core DSL2 module files
+ * -----------------------------------------------------
+ */
+
+/*
+ * Extract name of software tool from process name using $task.process
+ */
+def getSoftwareName(task_process) {
+    return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
+}
+
+/*
+ * Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
+ */
+def initOptions(Map args) {
+    def Map options = [:]
+    options.args          = args.args ?: ''
+    options.args2         = args.args2 ?: ''
+    options.publish_by_id = args.publish_by_id ?: false
+    options.publish_dir   = args.publish_dir ?: ''
+    options.publish_files = args.publish_files
+    options.suffix        = args.suffix ?: ''
+    return options
+}
+
+/*
+ * Tidy up and join elements of a list to return a path string
+ */
+def getPathFromList(path_list) {
+    def paths = path_list.findAll { item -> !item?.trim().isEmpty() }  // Remove empty entries
+    paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
+    return paths.join('/')
+}
+
+/*
+ * Function to save/publish module results
+ */
+def saveFiles(Map args) {
+    if (!args.filename.endsWith('.version.txt')) {
+        def ioptions = initOptions(args.options)
+        def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
+        if (ioptions.publish_by_id) {
+            path_list.add(args.publish_id)
+        }
+        if (ioptions.publish_files instanceof Map) {
+            for (ext in ioptions.publish_files) {
+                if (args.filename.endsWith(ext.key)) {
+                    def ext_list = path_list.collect()
+                    ext_list.add(ext.value)
+                    return "${getPathFromList(ext_list)}/$args.filename"
+                }
+            }
+        } else if (ioptions.publish_files == null) {
+            return "${getPathFromList(path_list)}/$args.filename"
+        }
+    }
+}

software/bwameth/index/main.nf

@@ -0,0 +1,35 @@
+// Import generic module functions
+include { initOptions; saveFiles; getSoftwareName } from './functions'
+
+params.options = [:]
+def options    = initOptions(params.options)
+
+process BWAMETH_INDEX {
+    tag "$fasta"
+    label 'process_high'
+    publishDir "${params.outdir}",
+        mode: params.publish_dir_mode,
+        saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:'') }
+
+    conda (params.enable_conda ? "bioconda::bwameth=0.2.2" : null)
+    if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
+        container "https://depot.galaxyproject.org/singularity/bwameth:0.20--py35_0"
+    } else {
+        container "quay.io/biocontainers/bwameth:0.20--py35_0"
+    }
+
+    input:
+    path fasta, stageAs: "bwameth/*"
+
+    output:
+    path "bwameth"      , emit: index
+    path "*.version.txt", emit: version
+
+    script:
+    def software = getSoftwareName(task.process)
+    """
+    bwameth.py index $fasta
+
+    echo \$(bwameth.py --version 2>&1) | cut -f2 -d" " > ${software}.version.txt
+    """
+}

software/bwameth/index/meta.yml

@@ -0,0 +1,53 @@
+name: bwameth_index
+description: Performs indexing of c2t converted reference genome
+keywords:
+    - bwameth
+    - 3-letter genome
+    - index
+    - methylseq
+    - bisulphite
+    - fasta
+tools:
+    - bwameth:
+        description: |
+            Fast and accurate alignment of BS-Seq reads
+            using bwa-mem and a 3-letter genome.
+        homepage: https://github.com/brentp/bwa-meth
+        documentation: https://github.com/brentp/bwa-meth
+        arxiv: arXiv:1401.1129
+params:
+    - outdir:
+        type: string
+        description: |
+            The pipeline's output directory. By default, the module will
+            output files into `$params.outdir/<SOFTWARE>`
+    - publish_dir_mode:
+        type: string
+        description: |
+            Value for the Nextflow `publishDir` mode parameter.
+            Available: symlink, rellink, link, copy, copyNoFollow, move.
+    - enable_conda:
+        type: boolean
+        description: |
+            Run the module with Conda using the software specified
+            via the `conda` directive
+    - singularity_pull_docker_container:
+        type: boolean
+        description: |
+            Instead of directly downloading Singularity images for use with Singularity,
+            force the workflow to pull and convert Docker containers instead.
+input:
+    - fasta:
+        type: file
+        description: Input genome fasta file
+output:
+    - index:
+        type: dir
+        description: Directory containing bwameth genome index
+        pattern: "index"
+    - version:
+        type: file
+        description: File containing software version
+        pattern: "*.{version.txt}"
+authors:
+    - "@phue"

software/gatk4/bedtointervallist/functions.nf

@@ -0,0 +1,59 @@
+/*
+ * -----------------------------------------------------
+ *  Utility functions used in nf-core DSL2 module files
+ * -----------------------------------------------------
+ */
+
+/*
+ * Extract name of software tool from process name using $task.process
+ */
+def getSoftwareName(task_process) {
+    return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
+}
+
+/*
+ * Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
+ */
+def initOptions(Map args) {
+    def Map options = [:]
+    options.args          = args.args ?: ''
+    options.args2         = args.args2 ?: ''
+    options.publish_by_id = args.publish_by_id ?: false
+    options.publish_dir   = args.publish_dir ?: ''
+    options.publish_files = args.publish_files
+    options.suffix        = args.suffix ?: ''
+    return options
+}
+
+/*
+ * Tidy up and join elements of a list to return a path string
+ */
+def getPathFromList(path_list) {
+    def paths = path_list.findAll { item -> !item?.trim().isEmpty() }  // Remove empty entries
+    paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
+    return paths.join('/')
+}
+
+/*
+ * Function to save/publish module results
+ */
+def saveFiles(Map args) {
+    if (!args.filename.endsWith('.version.txt')) {
+        def ioptions = initOptions(args.options)
+        def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
+        if (ioptions.publish_by_id) {
+            path_list.add(args.publish_id)
+        }
+        if (ioptions.publish_files instanceof Map) {
+            for (ext in ioptions.publish_files) {
+                if (args.filename.endsWith(ext.key)) {
+                    def ext_list = path_list.collect()
+                    ext_list.add(ext.value)
+                    return "${getPathFromList(ext_list)}/$args.filename"
+                }
+            }
+        } else if (ioptions.publish_files == null) {
+            return "${getPathFromList(path_list)}/$args.filename"
+        }
+    }
+}

software/gatk4/bedtointervallist/main.nf

@@ -0,0 +1,41 @@
+// Import generic module functions
+include { initOptions; saveFiles; getSoftwareName } from './functions'
+
+params.options = [:]
+def options    = initOptions(params.options)
+
+process GATK4_BEDTOINTERVALLIST {
+    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::gatk4:4.1.9.0' : null)
+    if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
+        container 'https://depot.galaxyproject.org/singularity/gatk4:4.1.9.0--py39_0'
+    } else {
+        container 'quay.io/biocontainers/gatk4:4.1.9.0--py39_0'
+    }
+
+    input:
+    tuple val(meta), path(bed)
+    path sequence_dict
+
+    output:
+    tuple val(meta), path('*.interval_list'), emit: interval_list
+    path  '*.version.txt'                   , emit: version
+
+    script:
+    def software = getSoftwareName(task.process)
+    def prefix   = options.suffix ? "${meta.id}.${options.suffix}" : "${meta.id}"
+    """
+    gatk BedToIntervalList \\
+        -I $bed \\
+        -SD $sequence_dict \\
+        -O ${prefix}.interval_list \\
+        $options.args
+
+    gatk --version | grep Picard | sed "s/Picard Version: //g" > ${software}.version.txt
+    """
+}

software/gatk4/bedtointervallist/meta.yml

@@ -0,0 +1,60 @@
+name: gatk4_bedtointervallist
+description: Creates an interval list from a bed file and a reference dict
+keywords:
+  - bed
+  - interval list
+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
+params:
+  - outdir:
+      type: string
+      description: |
+        The pipeline's output directory. By default, the module will
+        output files into `$params.outdir/<SOFTWARE>`
+  - publish_dir_mode:
+      type: string
+      description: |
+        Value for the Nextflow `publishDir` mode parameter.
+        Available: symlink, rellink, link, copy, copyNoFollow, move.
+  - enable_conda:
+      type: boolean
+      description: |
+        Run the module with Conda using the software specified
+        via the `conda` directive
+  - singularity_pull_docker_container:
+      type: boolean
+      description: |
+        Instead of directly downloading Singularity images for use with Singularity,
+        force the workflow to pull and convert Docker containers instead.
+input:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test']
+  - bed:
+      type: file
+      description: Input bed file
+      pattern: "*.bed"
+  - dict:
+      type: file
+      description: Sequence dictionary
+      pattern: "*.dict"
+output:
+  - interval_list:
+      type: file
+      description: gatk interval list file
+      pattern: "*.interval_list"
+  - version:
+      type: file
+      description: File containing software version
+      pattern: "*.version.txt"
+authors:
+  - "@kevinmenden"

software/gatk4/mergevcfs/functions.nf

@@ -0,0 +1,59 @@
+/*
+ * -----------------------------------------------------
+ *  Utility functions used in nf-core DSL2 module files
+ * -----------------------------------------------------
+ */
+
+/*
+ * Extract name of software tool from process name using $task.process
+ */
+def getSoftwareName(task_process) {
+    return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
+}
+
+/*
+ * Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
+ */
+def initOptions(Map args) {
+    def Map options = [:]
+    options.args          = args.args ?: ''
+    options.args2         = args.args2 ?: ''
+    options.publish_by_id = args.publish_by_id ?: false
+    options.publish_dir   = args.publish_dir ?: ''
+    options.publish_files = args.publish_files
+    options.suffix        = args.suffix ?: ''
+    return options
+}
+
+/*
+ * Tidy up and join elements of a list to return a path string
+ */
+def getPathFromList(path_list) {
+    def paths = path_list.findAll { item -> !item?.trim().isEmpty() }  // Remove empty entries
+    paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
+    return paths.join('/')
+}
+
+/*
+ * Function to save/publish module results
+ */
+def saveFiles(Map args) {
+    if (!args.filename.endsWith('.version.txt')) {
+        def ioptions = initOptions(args.options)
+        def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
+        if (ioptions.publish_by_id) {
+            path_list.add(args.publish_id)
+        }
+        if (ioptions.publish_files instanceof Map) {
+            for (ext in ioptions.publish_files) {
+                if (args.filename.endsWith(ext.key)) {
+                    def ext_list = path_list.collect()
+                    ext_list.add(ext.value)
+                    return "${getPathFromList(ext_list)}/$args.filename"
+                }
+            }
+        } else if (ioptions.publish_files == null) {
+            return "${getPathFromList(path_list)}/$args.filename"
+        }
+    }
+}

software/gatk4/mergevcfs/main.nf

@@ -0,0 +1,48 @@
+// Import generic module functions
+include { initOptions; saveFiles; getSoftwareName } from './functions'
+
+params.options = [:]
+def options    = initOptions(params.options)
+
+process GATK4_MERGEVCFS {
+    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::gatk4:4.1.9.0' : null)
+    if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
+        container 'https://depot.galaxyproject.org/singularity/gatk4:4.1.9.0--py39_0'
+    } else {
+        container 'quay.io/biocontainers/gatk4:4.1.9.0--py39_0'
+    }
+
+    input:
+    tuple val(meta), path(vcfs)
+    path(ref_dict)
+    val use_ref_dict
+
+    output:
+    tuple val(meta), path('*.vcf.gz')       , emit: vcf
+    path  '*.version.txt'                   , emit: version
+
+    script:
+    def software = getSoftwareName(task.process)
+    def prefix   = options.suffix ? "${meta.id}.${options.suffix}" : "${meta.id}"
+    // Make list of VCFs to merge
+    def input = ""
+    for (vcf in vcfs) {
+        input += " I=${vcf}"
+    }
+    def ref = use_ref_dict ? "D=${ref_dict}" : ""
+    """
+    gatk MergeVcfs \\
+        $input \\
+        O=${prefix}.merged.vcf.gz \\
+        $ref \\
+        $options.args
+
+    gatk --version | grep Picard | sed "s/Picard Version: //g" > ${software}.version.txt
+    """
+}

software/gatk4/mergevcfs/meta.yml

@@ -0,0 +1,63 @@
+name: gatk4_mergevcfs
+description: Merges several vcf files
+keywords:
+  - vcf
+  - merge
+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
+params:
+  - outdir:
+      type: string
+      description: |
+        The pipeline's output directory. By default, the module will
+        output files into `$params.outdir/<SOFTWARE>`
+  - publish_dir_mode:
+      type: string
+      description: |
+        Value for the Nextflow `publishDir` mode parameter.
+        Available: symlink, rellink, link, copy, copyNoFollow, move.
+  - enable_conda:
+      type: boolean
+      description: |
+        Run the module with Conda using the software specified
+        via the `conda` directive
+  - singularity_pull_docker_container:
+      type: boolean
+      description: |
+        Instead of directly downloading Singularity images for use with Singularity,
+        force the workflow to pull and convert Docker containers instead.
+input:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test']
+  - vcf:
+      type: list
+      description: Two or more VCF files
+      pattern: "*.{vcf,vcf.gz}"
+  - ref_dict:
+      type: file
+      description: Optional Sequence Dictionary as input
+      pattern: "*.dict"
+  - use_ref_dict:
+      type: boolean
+      description: Specify whether or not to use a given reference dictionary
+output:
+  - vcf:
+      type: file
+      description: merged vcf file
+      pattern: "*.vcf.gz"
+  - version:
+      type: file
+      description: File containing software version
+      pattern: "*.version.txt"
+authors:
+  - "@kevinmenden"

software/gatk4/revertsam/functions.nf

@@ -0,0 +1,59 @@
+/*
+ * -----------------------------------------------------
+ *  Utility functions used in nf-core DSL2 module files
+ * -----------------------------------------------------
+ */
+
+/*
+ * Extract name of software tool from process name using $task.process
+ */
+def getSoftwareName(task_process) {
+    return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
+}
+
+/*
+ * Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
+ */
+def initOptions(Map args) {
+    def Map options = [:]
+    options.args          = args.args ?: ''
+    options.args2         = args.args2 ?: ''
+    options.publish_by_id = args.publish_by_id ?: false
+    options.publish_dir   = args.publish_dir ?: ''
+    options.publish_files = args.publish_files
+    options.suffix        = args.suffix ?: ''
+    return options
+}
+
+/*
+ * Tidy up and join elements of a list to return a path string
+ */
+def getPathFromList(path_list) {
+    def paths = path_list.findAll { item -> !item?.trim().isEmpty() }  // Remove empty entries
+    paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
+    return paths.join('/')
+}
+
+/*
+ * Function to save/publish module results
+ */
+def saveFiles(Map args) {
+    if (!args.filename.endsWith('.version.txt')) {
+        def ioptions = initOptions(args.options)
+        def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
+        if (ioptions.publish_by_id) {
+            path_list.add(args.publish_id)
+        }
+        if (ioptions.publish_files instanceof Map) {
+            for (ext in ioptions.publish_files) {
+                if (args.filename.endsWith(ext.key)) {
+                    def ext_list = path_list.collect()
+                    ext_list.add(ext.value)
+                    return "${getPathFromList(ext_list)}/$args.filename"
+                }
+            }
+        } else if (ioptions.publish_files == null) {
+            return "${getPathFromList(path_list)}/$args.filename"
+        }
+    }
+}

software/gatk4/revertsam/main.nf

@@ -0,0 +1,39 @@
+// Import generic module functions
+include { initOptions; saveFiles; getSoftwareName } from './functions'
+
+params.options = [:]
+def options    = initOptions(params.options)
+
+process GATK4_REVERTSAM {
+    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::gatk4:4.1.9.0' : null)
+    if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
+        container 'https://depot.galaxyproject.org/singularity/gatk4:4.1.9.0--py39_0'
+    } else {
+        container 'quay.io/biocontainers/gatk4:4.1.9.0--py39_0'
+    }
+
+    input:
+    tuple val(meta), path(bam)
+
+    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}" : "${meta.id}"
+    """
+    gatk RevertSam \\
+        I=$bam \\
+        O=${prefix}.reverted.bam \\
+        $options.args
+
+    gatk --version | grep Picard | sed "s/Picard Version: //g" > ${software}.version.txt
+    """
+}

software/gatk4/revertsam/meta.yml

@@ -0,0 +1,56 @@
+name: gatk4_revertsam
+description: Reverts SAM or BAM files to a previous state.
+keywords:
+  - sam
+  - revert
+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
+params:
+  - outdir:
+      type: string
+      description: |
+        The pipeline's output directory. By default, the module will
+        output files into `$params.outdir/<SOFTWARE>`
+  - publish_dir_mode:
+      type: string
+      description: |
+        Value for the Nextflow `publishDir` mode parameter.
+        Available: symlink, rellink, link, copy, copyNoFollow, move.
+  - enable_conda:
+      type: boolean
+      description: |
+        Run the module with Conda using the software specified
+        via the `conda` directive
+  - singularity_pull_docker_container:
+      type: boolean
+      description: |
+        Instead of directly downloading Singularity images for use with Singularity,
+        force the workflow to pull and convert Docker containers instead.
+input:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test']
+  - bam:
+      type: file
+      description: The input bam/sam file
+      pattern: "*.{bam,sam}"
+output:
+  - bam:
+      type: file
+      description: The reverted bam/sam file
+      pattern: "*.reverted.bam"
+  - version:
+      type: file
+      description: File containing software version
+      pattern: "*.version.txt"
+authors:
+  - "@kevinmenden"

software/gatk4/samtofastq/functions.nf

@@ -0,0 +1,59 @@
+/*
+ * -----------------------------------------------------
+ *  Utility functions used in nf-core DSL2 module files
+ * -----------------------------------------------------
+ */
+
+/*
+ * Extract name of software tool from process name using $task.process
+ */
+def getSoftwareName(task_process) {
+    return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
+}
+
+/*
+ * Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
+ */
+def initOptions(Map args) {
+    def Map options = [:]
+    options.args          = args.args ?: ''
+    options.args2         = args.args2 ?: ''
+    options.publish_by_id = args.publish_by_id ?: false
+    options.publish_dir   = args.publish_dir ?: ''
+    options.publish_files = args.publish_files
+    options.suffix        = args.suffix ?: ''
+    return options
+}
+
+/*
+ * Tidy up and join elements of a list to return a path string
+ */
+def getPathFromList(path_list) {
+    def paths = path_list.findAll { item -> !item?.trim().isEmpty() }  // Remove empty entries
+    paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
+    return paths.join('/')
+}
+
+/*
+ * Function to save/publish module results
+ */
+def saveFiles(Map args) {
+    if (!args.filename.endsWith('.version.txt')) {
+        def ioptions = initOptions(args.options)
+        def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
+        if (ioptions.publish_by_id) {
+            path_list.add(args.publish_id)
+        }
+        if (ioptions.publish_files instanceof Map) {
+            for (ext in ioptions.publish_files) {
+                if (args.filename.endsWith(ext.key)) {
+                    def ext_list = path_list.collect()
+                    ext_list.add(ext.value)
+                    return "${getPathFromList(ext_list)}/$args.filename"
+                }
+            }
+        } else if (ioptions.publish_files == null) {
+            return "${getPathFromList(path_list)}/$args.filename"
+        }
+    }
+}

software/gatk4/samtofastq/main.nf

@@ -0,0 +1,40 @@
+// Import generic module functions
+include { initOptions; saveFiles; getSoftwareName } from './functions'
+
+params.options = [:]
+def options    = initOptions(params.options)
+
+process GATK4_SAMTOFASTQ {
+    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::gatk4:4.1.9.0' : null)
+    if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
+        container 'https://depot.galaxyproject.org/singularity/gatk4:4.1.9.0--py39_0'
+    } else {
+        container 'quay.io/biocontainers/gatk4:4.1.9.0--py39_0'
+    }
+
+    input:
+    tuple val(meta), path(bam)
+
+    output:
+    tuple val(meta), path('*.fastq.gz')     , emit: fastq
+    path  '*.version.txt'                   , emit: version
+
+    script:
+    def software = getSoftwareName(task.process)
+    def prefix   = options.suffix ? "${meta.id}.${options.suffix}" : "${meta.id}"
+    def output = meta.single_end ? "FASTQ=${prefix}.fastq.gz" : "FASTQ=${prefix}_1.fastq.gz SECOND_END_FASTQ=${prefix}_2.fastq.gz"
+    """
+    gatk SamToFastq \\
+        I=$bam \\
+        $output \\
+        $options.args
+
+    gatk --version | grep Picard | sed "s/Picard Version: //g" > ${software}.version.txt
+    """
+}

software/gatk4/samtofastq/meta.yml

@@ -0,0 +1,56 @@
+name: gatk4_samtofastq
+description: Converts BAM/SAM file to FastQ format
+keywords:
+  - bed
+  - interval list
+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
+params:
+  - outdir:
+      type: string
+      description: |
+        The pipeline's output directory. By default, the module will
+        output files into `$params.outdir/<SOFTWARE>`
+  - publish_dir_mode:
+      type: string
+      description: |
+        Value for the Nextflow `publishDir` mode parameter.
+        Available: symlink, rellink, link, copy, copyNoFollow, move.
+  - enable_conda:
+      type: boolean
+      description: |
+        Run the module with Conda using the software specified
+        via the `conda` directive
+  - singularity_pull_docker_container:
+      type: boolean
+      description: |
+        Instead of directly downloading Singularity images for use with Singularity,
+        force the workflow to pull and convert Docker containers instead.
+input:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test']
+  - bam:
+      type: file
+      description: Input SAM/BAM file
+      pattern: "*.{bam,sam}"
+output:
+  - fastq:
+      type: file
+      description: converted fastq file
+      pattern: "*.fastq"
+  - version:
+      type: file
+      description: File containing software version
+      pattern: "*.version.txt"
+authors:
+  - "@kevinmenden"

software/gatk4/splitncigarreads/functions.nf

@@ -0,0 +1,59 @@
+/*
+ * -----------------------------------------------------
+ *  Utility functions used in nf-core DSL2 module files
+ * -----------------------------------------------------
+ */
+
+/*
+ * Extract name of software tool from process name using $task.process
+ */
+def getSoftwareName(task_process) {
+    return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
+}
+
+/*
+ * Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
+ */
+def initOptions(Map args) {
+    def Map options = [:]
+    options.args          = args.args ?: ''
+    options.args2         = args.args2 ?: ''
+    options.publish_by_id = args.publish_by_id ?: false
+    options.publish_dir   = args.publish_dir ?: ''
+    options.publish_files = args.publish_files
+    options.suffix        = args.suffix ?: ''
+    return options
+}
+
+/*
+ * Tidy up and join elements of a list to return a path string
+ */
+def getPathFromList(path_list) {
+    def paths = path_list.findAll { item -> !item?.trim().isEmpty() }  // Remove empty entries
+    paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
+    return paths.join('/')
+}
+
+/*
+ * Function to save/publish module results
+ */
+def saveFiles(Map args) {
+    if (!args.filename.endsWith('.version.txt')) {
+        def ioptions = initOptions(args.options)
+        def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
+        if (ioptions.publish_by_id) {
+            path_list.add(args.publish_id)
+        }
+        if (ioptions.publish_files instanceof Map) {
+            for (ext in ioptions.publish_files) {
+                if (args.filename.endsWith(ext.key)) {
+                    def ext_list = path_list.collect()
+                    ext_list.add(ext.value)
+                    return "${getPathFromList(ext_list)}/$args.filename"
+                }
+            }
+        } else if (ioptions.publish_files == null) {
+            return "${getPathFromList(path_list)}/$args.filename"
+        }
+    }
+}

software/gatk4/splitncigarreads/main.nf

@@ -0,0 +1,41 @@
+// Import generic module functions
+include { initOptions; saveFiles; getSoftwareName } from './functions'
+
+params.options = [:]
+def options    = initOptions(params.options)
+
+process GATK4_SPLITNCIGARREADS {
+    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::gatk4:4.1.9.0' : null)
+    if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
+        container 'https://depot.galaxyproject.org/singularity/gatk4:4.1.9.0--py39_0'
+    } else {
+        container 'quay.io/biocontainers/gatk4:4.1.9.0--py39_0'
+    }
+
+    input:
+    tuple val(meta), path(bam)
+    tuple path(fasta), path(fai), path(dict)
+
+    output:
+    tuple val(meta), path('*.split_cigar.bam'), emit: bam
+    path  '*.version.txt'                     , emit: version
+
+    script:
+    def software = getSoftwareName(task.process)
+    def prefix   = options.suffix ? "${meta.id}.${options.suffix}" : "${meta.id}"
+    """
+    gatk SplitNCigarReads \\
+        -R $fasta \\
+        -I $bam \\
+        -O ${prefix}.split_cigar.bam \\
+        $options.args
+
+    gatk --version | grep Picard | sed "s/Picard Version: //g" > ${software}.version.txt
+    """
+}

software/gatk4/splitncigarreads/meta.yml

@@ -0,0 +1,61 @@
+name: gatk4_splitncigarreads
+description: Splits reads that contain Ns in their cigar string
+keywords:
+  - vcf
+  - merge
+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
+params:
+  - outdir:
+      type: string
+      description: |
+        The pipeline's output directory. By default, the module will
+        output files into `$params.outdir/<SOFTWARE>`
+  - publish_dir_mode:
+      type: string
+      description: |
+        Value for the Nextflow `publishDir` mode parameter.
+        Available: symlink, rellink, link, copy, copyNoFollow, move.
+  - enable_conda:
+      type: boolean
+      description: |
+        Run the module with Conda using the software specified
+        via the `conda` directive
+  - singularity_pull_docker_container:
+      type: boolean
+      description: |
+        Instead of directly downloading Singularity images for use with Singularity,
+        force the workflow to pull and convert Docker containers instead.
+input:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test']
+  - bam:
+      type: list
+      description: BAM/SAM/CRAM file containing reads
+      pattern: "*.{bam,sam,cram}"
+  - fasta:
+      type: tuple of files
+      description: |
+        Tuple of fasta file (first), sequence dict (second) and fasta index (third)
+      pattern: ["*.fasta", "*.dict", "*.fai"]
+output:
+  - bam:
+      type: file
+      description: Output file with split reads (BAM/SAM/CRAM)
+      pattern: "*.{bam,sam,cram}"
+  - version:
+      type: file
+      description: File containing software version
+      pattern: "*.version.txt"
+authors:
+  - "@kevinmenden"

software/methyldackel/extract/functions.nf

@@ -0,0 +1,59 @@
+/*
+ * -----------------------------------------------------
+ *  Utility functions used in nf-core DSL2 module files
+ * -----------------------------------------------------
+ */
+
+/*
+ * Extract name of software tool from process name using $task.process
+ */
+def getSoftwareName(task_process) {
+    return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
+}
+
+/*
+ * Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
+ */
+def initOptions(Map args) {
+    def Map options = [:]
+    options.args          = args.args ?: ''
+    options.args2         = args.args2 ?: ''
+    options.publish_by_id = args.publish_by_id ?: false
+    options.publish_dir   = args.publish_dir ?: ''
+    options.publish_files = args.publish_files
+    options.suffix        = args.suffix ?: ''
+    return options
+}
+
+/*
+ * Tidy up and join elements of a list to return a path string
+ */
+def getPathFromList(path_list) {
+    def paths = path_list.findAll { item -> !item?.trim().isEmpty() }  // Remove empty entries
+    paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
+    return paths.join('/')
+}
+
+/*
+ * Function to save/publish module results
+ */
+def saveFiles(Map args) {
+    if (!args.filename.endsWith('.version.txt')) {
+        def ioptions = initOptions(args.options)
+        def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
+        if (ioptions.publish_by_id) {
+            path_list.add(args.publish_id)
+        }
+        if (ioptions.publish_files instanceof Map) {
+            for (ext in ioptions.publish_files) {
+                if (args.filename.endsWith(ext.key)) {
+                    def ext_list = path_list.collect()
+                    ext_list.add(ext.value)
+                    return "${getPathFromList(ext_list)}/$args.filename"
+                }
+            }
+        } else if (ioptions.publish_files == null) {
+            return "${getPathFromList(path_list)}/$args.filename"
+        }
+    }
+}

software/methyldackel/extract/main.nf

@@ -0,0 +1,40 @@
+// Import generic module functions
+include { initOptions; saveFiles; getSoftwareName } from './functions'
+
+params.options = [:]
+def options    = initOptions(params.options)
+
+process METHYLDACKEL_EXTRACT {
+    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::methyldackel=0.5.0" : null)
+    if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
+        container "https://depot.galaxyproject.org/singularity/methyldackel:0.5.0--hed50d52_0"
+    } else {
+        container "quay.io/biocontainers/methyldackel:0.5.0--hed50d52_0"
+    }
+
+    input:
+    tuple val(meta), path(bam), path(bai)
+    path fasta
+    path fai
+
+    output:
+    tuple val(meta), path("*.bedGraph"), emit: bedgraph
+    path  "*.version.txt"              , emit: version
+
+    script:
+    def software = getSoftwareName(task.process)
+    """
+    MethylDackel extract \\
+        $options.args \\
+        $fasta \\
+        $bam
+
+    echo \$(methyldackel --version 2>&1) | cut -f1 -d" " > ${software}.version.txt
+    """
+}

software/methyldackel/extract/meta.yml

@@ -0,0 +1,78 @@
+name: methyldackel_extract
+description: Extracts per-base methylation metrics from alignments
+keywords:
+    - methylation
+    - 5mC
+    - methylseq
+    - bisulphite
+    - consensus
+    - bedGraph
+    - bam
+    - cram
+tools:
+    - methyldackel:
+        description: |
+            A (mostly) universal methylation extractor
+            for BS-seq experiments.
+        homepage: https://github.com/brentp/bwa-meth
+        documentation: https://github.com/brentp/bwa-meth
+        arxiv: arXiv:1401.1129
+params:
+    - outdir:
+        type: string
+        description: |
+            The pipeline's output directory. By default, the module will
+            output files into `$params.outdir/<SOFTWARE>`
+    - publish_dir_mode:
+        type: string
+        description: |
+            Value for the Nextflow `publishDir` mode parameter.
+            Available: symlink, rellink, link, copy, copyNoFollow, move.
+    - enable_conda:
+        type: boolean
+        description: |
+            Run the module with Conda using the software specified
+            via the `conda` directive
+    - singularity_pull_docker_container:
+        type: boolean
+        description: |
+            Instead of directly downloading Singularity images for use with Singularity,
+            force the workflow to pull and convert Docker containers instead.
+input:
+    - meta:
+        type: map
+        description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test', single_end:false ]
+    - fasta:
+        type: file
+        description: Input genome fasta file
+        pattern: "*.{fasta,fa}"
+    - fai:
+        type: file
+        description: FASTA index file
+        pattern: "*.{fai}"
+    - bam:
+        type: file
+        description: BAM/CRAM file
+        pattern: "*.{bam,cram}"
+    - bai:
+        type: file
+        description: BAM/CRAM index file
+        pattern: "*.{bai,crai}"
+output:
+    - meta:
+        type: map
+        description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test', single_end:false ]
+    - bedgraph:
+        type: file
+        description: bedGraph file containing per-base methylation metrics
+        pattern: "*.{bedGraph}"
+    - version:
+        type: file
+        description: File containing software version
+        pattern: "*.{version.txt}"
+authors:
+    - "@phue"

software/methyldackel/mbias/functions.nf

@@ -0,0 +1,59 @@
+/*
+ * -----------------------------------------------------
+ *  Utility functions used in nf-core DSL2 module files
+ * -----------------------------------------------------
+ */
+
+/*
+ * Extract name of software tool from process name using $task.process
+ */
+def getSoftwareName(task_process) {
+    return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
+}
+
+/*
+ * Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
+ */
+def initOptions(Map args) {
+    def Map options = [:]
+    options.args          = args.args ?: ''
+    options.args2         = args.args2 ?: ''
+    options.publish_by_id = args.publish_by_id ?: false
+    options.publish_dir   = args.publish_dir ?: ''
+    options.publish_files = args.publish_files
+    options.suffix        = args.suffix ?: ''
+    return options
+}
+
+/*
+ * Tidy up and join elements of a list to return a path string
+ */
+def getPathFromList(path_list) {
+    def paths = path_list.findAll { item -> !item?.trim().isEmpty() }  // Remove empty entries
+    paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
+    return paths.join('/')
+}
+
+/*
+ * Function to save/publish module results
+ */
+def saveFiles(Map args) {
+    if (!args.filename.endsWith('.version.txt')) {
+        def ioptions = initOptions(args.options)
+        def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
+        if (ioptions.publish_by_id) {
+            path_list.add(args.publish_id)
+        }
+        if (ioptions.publish_files instanceof Map) {
+            for (ext in ioptions.publish_files) {
+                if (args.filename.endsWith(ext.key)) {
+                    def ext_list = path_list.collect()
+                    ext_list.add(ext.value)
+                    return "${getPathFromList(ext_list)}/$args.filename"
+                }
+            }
+        } else if (ioptions.publish_files == null) {
+            return "${getPathFromList(path_list)}/$args.filename"
+        }
+    }
+}

software/methyldackel/mbias/main.nf

@@ -0,0 +1,44 @@
+// Import generic module functions
+include { initOptions; saveFiles; getSoftwareName } from './functions'
+
+params.options = [:]
+def options    = initOptions(params.options)
+
+process METHYLDACKEL_MBIAS {
+    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), publish_id:meta.id) }
+
+    conda (params.enable_conda ? "bioconda::methyldackel=0.5.0" : null)
+    if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
+        container "https://depot.galaxyproject.org/singularity/methyldackel:0.5.0--hed50d52_0"
+    } else {
+        container "quay.io/biocontainers/methyldackel:0.5.0--hed50d52_0"
+    }
+
+    input:
+    tuple val(meta), path(bam), path(bai)
+    path fasta
+    path fai
+
+    output:
+    tuple val(meta), path("*.txt"), emit: txt
+    path  "*.version.txt"         , emit: version
+
+    script:
+    def software = getSoftwareName(task.process)
+    def prefix   = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
+    """
+    MethylDackel mbias \\
+        $options.args \\
+        $fasta \\
+        $bam \\
+        $prefix \\
+        --txt \\
+        > ${prefix}.txt
+
+    echo \$(methyldackel --version 2>&1) | cut -f1 -d" " > ${software}.version.txt
+    """
+}

software/methyldackel/mbias/meta.yml

@@ -0,0 +1,79 @@
+name: methyldackel_mbias
+description: Generates methylation bias plots from alignments
+keywords:
+    - methylation
+    - 5mC
+    - methylseq
+    - bisulphite
+    - methylation bias
+    - mbias
+    - qc
+    - bam
+    - cram
+tools:
+    - methyldackel:
+        description: |
+            A (mostly) universal methylation extractor
+            for BS-seq experiments.
+        homepage: https://github.com/brentp/bwa-meth
+        documentation: https://github.com/brentp/bwa-meth
+        arxiv: arXiv:1401.1129
+params:
+    - outdir:
+        type: string
+        description: |
+            The pipeline's output directory. By default, the module will
+            output files into `$params.outdir/<SOFTWARE>`
+    - publish_dir_mode:
+        type: string
+        description: |
+            Value for the Nextflow `publishDir` mode parameter.
+            Available: symlink, rellink, link, copy, copyNoFollow, move.
+    - enable_conda:
+        type: boolean
+        description: |
+            Run the module with Conda using the software specified
+            via the `conda` directive
+    - singularity_pull_docker_container:
+        type: boolean
+        description: |
+            Instead of directly downloading Singularity images for use with Singularity,
+            force the workflow to pull and convert Docker containers instead.
+input:
+    - meta:
+        type: map
+        description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test', single_end:false ]
+    - fasta:
+        type: file
+        description: Input genome fasta file
+        pattern: "*.{fasta,fa}"
+    - fai:
+        type: file
+        description: FASTA index file
+        pattern: "*.{fai}"
+    - bam:
+        type: file
+        description: BAM/CRAM file
+        pattern: "*.{bam,cram}"
+    - bai:
+        type: file
+        description: BAM/CRAM index file
+        pattern: "*.{bai,crai}"
+output:
+    - meta:
+        type: map
+        description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test', single_end:false ]
+    - txt:
+        type: file
+        description: Text file containing methylation bias
+        pattern: "*.{txt}"
+    - version:
+        type: file
+        description: File containing software version
+        pattern: "*.{version.txt}"
+authors:
+    - "@phue"

software/qualimap/bamqc/functions.nf

@@ -0,0 +1,59 @@
+/*
+ * -----------------------------------------------------
+ *  Utility functions used in nf-core DSL2 module files
+ * -----------------------------------------------------
+ */
+
+/*
+ * Extract name of software tool from process name using $task.process
+ */
+def getSoftwareName(task_process) {
+    return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
+}
+
+/*
+ * Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
+ */
+def initOptions(Map args) {
+    def Map options = [:]
+    options.args          = args.args ?: ''
+    options.args2         = args.args2 ?: ''
+    options.publish_by_id = args.publish_by_id ?: false
+    options.publish_dir   = args.publish_dir ?: ''
+    options.publish_files = args.publish_files
+    options.suffix        = args.suffix ?: ''
+    return options
+}
+
+/*
+ * Tidy up and join elements of a list to return a path string
+ */
+def getPathFromList(path_list) {
+    def paths = path_list.findAll { item -> !item?.trim().isEmpty() }  // Remove empty entries
+    paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
+    return paths.join('/')
+}
+
+/*
+ * Function to save/publish module results
+ */
+def saveFiles(Map args) {
+    if (!args.filename.endsWith('.version.txt')) {
+        def ioptions = initOptions(args.options)
+        def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
+        if (ioptions.publish_by_id) {
+            path_list.add(args.publish_id)
+        }
+        if (ioptions.publish_files instanceof Map) {
+            for (ext in ioptions.publish_files) {
+                if (args.filename.endsWith(ext.key)) {
+                    def ext_list = path_list.collect()
+                    ext_list.add(ext.value)
+                    return "${getPathFromList(ext_list)}/$args.filename"
+                }
+            }
+        } else if (ioptions.publish_files == null) {
+            return "${getPathFromList(path_list)}/$args.filename"
+        }
+    }
+}

software/qualimap/bamqc/main.nf

@@ -0,0 +1,61 @@
+// Import generic module functions
+include { initOptions; saveFiles; getSoftwareName } from './functions'
+
+params.options = [:]
+def options    = initOptions(params.options)
+
+process QUALIMAP_BAMQC {
+    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::qualimap=2.2.2d" : null)
+    if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
+        container "https://depot.galaxyproject.org/singularity/qualimap:2.2.2d--1"
+    } else {
+        container "quay.io/biocontainers/qualimap:2.2.2d--1"
+    }
+
+    input:
+    tuple val(meta), path(bam)
+    path gff
+    val use_gff
+
+    output:
+    tuple val(meta), path("${prefix}"), emit: results
+    path  "*.version.txt"             , emit: version
+
+    script:
+    def software   = getSoftwareName(task.process)
+    prefix         = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
+
+    def collect_pairs = meta.single_end ? '' : '--collect-overlap-pairs'
+    def memory     = task.memory.toGiga() + "G"
+    def regions = use_gff ? "--gff $gff" : ''
+
+    def strandedness = 'non-strand-specific'
+    if (meta.strandedness == 'forward') {
+        strandedness = 'strand-specific-forward'
+    } else if (meta.strandedness == 'reverse') {
+        strandedness = 'strand-specific-reverse'
+    }
+    """
+    unset DISPLAY
+    mkdir tmp
+    export _JAVA_OPTIONS=-Djava.io.tmpdir=./tmp
+    qualimap \\
+        --java-mem-size=$memory \\
+        bamqc \\
+        $options.args \\
+        -bam $bam \\
+        $regions \\
+        -p $strandedness \\
+        $collect_pairs \\
+        -outdir $prefix \\
+        -nt $task.cpus
+
+    echo \$(qualimap 2>&1) | sed 's/^.*QualiMap v.//; s/Built.*\$//' > ${software}.version.txt
+    """
+}

software/qualimap/bamqc/meta.yml

@@ -0,0 +1,70 @@
+name: qualimap_bamqc
+description: Evaluate alignment data
+keywords:
+    - quality control
+    - qc
+    - bam
+tools:
+    - qualimap:
+        description: |
+          Qualimap 2 is a platform-independent application written in
+          Java and R that provides both a Graphical User Interface and
+          a command-line interface to facilitate the quality control of
+          alignment sequencing data and its derivatives like feature counts.
+        homepage: http://qualimap.bioinfo.cipf.es/
+        documentation: http://qualimap.conesalab.org/doc_html/index.html
+        doi: 10.1093/bioinformatics/bts503
+params:
+    - outdir:
+        type: string
+        description: |
+            The pipeline's output directory. By default, the module will
+            output files into `$params.outdir/<SOFTWARE>`
+    - publish_dir_mode:
+        type: string
+        description: |
+            Value for the Nextflow `publishDir` mode parameter.
+            Available: symlink, rellink, link, copy, copyNoFollow, move.
+    - enable_conda:
+        type: boolean
+        description: |
+            Run the module with Conda using the software specified
+            via the `conda` directive
+    - singularity_pull_docker_container:
+        type: boolean
+        description: |
+            Instead of directly downloading Singularity images for use with Singularity,
+            force the workflow to pull and convert Docker containers instead.
+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}"
+    - gff:
+        type: file
+        description: Feature file with regions of interest
+        pattern: "*.{gff,gtf,bed}"
+    - use_gff:
+        type: boolean
+        description: Specifies if feature file should be used or not
+output:
+    - meta:
+        type: map
+        description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test', single_end:false ]
+    - results:
+        type: dir
+        description: Qualimap results dir
+        pattern: "*/*"
+    - version:
+        type: file
+        description: File containing software version
+        pattern: "*.{version.txt}"
+authors:
+    - "@phue"

software/samtools/faidx/functions.nf

@@ -0,0 +1,59 @@
+/*
+ * -----------------------------------------------------
+ *  Utility functions used in nf-core DSL2 module files
+ * -----------------------------------------------------
+ */
+
+/*
+ * Extract name of software tool from process name using $task.process
+ */
+def getSoftwareName(task_process) {
+    return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
+}
+
+/*
+ * Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
+ */
+def initOptions(Map args) {
+    def Map options = [:]
+    options.args          = args.args ?: ''
+    options.args2         = args.args2 ?: ''
+    options.publish_by_id = args.publish_by_id ?: false
+    options.publish_dir   = args.publish_dir ?: ''
+    options.publish_files = args.publish_files
+    options.suffix        = args.suffix ?: ''
+    return options
+}
+
+/*
+ * Tidy up and join elements of a list to return a path string
+ */
+def getPathFromList(path_list) {
+    def paths = path_list.findAll { item -> !item?.trim().isEmpty() }  // Remove empty entries
+    paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
+    return paths.join('/')
+}
+
+/*
+ * Function to save/publish module results
+ */
+def saveFiles(Map args) {
+    if (!args.filename.endsWith('.version.txt')) {
+        def ioptions = initOptions(args.options)
+        def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
+        if (ioptions.publish_by_id) {
+            path_list.add(args.publish_id)
+        }
+        if (ioptions.publish_files instanceof Map) {
+            for (ext in ioptions.publish_files) {
+                if (args.filename.endsWith(ext.key)) {
+                    def ext_list = path_list.collect()
+                    ext_list.add(ext.value)
+                    return "${getPathFromList(ext_list)}/$args.filename"
+                }
+            }
+        } else if (ioptions.publish_files == null) {
+            return "${getPathFromList(path_list)}/$args.filename"
+        }
+    }
+}

software/samtools/faidx/main.nf

@@ -0,0 +1,33 @@
+// Import generic module functions
+include { saveFiles; getSoftwareName } from './functions'
+
+params.options = [:]
+
+process SAMTOOLS_FAIDX {
+    tag "$fasta"
+    label 'process_low'
+    publishDir "${params.outdir}",
+        mode: params.publish_dir_mode,
+        saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:'') }
+
+    conda (params.enable_conda ? "bioconda::samtools=1.10" : null)
+    if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
+        container "https://depot.galaxyproject.org/singularity/samtools:1.10--h9402c20_2"
+    } else {
+        container "quay.io/biocontainers/samtools:1.10--h9402c20_2"
+    }
+
+    input:
+    path fasta
+
+    output:
+    path "*.fai"        , emit: fai
+    path "*.version.txt", emit: version
+
+    script:
+    def software = getSoftwareName(task.process)
+    """
+    samtools faidx $fasta
+    echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//' > ${software}.version.txt
+    """
+}

software/samtools/faidx/meta.yml

@@ -0,0 +1,53 @@
+name: samtools_faidx
+description: Index FASTA file
+keywords:
+    - index
+    - fasta
+tools:
+    - samtools:
+        description: |
+            SAMtools is a set of utilities for interacting with and post-processing
+            short DNA sequence read alignments in the SAM, BAM and CRAM formats, written by Heng Li.
+            These files are generated as output by short read aligners like BWA.
+        homepage: http://www.htslib.org/
+        documentation: http://www.htslib.org/doc/samtools.html
+        doi: 10.1093/bioinformatics/btp352
+params:
+    - outdir:
+        type: string
+        description: |
+            The pipeline's output directory. By default, the module will
+            output files into `$params.outdir/<SOFTWARE>`
+    - publish_dir_mode:
+        type: string
+        description: |
+            Value for the Nextflow `publishDir` mode parameter.
+            Available: symlink, rellink, link, copy, copyNoFollow, move.
+    - enable_conda:
+        type: boolean
+        description: |
+            Run the module with Conda using the software specified
+            via the `conda` directive
+    - singularity_pull_docker_container:
+        type: boolean
+        description: |
+            Instead of directly downloading Singularity images for use with Singularity,
+            force the workflow to pull and convert Docker containers instead.
+input:
+    - fasta:
+        type: file
+        description: FASTA file
+        pattern: "*.{fa,fasta}"
+output:
+    - fai:
+        type: file
+        description: FASTA index file
+        pattern: "*.{fai}"
+    - version:
+        type: file
+        description: File containing software version
+        pattern: "*.{version.txt}"
+authors:
+    - "@drpatelh"
+    - "@ewels"
+    - "@phue"

software/seqwish/induce/functions.nf

@@ -0,0 +1,59 @@
+/*
+ * -----------------------------------------------------
+ *  Utility functions used in nf-core DSL2 module files
+ * -----------------------------------------------------
+ */
+
+/*
+ * Extract name of software tool from process name using $task.process
+ */
+def getSoftwareName(task_process) {
+    return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
+}
+
+/*
+ * Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
+ */
+def initOptions(Map args) {
+    def Map options = [:]
+    options.args          = args.args ?: ''
+    options.args2         = args.args2 ?: ''
+    options.publish_by_id = args.publish_by_id ?: false
+    options.publish_dir   = args.publish_dir ?: ''
+    options.publish_files = args.publish_files
+    options.suffix        = args.suffix ?: ''
+    return options
+}
+
+/*
+ * Tidy up and join elements of a list to return a path string
+ */
+def getPathFromList(path_list) {
+    def paths = path_list.findAll { item -> !item?.trim().isEmpty() }  // Remove empty entries
+    paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
+    return paths.join('/')
+}
+
+/*
+ * Function to save/publish module results
+ */
+def saveFiles(Map args) {
+    if (!args.filename.endsWith('.version.txt')) {
+        def ioptions = initOptions(args.options)
+        def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
+        if (ioptions.publish_by_id) {
+            path_list.add(args.publish_id)
+        }
+        if (ioptions.publish_files instanceof Map) {
+            for (ext in ioptions.publish_files) {
+                if (args.filename.endsWith(ext.key)) {
+                    def ext_list = path_list.collect()
+                    ext_list.add(ext.value)
+                    return "${getPathFromList(ext_list)}/$args.filename"
+                }
+            }
+        } else if (ioptions.publish_files == null) {
+            return "${getPathFromList(path_list)}/$args.filename"
+        }
+    }
+}

software/seqwish/induce/main.nf

@@ -0,0 +1,44 @@
+// Import generic module functions
+include { initOptions; saveFiles; getSoftwareName } from './functions'
+params.options = [:]
+def options    = initOptions(params.options)
+
+def VERSION = '0.4.1'
+
+process SEQWISH_INDUCE {
+    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::seqwish=0.4.1" : null)
+
+    if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
+        container "https://depot.galaxyproject.org/singularity/seqwish:0.4.1--h8b12597_0"
+    } else {
+        container "quay.io/biocontainers/seqwish:0.4.1--h8b12597_0"
+    }
+
+    input:
+    tuple val(meta), path(paf), path(fasta)
+
+    output:
+    tuple val(meta), path("*.gfa"), emit: gfa
+    path "*.version.txt"          , emit: version
+
+
+    script:
+    def software = getSoftwareName(task.process)
+    def prefix   = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
+    """
+    seqwish \\
+        --threads $task.cpus \\
+        --paf-alns=$paf \\
+        --seqs=$fasta \\
+        --gfa=${prefix}.gfa \\
+        $options.args
+
+    echo $VERSION > ${software}.version.txt
+    """
+}

software/seqwish/induce/meta.yml

@@ -0,0 +1,67 @@
+name: seqwish_induce
+description: Induce a variation graph in GFA format from alignments in PAF format
+keywords:
+    - induce
+    - paf
+    - gfa
+    - graph
+    - variation graph
+tools:
+    - seqwish:
+        description: |
+            seqwish implements a lossless conversion from pairwise alignments between
+            sequences to a variation graph encoding the sequences and their alignments.
+        homepage: https://github.com/ekg/seqwish
+        documentation: https://github.com/ekg/seqwish
+params:
+    - outdir:
+        type: string
+        description: |
+            The pipeline's output directory. By default, the module will
+            output files into `$params.outdir/<SOFTWARE>`
+    - publish_dir_mode:
+        type: string
+        description: |
+            Value for the Nextflow `publishDir` mode parameter.
+            Available: symlink, rellink, link, copy, copyNoFollow, move.
+    - enable_conda:
+        type: boolean
+        description: |
+            Run the module with Conda using the software specified
+            via the `conda` directive
+    - singularity_pull_docker_container:
+        type: boolean
+        description: |
+            Instead of directly downloading Singularity images for use with Singularity,
+            force the workflow to pull and convert Docker containers instead.
+input:
+    - meta:
+        type: map
+        description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test', single_end:false ]
+    - paf:
+        type: file
+        description: PAF file of alignments
+        pattern: "*.{paf,paf.gz}"
+    - fasta:
+        type: file
+        description: FASTA file used to generate alignments
+        pattern: "*.{fa,fa.gz,fasta,fasta.gz}"
+
+output:
+    - meta:
+        type: map
+        description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test', single_end:false ]
+    - gfa:
+        type: file
+        description: Variation graph in GFA1 format
+        pattern: "*.{gfa}"
+    - version:
+        type: file
+        description: File containing software version
+        pattern: "*.{version.txt}"
+authors:
+    - "@heuermh"

tests/data/bed/sarscov2.bed

@@ -0,0 +1,4 @@
+MT192765.1	1242	1264	nCoV-2019_5_LEFT	1	+
+MT192765.1	1623	1651	nCoV-2019_5_RIGHT	1	-
+MT192765.1	1573	1595	nCoV-2019_6_LEFT	2	+
+MT192765.1	1942	1964	nCoV-2019_6_RIGHT	2	-

tests/data/fasta/E_coli/NC_010473.fa.fai

@@ -0,0 +1 @@
+gi|170079663|ref|NC_010473.1|	4686137	89	70	71

tests/data/fasta/sarscov2/GCA_011545545.1_ASM1154554v1_genomic.dict

@@ -0,0 +1,2 @@
+@HD	VN:1.6
+@SQ	SN:MT192765.1	LN:29829	M5:c95f3e5592d0ad9974e41e7f0ea14eb0	UR:file:/Users/kevin/Documents/nfcore/modules/tests/data/fasta/sarscov2/GCA_011545545.1_ASM1154554v1_genomic.fna

tests/data/fasta/sarscov2/GCA_011545545.1_ASM1154554v1_genomic.fna.fai

@@ -0,0 +1 @@
+MT192765.1	29829	120	80	81

tests/data/fasta/test.consensus.for_vcf.dict

@@ -0,0 +1,3 @@
+@HD	VN:1.6
+@SQ	SN:1	LN:500	M5:98994ca39b95ec4c96496f6aa8c5c118	UR:file:/Users/kevin/Documents/nfcore/modules/tests/data/fasta/test.consensus.fa
+@SQ	SN:2	LN:501	M5:6cb9f5c857251ffe4420b42453dc9ca3	UR:file:/Users/kevin/Documents/nfcore/modules/tests/data/fasta/test.consensus.fa

tests/data/fasta/test.consensus.for_vcf.fa

@@ -0,0 +1,20 @@
+>1
+TACcAtATgTgACAtATAAaAAAGAACATAACCTACGTATCAACTAAAGTGGTTGTTTG
+cAGAAAAGGAAGACTTAAAAAGAGTCAGTACTAACCTACATAATATATACAATGTTCATT
+AAATAATAAAATGAGCTCATCATACTTAGGTCATCATAAATATATCTGAAATTCACAAAT
+ATTGATCAAATGGTAAAATAGACAAGTAGATTTTAATAGGTTAAACAATTACTGATTCTC
+TTGAAAGAATAAATTTAATATGAGACCTATTTCATTATAATGAACTCACAAATTAGAAAC
+TTCACACTGGGGGCTGGAGAGATGGCTCAGTAGTTAAGAACACTGACTGCTCTTCTGAAG
+GTCCTGAGTTCAAATCCCAGCAACCACATGGTGACTTACAACCATCTGTAATGACATCTG
+ATGCCCTCTGGTGTGTCTGAAGACAGCTACAGTGTACTTACATAAAATAATAAATAAATC
+TTTAAAAACAAAAAAAAAGAA
+>2
+gaagatcttttccttattaaggatctgaagctctgtagatttgtattctattaaacatgg
+AgagattagtgattttccatattctttaagtcattttagagtaatgtgttcttaagatAa
+atcagaaaaacaaaaacttgtgctttcctgtttgaaaaacaaacagctgtggggaatgGt
+gtcgggacagcctttttatAaaatttttctaaataatgttgaggctttgatacgtcaaag
+ttatatttcaaatggaatcacttagacctcgtttctgagtgtcaatggccatattggggA
+tttgctgctgccaatgacaGcacaccctgggaatgccccaactacttactacaaagcagt
+gttacatggagaagatcttcaagagtctttttgctagatctttccttggcttttgatgtg
+actcctctcaataaaatccacagtaatatagtgagtggtctcctgctccaaaccagtatt
+Tcagacacagttaatccagac

tests/data/fastq/dna/sarscov2_1.fastq.gz

@@ -0,0 +1,400 @@
+@ERR5069949.2151832 NS500628:121:HK3MMAFX2:2:21208:10793:15304/1
+TCATAAACCAAAGCACTCACAGTGTCAACAATTTCAGCAGGACAACGCCGACAAGTTCCGAGGAACATGTCTGGACCTATAGTTTTCATAAGTCTACACACTGAATTGAAATATTCTGGTTCTAGTGTGCCCTTAGTTAGCAATGTGCGT
++
+AAAAAAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAAEEEEAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAAEEEEE<EEAAAEEEEEEEEEAAAAEAEEEAEEEEEE<AAAA
+@ERR5069949.576388 NS500628:121:HK3MMAFX2:4:11501:11167:14939/1
+ACTGTTTTCTTTGTAGAAAACATCCGTAATAGGACCTTTGTATTCTGAGGACTTTGTAAGTAAAGCACCGTCTATGC
++
+AAA6AEEEEEEEEEAEEE/6EEAEEEAEEEEEAEEEEEEEEEEEEEEEEEEEEE<AAEEEEEEEEEEE</EEEA/AE
+@ERR5069949.501486 NS500628:121:HK3MMAFX2:1:21305:3080:7962/1
+GTACATAACAGCTTCTACACCCTTAAGGGTTGTCTGCTGTTGTCCACAAGTTTTACACACCACGTTCAAGACTCTTTTGCAAGAATCTAAATTGGCATGTTGAAACAAGTAACTCATTGTTTCTCTAACATCACCTAACTCACCTA
++
+AAAAAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAEEEEEEEEEEAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAEEEEEE</EEEEEE/EEAAEEEEEE<EEEEEEEEA<E6EEEEAEAAAAE
+@ERR5069949.1331889 NS500628:121:HK3MMAFX2:3:11605:17658:18222/1
+GTCTACAAGCTGGTAATGCAACAGAAGTGCCTGCCAATTCAACTGTATTATCTTTCTGTGCTTTTGCTGTAGATGCTGCTAAAGCTTACAAAGATTATCTAGCTAGTGGGGGACAACCAATCACTAATTGTG
++
+A/AAAEEEEEEEEEEEEEEEEEEEAEEEEAEEEEEEEEEEEAEEEEEEEEEEEEEEE/EEEEE<AEAEEEEE/EAEAEEE/AEEEEEEEEEEEEEEEEEEEEAE/EEEEEEEEEEEEEEEEEEEEEEEA<EE
+@ERR5069949.2161340 NS500628:121:HK3MMAFX2:2:21107:15810:18317/1
+AACCAGAATATTTCAATTCAGTGTGTAGACTTATGAAAACTATAGGTCCAGACATGTTCCTCGGAACTTGTCGGCGTTGT
++
+A/AA//EEAEA/E/AEEEE6EE/EEEA/6AEEEEEEEEE6EEEAEAEE//A/EEEEEE//E/E/A//E/E/<<EE</E/E
+@ERR5069949.973930 NS500628:121:HK3MMAFX2:2:21105:5548:5659/1
+CTAAAAGTGAAGTCAAAATTGTGAGTAACAACCAGTGGTGTGTACCCGTGATTGTTCTTTTGACTGCACTTTGGAAAGT
++
+AAAAAEEEEEEEEEEEEEEEEEEEEEEEEE/EEEEEEEAE/E///EE/EE/AE6/A//E/E//</E//E/EE/E////<
+@ERR5069949.2417063 NS500628:121:HK3MMAFX2:1:11310:4428:10115/1
+CCTGTTGTCTATGTGATAGACGTGCCACATGCTTTTCCACTGCTTCAGACACTTATGCCTGTTGGCATCATTCTATTGGATTTGATTACGTCTATAATCCGTTTATGATTGATGTTCAACAATGGGGTTTTACAGGTAACCTACAAAGCA
++
+AAAAAEEEAEEEEEEEEEEEEEEEEEEAEEEEEEEEEEEEEEEAEEEE/EEEEAEEEEE<EEEEAEE<AAEAEEAAEEEEAEEEEEEEEEEEEEEEEEEEEEAEAEEE<AEE<EAE/EEA<EEEEAEEEAEEEEEEEA/EEEAE/AEEEA
+@ERR5069949.376959 NS500628:121:HK3MMAFX2:1:21205:12113:10369/1
+GCTCCATATATAGTGGGTGATGTTGTTCAAGAGGGTGTTTTAACTGCTGTGGTTATACCTACTAAAAAGGCTGGTGGCACTACTGAAATGCTAGCGAAAGCTTTGAGAAAAGTGCCAACAGACAATTATATAACCACTTACCCGGGTCAGG
++
+AAAAAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAEEEEEEEEEEEEEEEEEEEEEEEEEEAEEEEEEEAAAAAEEEEEEEEEAEEAEEEEEEEEEEEEAAAEEAEA
+@ERR5069949.1088785 NS500628:121:HK3MMAFX2:1:21109:26270:17779/1
+CAGTAGTCTTACTCTCAGTTTTGCAACAACTCAGAGTAGAATCATCATCTAAATTGTGGGCTCAATGTGTCCAGTTACACAATGACATTCTCTTAGCTAAAGATACTACTGAATCCTTTGAAAAAAAGGTTTCACTACTTTCGGTTTTG
++
+AAAAAE/EAEE<EEA///<AEEE/EE<AEEE<EA/EEEEEEE/EAAAEEEEEE<E/E6AE<<E/EEA//</E/EEE/EEE/EE/E/<<EEAAAE<EEEEEE/EAEA//<//AA/E</A<<E/EEEE/AEE<E/<EAE</A6///AEEAA
+@ERR5069949.1066259 NS500628:121:HK3MMAFX2:1:11312:18369:8333/1
+CCTTATGACAGCAAGAACTGTGTATGATGATGGTGCTAGGAGAGTGTGGACACTTATGAATGTCTTGACACTCGTTTATAAAGTTTATTATGGTAATGCTTTAGATCAAGCCATTTCCATGTGGGCTCTTATAATCTCTGTTACTTC
++
+AAAAAEAEEAEEEEEEEEEEEEEEEEAEEEEAEEEEEEEEAEEEEEEEEEEEEEEEEE/EAEEEEEE/6EEEEEEEEEEAEEAEEE/EE/AEEAEEEEEAEEEA/EEAAEAE<AEEAEEEAEAEEEAEAEEAE/AEEEEAEEEEAEA
+@ERR5069949.2832676 NS500628:121:HK3MMAFX2:4:11602:20035:16369/1
+GTCAACCAAAATGCACAAGCTTTAAACACGCTTGTTAAACAACTTAGCTCCAATTTTGGTGCAATTTCAAGTGTTTTAAATGATATCCTTTCACGTCTTGACAAAGTTGAGGCTGAAGTGCAAATTGATAGGTTGATCA
++
+AAAA6EEEEEEEEEEEEEEEEAEEAEEEEEEEEEEEEEEEEEEEEEEEEEEEEE<E/EAEEAEEEAEEAEEEEEAEEEEEEEEEEEEEEAEEAEEEEEAAEEEEEEA<AEEEAAAAEEEEE<EEAAAEEAEEAAEEEEA
+@ERR5069949.2953930 NS500628:121:HK3MMAFX2:3:21504:10316:13537/1
+GTGCTCAAAGGAGTCAAATTACATTACACATAAACGAACTTATGGATTTGTTTATGAGAATCTTCACAATTGGAACTGTAACTTTGAAGCAAGGTGAAATCAAGGATGCTACTCCTTCAGATTTTGTTCGCGCTACTGCAACGATACCGAT
++
+AAAAAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAEEEEEEEEEEEEEEEEEEEAEEAEEEEEEEEEEEEEEEEEEEEE/EEEEEE<AA/EA<A<AAAA<AAEAAEAEE/E<<E<EAAEA
+@ERR5069949.324865 NS500628:121:HK3MMAFX2:1:11102:17526:14721/1
+CACAAACTCTAAAAGAATGTATAGGGTCAGCACCAAAAATACCAGCAGATAATAATGTTGCAAGTAGAACTTCGTGCAGATTAAAATTTTCATAAGCACTCTAAAGAAGTTGAATGTCTTCAAATTTCTTAACATTAGGGCCCACAACAAG
++
+AAAAAEA/A<EAA/AE/EE/EE//////EA/EEE/E/EEEE//E/6//EA//<AA/A/EEEAA/EEEE/EEEA/E/</AEE////AEEEE//<E//EAE/A///<EEE//<E<<EEE<///A//E/E/EEEAA/<A////<A/AEAAA//E
+@ERR5069949.2185111 NS500628:121:HK3MMAFX2:2:11210:1473:2754/1
+GATGAAACATCATGCGTGATAACACCCTTATAAAACATTTTAAAGCATTGAGCTGATTTGTCTTTATGTGCTTAAAGCTTATTATCATAAACCAAAGCACTCACAGTGTCAACAATTTCAGCAGGACAACGCCGACAAGTTCCGAGGAAC
++
+AAAA6EEAEAAAAAEEEAEEEEEEA<<EEE/AEEE</EEEE/EEE<AA//EAA</A/E<A</EEAE/E/<EEE/AEAA/AE//EEEEEEAEAEE/EEAEA/AEEA/A//A<EEAAAEEEEEEEEE/A6<6//AE<<A<E/AEE<EE/AEA
+@ERR5069949.937422 NS500628:121:HK3MMAFX2:2:11104:8644:10925/1
+TTACCAATGTGCTATGAGGCCCAATTTCACTATTAAGGGTTCATTCCTTAATGGTTCATGTGGTAGTGTTGGTTTTAACATAGATTATGGAATTACCAACTGGAGTTCATGCTGGCACAGACTTAGAAGGTAACTTTTATGGACCTTTTGT
++
+AAAAAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAAEEEEEEEEEEEEEEEEA<E<EE/EAE/E//EE/EEEEEEEAEEE<E/EEE/EEA<EEE</66EE<A/AA<EEEA<EAE/A//AEEAEE///<A<EEEEEEA
+@ERR5069949.2431709 NS500628:121:HK3MMAFX2:3:21609:20858:5879/1
+GTTTATGATTGATGTTCAACAATGGGGTTTTACAGGTAACCTACAAAGCAACCATGATCTGTATTGTCAAGTCATGGTAATGCACATGTAGCTAGTTGTGATGCAATCATGACTAGGTGTCTAGCTGTCCACGAGTGCTTTGTTAAGCGT
++
+AAAAAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAAAAAAEAEAEE<AEEEEAEEAA<AEA
+@ERR5069949.1246538 NS500628:121:HK3MMAFX2:4:11505:20131:7933/1
+AGTATGGACAATTCACCTAATTTAGCATGGCCTCTTATTGTAACAGCTTTAAGGGCCAATTCTGCTGTCAAATTACAGAATAATGAGCTTAGTCCTGTTGCACTACGACAGATGTCTTGTGCTGCCGGTACTACACAAACTGCTTGCA
++
+AAAAAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAAEEEEEEEEEEEEEEEEEEA/EEEEEAEEEEEE/EEEEEEEEEEEEAAAAEEAEEEEEEEEEEEEEEEEE
+@ERR5069949.1189252 NS500628:121:HK3MMAFX2:2:21308:10087:1427/1
+CTATAACACATATAAAAATACGTGTGATGGTACAACATTTACTTATGCATCAGCATTGTGGGAAATCCAACAGGTTGTAGATGCAGATAGTAAAATTG
++
+AAAAAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAEEEEE/EEEEEEEEEEEEEEEEEEEEEEEEAEEE
+@ERR5069949.2216307 NS500628:121:HK3MMAFX2:1:21302:10479:19538/1
+CCAAGCAGGGTTACGTGTAAGGAATTCTCTTACCACGCCTATTTGTGGCCTGATAATTGCAGATGAAACATCATGCGTGATAACACCCTTATAAAACATTTTAAAGCATTGAGCTGATTTGTCTTTATGTGCTTTAAGCTTATTATC
++
+AAAE/AEAA/EEE/AE6EEEA/EEEEEEEEEE/<EAE<<6E/EE6E<A/AEE/EAE<</<EAEE/EEEEEEAEA/EAEEEEEEAEA//EAE<<EEA<EEE</<AA<</A<<A<AAAEEE/A6A6A//<AAAAEA6<A<<EAAA/AEA
+@ERR5069949.3273002 NS500628:121:HK3MMAFX2:4:11506:23944:16676/1
+GGTGTATTCAAGGCTCCCTCAGTTGCAACCCATATGATGCCGTCTTTGTTAGCACCATAGGGAAGTCCAGCTTCTGGCCCAGTTCCGAGGTAGTAGAAATACCATCTTGGACTGAGATCTTTCATTTTACCGTCACCACCACCCATTC
++
+AAAAAAEEEEEEEEEEEEEEEEEEEE/EEEE/EAEEEEEEEEEAEEEAEAEEEEEEEEEEEE<EEEAE/AEAEE/<EEEE/A/E/E/<AE<EEEAE//<EEAAAEA/E<<<EE<AA/E/6E6A//AEEE<EAEA/EE/<E/A//A/EA
+@ERR5069949.3277445 NS500628:121:HK3MMAFX2:4:11601:26589:14031/1
+TGACCAAATTGGCTACTACCGAAGAGCTACCAGACGAATTCGTGGTGGTGACGGTAAAATGAAAGATCTCAGTCCAAGATGGTATTTCTACTACCTAGGAACTGGGCCAGAAGCTGGACTTCCCTATGGTGCTAACAAAGACGGCATCATA
++
+AA/AAEEEEEEEEEEEEEEEEEEEAEEEEEEEEAEEEEAEEEEEEEEEEEAEEEEEEEEEEEEEE/AEEEAEEEAAEEAEEE<E/EEEEEEEEAEEEEA/EEEEEEEAAA//EEEEEAEA<AEEAAEAEAEAEAEEEEAEEEEEEA/EEAA
+@ERR5069949.3022231 NS500628:121:HK3MMAFX2:1:21102:10897:17190/1
+GTACGAACTTATGTACTCATTCGTTTCGGAAGAGACAGGTACGTTAATAGTTAATAGCGTACTTCTTTTTCTTGCTTTCGTGGTATTCTTGCTAGTTACACTAGCCATCCTTACTGCGCTTCGATTGTGTGCGTACTGCTGCAATAT
++
+AAAAAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAEEEEEEEEEEEEEEEEEAEEEEEEEEEEEEEEEEEEEEEEEEEE<EEEEEEEEEEEEEEEEEEEEEEEAAEEEEEEEEEEEEAAAAEEEEEEEEAEEE
+@ERR5069949.184542 NS500628:121:HK3MMAFX2:2:21205:8408:1786/1
+TCAATGGGGAATGTCCAAATTTTGTATTTCCCTTAAATTCCATAATCAAGACTATTCAACAAAGGGTTGAAAAGAAAAAGCTTGATGGCTTTATGGGTAGAATTCGATCTGTCTATCCAGTTGCGTCTCCAAATGAATGCAACCAAATGTG
++
+AAAAAEEEEE/EA/E/EEE/EEAEE/E/EE/EEEE//AEE/E/EEE//EEE/</E/EE<<//EE/EE<EEEEEAE/E/EAAEEEAEAEE<E</EEEE/E//E<<<///E<//A<AE</<AEEEAAE///EE</EE//AA///<E</A<AEA
+@ERR5069949.540529 NS500628:121:HK3MMAFX2:3:21609:5345:11242/1
+CCGTCTATGCAATACAAAGTTTCTTTAGAAGTTATATGTTTATAGTGACCACACTGGTAATTACCAGTGTACTCACTAGCACAAGTAAATGTACCATGCTTAAGTTCATACTGAGCAGGTGGTGCTGACATCATAACAAAAGGTGACTC
++
+AAAAAE/A/EEEEAA/EEAEEEAEEEEEEE6EEAEEEEEEAE/E<AE/EEEEEEEEEEAEEEEEEEEEEEEEEAAEAEAEEEAEEE<EEEEEEEAE</E<EEEA<E/EEE<EEEE<EE<EEEA<A6EE</EEE<AEAA<EE<EEAEAEA
+@ERR5069949.686090 NS500628:121:HK3MMAFX2:1:11212:8601:4499/1
+ATGTCAGATTTATGTGACAATTTAAGACATTCAACAACATCTTTAGTTTCTACATCTGAATCAACAAACCCTTGCCGAGCTGCTGAAATAAAAGTAGATAAGACATTGTCTAAGGACACATTCTTTGCAAGTTCAGCTTCTGCAGTTGCA
++
+AAAAAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAEEEEEAEEEE/EEAEEEEEEEEEEEEEEEEEEEEEEEEEEEEAEEEEEE6EEEAEEEEEEEE/EEAE<EEEAEEEEEAEEEEEEEEEEEEEAEAEEE
+@ERR5069949.2787556 NS500628:121:HK3MMAFX2:4:11609:10602:17177/1
+GCTGCTAGAGACCTCGTTTGTGCACAAAAGTTTAACGGCCTTACTGTTTTGCCACCTTTGCTCACAGATGAAATGATTGCTCAATACACTTCTGCACTGTTAGCGG
++
+AAAAAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEE<EEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAAE
+@ERR5069949.2650879 NS500628:121:HK3MMAFX2:1:21111:16524:5801/1
+GCTATAACGCAGCCTGTAAAATCATCTGGTAATTTATAATTATAATCAGCAATCTTTCCAGTTTGCCCTGGAGCGATTTGTCTGACTTCATCACCTCTAATTACAAATGAATCTGCATAGACATTAGTAAAGCAGAGATCATTTAATTTA
++
+AAAAAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAEEEEEEEEEEEEEEEEEAEEEEEEE/EEEEEEEEEEEEEEEEEEEEEEAA<AEEEEEEEEEEEAEEEEEE/EEE<EEAEEEAE
+@ERR5069949.2064910 NS500628:121:HK3MMAFX2:3:21608:24504:13289/1
+CTACCCTTCTGCTCGCATAGTGTATACAGCTTGCTCTCATGCCGCTGTTGATGCACTATGTGAGAAGGCATTAAAATATTTGCATATAGATAAATGTAGTAGAATTATACCTGCACGTGCTCGTGTAGAGTGTTTTGATAAATTCAAAG
++
+AAAAAEA<AEEE/EE/EE/EEE/EEE//E/EA/EEEEEEEEEEE<E/A</</A/AEAEEEE/EAE/AEEE<AAE/E//EA</<//E<A/AE<EAEEE///<EA/E<AEAAAA/A/</EEEEEAE/A/<A/AA/EAE<AE/6/<<A</<A
+@ERR5069949.2328704 NS500628:121:HK3MMAFX2:4:21612:9379:15958/1
+GATTTTTAAGTGTGTCACTTAACATTTGTACAATCTTTATACGCACTACATTCCAAGGAAGTCCTTTGTACATAAGTGGTATGAGGTGTTTAAATTGATCTCCAGGCGGTGGTTTAGCACTAACTCTGGAAAAATCTGTATTATTAGGTG
++
+AAAAAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEE/E/EEEEEEEAAEEEEEAAEAEEEEE<AEA/EEEEEEAEAEEAEAAAE/<EEAAE/EEAEEEEEEEAAEEEEEEAEAAEA
+@ERR5069949.1067032 NS500628:121:HK3MMAFX2:4:21403:19263:10183/1
+GTACAAAAATAGCCTAAGAAACAATAAACTAGCATTATACACTGAAGTGTATTTCCAGTTATGAAGAAAATAGGGCAATACTCAACACACATAAAAACAATACCTCTGGCCAAAAACATGACAGTTGTAACTACACCTGAGTAGTTAGAA
++
+AAAAA/EEEAE/EAEEEEEEEEEEEE/E/EEEEEEEE/EEEE<EE//EAEEEE/EAAAEEEEAEEEEEE6AEEEA6EEE//EAE6A/EE<EE/EEEEAA///A<EEEEEEAAEEE/EE/AAA/E/<6<AAEEEA<</EEAEE/EAAE<EE
+@ERR5069949.3338256 NS500628:121:HK3MMAFX2:1:11108:15722:2450/1
+AGAGTAGACTATATATCGTAAACGGAAAAGCGAAAACGTTTATATAGCCCATCTGCCTTGTGTGGTCTGCATGAGTTTAGGCCTGAGTTGAGTCAGCACTGCTCATGGATTGTTGCAATTGTTTGGAGAAATCATCCAAATCTGCAGCAGG
++
+AAAAAEEEEEEEEEEEEEEEEEEEEEEEEEEEEE/AEEAEEEEEEEEEEAEEEEE<EAAEEEEEEEEEEEEEEEEEEEEEEAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAEAEEEEEE<AAEEEEEEAEEA<AEEEEEEEEEEEA
+@ERR5069949.1412839 NS500628:121:HK3MMAFX2:3:11609:15519:12102/1
+CATTAGCACAAGTTGTAGGTATTTGTACATACTTACCTTTTAAGTCACAAAATCCTTTAGGATTTGGATGATCTATGTGGCAACGGCAGTACAGACAACACGATGCACCACCAAAGGATTCTTGATCCATATTGGCTTCCGGTGTAA
++
+AAAAAEEAEEEEEEEEAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAAEEEEEEE<AEEEEEEEEEEEEEEEEEEEEEEEEEEEEAEE/EEEE/EEEAAAEEEE/EEEEE<E/<EAE<AE<<A<EAAAAAAEAA<AEE
+@ERR5069949.1538968 NS500628:121:HK3MMAFX2:2:11304:14669:15804/1
+AAGTTGGCGTATACGCGTAATATATCTGGGTTTTCTACAAAATCATACCAGTCCTTTTTATTGAAATAATCATCATCACAACAATTGTATGTGACAAGTATTTCTTTTAATGTGTCACAATTACCTTCATCAAAATGCCTTAAAGCATAG
++
+AAAAAEEEEEEEAEEAEEEEEEE/EEEEEEEEEEEEEEEEEEEEEEAEAEEEEAEEEEA<EEEEEEAE/EEEE/EEAEEE/AEEE/EEEAEEE//EEEE/EEEEEEE<EEEEA/<6/6AAAEEEAA6AA6<AEA<EA</AE/E<AA6EEA
+@ERR5069949.147998 NS500628:121:HK3MMAFX2:3:21611:12530:12698/1
+GCAATTCATAGCTCTTTTCAGAACGTTCCGTGTACCAAGCAATTTCATGCTCATGTTCACGGCAGCAGTATACACCCCTCTTAGTGTCAATAAA
++
+AAAAAEAEEEEEEEEEEEEEEAAEE/EEE/EE/E/EEE6EEE/EEEE//<EAEAE/A/EEE/EE6<AEEE<EAEA<E/<A/EEE/A//EEE<EE
+@ERR5069949.366975 NS500628:121:HK3MMAFX2:1:11105:12446:15727/1
+GTGTAACCATTTAAACCCTGACCCGGGTAAGTGGTTATATAATTGTCTGTTGGCACTTTTCTCAAAGCTTTCGCTAGCATTTCAGTAGTGCCACCAGCCTTTTTAG
++
+AAAAAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAEEEAEA<EEEEEEEEEEAEEEEEEEEEE6EEEEEEEEEEEEEEEEEEEEEEEEEEAEEEEEEEEEEEEE
+@ERR5069949.1372331 NS500628:121:HK3MMAFX2:3:11601:26764:8562/1
+ATCCTTTAGGATTTGGATGATCTATGTGGCAACGGCAGTACAGACAACACGATGCACCACCAAAGGATTCTTGATCCATATTGGCTTCCGGTGTAACTGTTATTGCCTGACCAGTACCAGTGTGTGTACACAACATCTTAACACAATTAGT
++
+AAAAAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAEEEEAEEEEEEEEEEEEEEEEEEEEE/EEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAEAEEEEAEEEEEEEEAEEEEEEEEEAEEEEEAAAEEEEEEE<<EE
+@ERR5069949.1709367 NS500628:121:HK3MMAFX2:1:11301:9990:2022/1
+AAGTGTATCTTGATCCTCATAACTCATTGAATCATAATAAAGTCTAGCCTTACCCCATTTATTAAATGGAAAACCAGCTGATTTGTCTAGGTTGTTGACGATGACTTGGTTAGCATTAATACAGCCACC
++
+AAAAAEEEAEEEAEEEEEEEEEEEEEEEEEEEEEEEEEAEEEEAAEAAE<AEA<EEE/EEA<AAEE/AEEEEEEEE/EAEAEEA<EAEA/EEEAEEAAAAAAAAEAAEAAE/A6EEAEEEEAAAEE/AA
+@ERR5069949.2388984 NS500628:121:HK3MMAFX2:2:21306:17580:3896/1
+TGTCTATGTGATAGACGTGCCACATGCTTTTCCACTGCTTCAGACACTTATGCCTGTTGGCATCATTCTATTGGATTTGATTACGTCTATAATCCGTTTATGATTGATGTTCAACAATGGGGTTTTACAGGTAACCTACAAAGCAACCAT
++
+AAAAAEEEEEEEEE/EEEEEEEEEEEEEEEEEEAEEEEEEEEEEEEEEEEEEAAEEEEEEEEEEEAEEEEEEEEEEEEEEEEEEEEEAEEEEAE/EAEEEEEEEEEEAEEEE/EEEEEEEEAEEAEEAEEEEEAEEEEAEEEE<A/EA<E
+@ERR5069949.1132353 NS500628:121:HK3MMAFX2:2:21111:21744:6806/1
+GATTTAGCCACATTCAAAGACTTCTTCAACTTTTTAAGAACAACTTCAGAATCACCATTAGCAACAGCCTGCTCATAAGCTTCTTGAGCAGTAGCAAAAGCTGCATATGATGGAAGGGAACTAAACTCTGAGGCTATAGCTTGTAAGGTT
++
+AAAAAEEEEEEEEEEEEEE6EEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAEEEEEEEEEEEEEEEEEEAEEEEEEEAEEEEEEEEEEEAEAAEEAE<EEAAEEEEEEEEEEE<A<EEEEEEEEEEEEEEAEE
+@ERR5069949.1151736 NS500628:121:HK3MMAFX2:4:21406:11928:13664/1
+TCTAAGCATAGTGAAAAGCATTGTCTGCATAGCACTAGTAACTTTTGCCCTCTTGTCCTCAGATCTAGCCTGTTTATACATTTGGGTCATAGCTTGATCAGCCATCTTTTCCAACTTACGTTGCATGGCTGCATCACGGTCAAATTCAGAT
++
+AAAAAEEAEEEEEAEE/EEEEAEEEEEEEEEEE/EEEEEEEEEE/EEAEEEEEE/EE<EEEEEEEEEAEEEEEEEEEEEEEEEEEEEEAEEEEEAEEEEEE<AEEEEEAAEAAEEEEEEA/<AAEEAAEEEEAEAAAE/EE//AEAAAAAA
+@ERR5069949.479807 NS500628:121:HK3MMAFX2:3:11402:16906:16736/1
+TATCTGCCCATTTAATAGAAGTTAAACCATTAACTTGTGGGTATTTCCACTTTTTAGTGTGATTTAATGCTGACATGTACCTACCCAGAAAACTAGGATCAGTTGTGTGGTAGTACTCAAAAGCCTCAACACGTAGAGTGTCATCATTAG
++
+AAAAAEEEEEEEEEEEEEEEEEEEEAEEEAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAEEEEEEEAEEEEEEEEEEEEEAEEEEEEEEEEEAAAAEAAA/EEAAEAA/AEEAAAEEEAEAAAEEEE/AA
+@ERR5069949.2176303 NS500628:121:HK3MMAFX2:4:11608:21150:1680/1
+TTACCTGCACCACGCACATTGCTAACTAAGGGCACACTAGAACCAGAATATTTCAATTCAGTGTGTAGACTTATGAAAACTATAGGTCCAGACATGTTCCTCGGAACTTGTCGGCGTTGTCCTGCTGAAATTGTTGACACTGTGAGTGCTT
++
+AAAAAEEEEEEAEEEEEEAEEEEEEEEEEEEEEAEAEEEEEAEEEEEEEEEAEEEEEEEEEEE<EEEEAEEEEEEEEEEEEEEEEEEEEEEAEEEE<A<AEEEAE/EE<EEEEAAAAAAEEAA<AAAEEEEEE<EEEEEEEEAEE<EEEEA
+@ERR5069949.2772897 NS500628:121:HK3MMAFX2:1:11106:12629:15009/1
+GTTGAAAGTAGATCTTCAATAAATGACCTCTTGCTTGGTTTTGATGGATCTGGTAATATTTGTGAAAAATTAAAACCACCAAAATCTTTAATTGGTGGTGTTTTGTAAATTTGTTTGACTTGTGCAAAAACTTCTTGGGTGTTTTTGTCTT
++
+AAAAAEEEEEEEEEEEEEEEEEEEE6EEEEEEEEEEEEEEEEEEEEAEEEEEEEAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAEEEEAAEEEEEEEEAEEEEEEEEEEEEEEEEEEEEAAEEAA<EEEEEEA
+@ERR5069949.1020777 NS500628:121:HK3MMAFX2:3:11408:13234:17983/1
+GGATTAGTAACACTACAGCTGATGCATACATAACACAGTCTTTTAGCTTAAAACCAGACAAACTAGTATCAACCATATCCAACCATGTCATAATACGCATCACCCAACTAGCAGGCATATAG
++
+AAAAAEEEE6E6EEAEEE<EEEEEE/EEEEEE6EEEEEEEEEEEEE/EEEEE/EEEEEEEEAEEEEAAEEA/EEEEE<EAEAEAEAE<EAEEEA<EE<AEE/EAAA6AA/E6AAAA6AEEEE
+@ERR5069949.465452 NS500628:121:HK3MMAFX2:3:11503:20241:8941/1
+ACCTGATGCTGTTACAGCGTATAATGGTTATCTTACTTCTTCTTCTAAAACACCTGAAGAACATTTTATTGAAACCATCTCACTTGCTGGTTCTTATAAAGATTGGTCCTATTCTGGACAATCTACACAACTAGGTATAGAATTTCTTAAG
++
+AAAAAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAEEEEEEEEEEEEEEEEEEEEEEEEEAEEEEEE/EEAEEEE/EEEEEEEEEEAEEEEEEEEEEEEEEE<EEEEAAAEAEEEEEEAA6AAEEEEEA<EEEEE</EEAEE/EE
+@ERR5069949.1704586 NS500628:121:HK3MMAFX2:3:11408:18502:19140/1
+GATAAACGCACTACGTGCTTTTCAGTAGCTGCACTTACTAACAATGTTGCTTTTCAAACTGTCAAACCCGGTAATTTTAACAAAGACTTCTATGACTTTGCTGTGTCTAAGGGTTTCTTTAAGGAAGGAAGTTCTGTTGAATTAAAACA
++
+AAAA6EEEE/EE6EEEEEEEEEEEEEEEEEE<EEEEEEEE6EEAEEEEEA<EEEEE66EEEEE///EEEAEEEE<EEEEEEA/EE/EEEEEEEAE<E<AA<AAAEEAE/AEE<E<AA<EAAEEAE/AEE/E/EAEAAAEE/EA/A//EE
+@ERR5069949.1258508 NS500628:121:HK3MMAFX2:2:21106:23201:10887/1
+CCCTTTGTTGTGTTGTAGTAAGCTAACGCATTGTCATCAGTGCAAGCAGTTTGTGTAGTACCGGCAGCACAAGACATCTGTCGTAGTGCAACAGGACTAAGCTCATTATTCTGTAATTTGACAGCAGAATTGGCCCTTAAAGCTGTTACAA
++
+AAAAAEEEEEEEEEEEAEEEEEEEEEEEEEEEEEEEEEEEAEEEEEEEEEEEEEEEEEEEEEAEEEEEEEEEEEEEEEEEEEEEEEEEEEAEEEEEEEEEEEAAAAAAEEEAAE/AE</EEEEAA/AAEEEEEEAEEEAAAEEE/AEEAAE
+@ERR5069949.986441 NS500628:121:HK3MMAFX2:2:11310:5407:13956/1
+GTTACTCACAATTTTGACTTCACTTTTAGTCTTAGTCCAGAGTACTCAATGGTCTTTGTTCTTTTTTTTGTATGAAAATGCCTTTTTACCTTTTGCTATGGGTATTATTGCTATGTCTG
++
+AAAAAEAEEEEEEE/EEE/EEEEEAEEEEEEEEEEEEEEEEEEEEE</EAAEA/EEEEEEEEAEAAEEEEEEEEEEEEE/E//<EAE/6///EE//E/EEE///E<EEEEA</A<<//<
+@ERR5069949.2674295 NS500628:121:HK3MMAFX2:1:21303:10381:8722/1
+GTTATAACACTGACACCACCAAAAGAACATGGTGTAATGTCAAGAATCTCAAGTGTCTGTGGATCACGGACAGCATCAGTAGTGTCAGCAATGTCTCTGCCAAATTGTTGGAAAGGCAGAAACTTTTTGTTAGACTCAGTAAGAACAC
++
+AAAAAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAEAEEEEEEEEEEEEEE<EEEEEE<EEEEEEE<AEAAA<EAAE/EEEAA<AAEEE<AAEEEE<EEEEEEEEEEEEAEEE
+@ERR5069949.885966 NS500628:121:HK3MMAFX2:4:11610:19682:20132/1
+GTCTAATCATAATTTCTTGGTACAGGCTGGTATTGTTCATCTCAGGGTTATTGGACATTCTATGCAAAATTGTGTACTT
++
+AAA//E/EAA/E//E//E//E/E//AE/A/E//EAEA///AE//E///E/EEE6EEEAEEA///E/AEE/EAEE/E//E
+@ERR5069949.2342766 NS500628:121:HK3MMAFX2:4:21501:7762:9816/1
+CAGGTTATGTTGATACACCTAATAATACAGATTTTTCCAGAGTTAGTGCTAAACCACCGCCTGGAGATCAATTTAAACACCTCATACCACTTATGTACAAAGGACTTCCTTGGAATGTAGTGCGTATAAAGATTGTACAAATGTTAAGTGA
++
+AAAAAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAAEEAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAEAEEEEEEEAEAEAAAAEAEEEAEEAEEE/EEEE<AAEEAEA
+@ERR5069949.3122970 NS500628:121:HK3MMAFX2:2:21304:20157:2460/1
+TGCCAATCCTGTAGCGACTGTATGCAGCAAAACCTGAGTCACCTGCTACACGCTGCGAAGCTCCCAATTTGTAATAAGAAAGCGTTCGTGATGTAGCAACAGTGATTTCTTTAGGCAGGTCCTTGAT
++
+AAA/AEEEEEEEAEEEAEEEEEEEEEEEEE6AEEAEAEAEEAE<AEEEEEEEEAEEAEEAEEEEEAEE</EEEEAEEAAEE/EEEAEEEEEEEEE<A//EEE/EAAEEEEEEAA/AEEAEAAA6//A
+@ERR5069949.3279513 NS500628:121:HK3MMAFX2:1:21110:4328:5711/1
+TGCGTCTTGGGTCCCCGCTCTCACTCAACATGGCAAGGAAGACCTTAAATTCCCTCGAGGACAAGGCGGTCC
++
+AAAAAEEEEA/E//AE/E/EEEE6EEEE/E6/6A/E6E/6AEA/E<EEEE//E/EEEA//AEE///A//E/A
+@ERR5069949.309410 NS500628:121:HK3MMAFX2:1:11107:4644:2079/1
+GAAGAAGATTGGTTAGATGATGATAGTCAACAAACTGTTGGTCAACAAGACGGCAGTGAGGACAATCAGACAACTACTATTCAAACAATTGTTGAGGTTCAACCTCAATTAGAGATGGAACTTACACCAGTTGTTCAGACTATTGAAGTGA
++
+AAAAA//EEEEA6EEEAE</EEE/EEEEE/EE6EEEEEEEEEEEEEEEAEEAAEEEEEEEEEAEEEEEE/EEAEEEEEAEAEEE/EEAEEE<AEEEAA////EEEEEEEEA//A/EE/EAAEA/AE<EE/E//E/</AEAEAE/AEA/AEA
+@ERR5069949.532979 NS500628:121:HK3MMAFX2:2:21104:15575:19089/1
+CATGGGCACACTTTCTTATGAACAATTTAAGAAAGGTGTTCAGATACCTTGTACGTGTGGTAAACAAGCTACAAAATATCTAGTACAACAGGAGTCACCTTTTGTTATGATGTCAGCACCACCTGCTCAGTATGAACTTAAGCATGGTA
++
+AAAAAEEEEEEEEEEEEEEEEEEE/EEEAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEE/A/</EEE<EEE<<AEEEEEA/AA/AE/EE/EEEEAEA</EAEEE<<AEEEEE
+@ERR5069949.2888794 NS500628:121:HK3MMAFX2:3:11604:17798:16811/1
+CCTTGAATGAGTCTAATTCAGGTTGCAAAGGATCATAAACTGTGTTGTTGACAATTCCTATTACAACATCACAGTTACCAGACACAAATGTGTTGTCTGTAGTAATGATTTGTGGTTCATAAAAATTCCTTTGTGTTACAAACCAGTGTGT
++
+AAAAAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAEEEEEEEEEEEEEEEEEE/EEEEEEEEEAEEEEAAAAEEAAEEEEAAAEEEEEEEEEEEEEEEAAAEAA
+@ERR5069949.2205229 NS500628:121:HK3MMAFX2:1:11212:26331:4199/1
+CACTAGAACCAGAATATTTCAATTCAGTGTGTAGACTTATGAAAACTATAGGTCCAGACATGTTCCTCGGAACTTGTCGGCGTTGTCCTGCTGAAATTGTTGACACTGTGAGTGCTTTGGTTTATGATAATAAGCTTAAGCACATAAAGA
++
+AAAAAEEEEEEA/EEEEEEEAEEEEEEEEEAEAEAEEEEEEEEEEEEEEEEEEEEEE6EEEEEEEEEEEEEEAEEEEEEAEEEEEE6EE<E<<EEEAEEEEEEEEEEEEEEEEA<AEEEEEEAAAEEEEEEEEEEEEEEEE<EAAEEEEE
+@ERR5069949.786562 NS500628:121:HK3MMAFX2:2:11109:4461:9003/1
+AACACCAGCTTCTGATCTTTCACAAGTGCCGTGCCTACAGTACTCAGAATCAAAAGTTGTTACCACTCTAACAGAACCTTCAAGGTAGGTGTTAGGAAATTGAATAATAGAGCCATCCATGAGCACATAACGTGTGTCAGGGCGTAAACTT
++
+A6AAAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAEEEEEEAEEEEEEEEEEEEEEEEEEEEEEEEEEEAEEEEEAAEEEEEEEEAEAEAEEEA/AAAEEEEAEEEEAEE<EEAAEEAAA/EA<EAEA
+@ERR5069949.919671 NS500628:121:HK3MMAFX2:4:21608:23884:15511/1
+CTGTAATAGTTGTGTCCGTACCAGCTGCTTGTGCTGTTTGCCTGTCAACAAAAGGTCCATAAAAGTTACCTTCTAAGTCTGTGCCAGCATGAACTCCAGTTGGTAATTCCATATGGTGCATGTAACAAAAAGAGACACAGTCATAATCTAT
++
+AAAAAEEAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAAEEEEEEEEEEEEEEEEEEEEEE<EEEEEEEEAAEEEEEEEEEEEEEEEEEEEEAEEEAEEEAEEEA/EAAAAEEAEEEEEEEEA6AAEEAAAEAAEEEEEEEE
+@ERR5069949.1328186 NS500628:121:HK3MMAFX2:3:21510:25432:14327/1
+TCTTTGTAAGCTTTAGCAGCATCTACAGCAAAAGCACAGAAAGATAATACAGTTGAATTGGCAGGCACTTCTGTTGCATTACCAGCTTGTAGACGTACTGTGGCAGCTAAACTACCAAGTACCATACCTCTATTTAGGTTGTTTAATCCTT
++
+AAAAAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAEEEEEEEEEEEEEEEEEEEEAEEEEEEEEEEAE/EEEEEEEEAEEE/EEAEEEEEEAEEEEEEEEAAA<EEEEEAEE/<6A<AEEEEE//EEAA<EEAEE<E<EAA<E/6E</EE
+@ERR5069949.870926 NS500628:121:HK3MMAFX2:4:11510:4100:9432/1
+CAACTACACTTAACGGTCTTTGGCTTGATGACGTAGTTTACTGTCCAAGACATGTGATCTGCACCTCTGAAGACATGCTTAACCCTAATTATGAAGATTTACTCATTCGTAAGTCTAATCATAATTTCTTGGTACAGGCTGGTAATGTT
++
+AAAAAEEAEEEEEEEEEAEEEEEEAEEEEEEEEE/EEEEEEEAEEEEEEEAEEA<AE/AEEEEEEEEE<EEEEEEE/AEAEEEEAAEEEEAAEEEEEAEEEEEEEEAEEAAEEEEEAEAA/EEEAAEEEAAAA/A/EA/E/AEEEE/EE
+@ERR5069949.2257580 NS500628:121:HK3MMAFX2:3:11512:13762:8305/1
+AGTTGCAATTTACAAGTCTTGAAATTCCACGTAGGAATGTGGCAACTTTACAAGCTGAAAATGTAACAGGACTCTTTAAAGATTGTAGTAAGGTAATCACTGGGTTACATCCTACACAGGCACCTACACACCTCAGTGTTGACACTAAATT
++
+AAAAAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAEEEEEAEEEEEEEEEAEEEEEEAEEEEEEEEEEEEAEEEEEEEEEAEEEEEEAEE/EEAEA<EAEEEAEEEEEEEEE<EEAAAEAEEE<EA
+@ERR5069949.3249622 NS500628:121:HK3MMAFX2:2:21101:6979:17698/1
+TTGCCATGTTGAGTGAGAGCGGTGAACCAAGACGCAGTATTAATGGGTAAACCTTGGGGCCGACCTTGTTTTTATCG
++
+AAAAAE/EA/EEAEEEAEEAE/EE/EEE/EEEEEEEE/E//A//EEEEE/EEEEEE/AEE/EA////<<E<///E/E
+@ERR5069949.611123 NS500628:121:HK3MMAFX2:4:21402:10868:14846/1
+ACTCTAGATAATTCATTAGGTTTCTTAATAGTAAGACTAGAATTGTCTACATAAGCAGCCATTAGATCTGTGTGGCCAACCTCTTCTGTAATTTTTAAACTATTATTTGCTGGTTTAAGTATAAT
++
+AAAAAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAEEAEEEEEEEEEEEEEEEEEEEE/EEEEEEEEEAEEEEEEEEE/AEEEEAEEE<AEEEEEEEEEEEAEEE
+@ERR5069949.651338 NS500628:121:HK3MMAFX2:2:11307:9572:4021/1
+CTATAACATTAATAGGCAATGAACCTTTAGTGTTATTAGCTCTCAGGTTGTCTAAGTTAACAAAATGAGAGAGAGAATGTCTTTCATAAGTCTTTTGACCAGCTTTAACAAAGTAAAGATGGATGGAACCATTCTTCAGAGT
++
+AAAAAEEEAEAEEEEEEEEEAEEEEA/EEEEA/EE/<AEEAEEE/EA<//EE/A/E/EEEEEEEEEEEEEE/EAEEEEAAEE/E<AEEE/<<EEEEE<E/EEE<A/A/<<EAE/A</EEEA<EE/EE//AEEE</6/A///A
+@ERR5069949.169513 NS500628:121:HK3MMAFX2:2:21303:6012:2171/1
+AATCAAGACTATTCAACCAAGGGTTGAAAAGAAAAAGCTTGATGGCTTTATGGGTAGAATTCGATCTGTCTATCCAGTTGCGTCACCAAATG
++
+AAAAAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEE/EE6EEEE
+@ERR5069949.155944 NS500628:121:HK3MMAFX2:2:21111:24075:19469/1
+GGATAGACAGATCGAATTCTACCCATAAAGCCATCAAGCTTTTTCTTTTCAACCCTTGGTTGAATAGTCTTGATTATGGAATTTAAGTGAAATACAAAATTTGGACATTCCCCATTGAAGGTGTCAAATTTCTTTGCCAATTTAATTTCA
++
+AAAAAEEAEEEEEEE6EEEEEEEEEAEEEA<EEEEEEEEEA66AEA/EAEEEAEE/EEEEEAE/A/EEEEA6EEE/EA/EEEEE/A//EEE/AAEEEAAEEEEAA/<EEAAAAAA6/AEE/EEEAEAAA/66/6/AEA/A6/A</AE<AE
+@ERR5069949.2033605 NS500628:121:HK3MMAFX2:4:21508:23814:9228/1
+CTACACGAGCACGTGCAGGTATAATTCTACTACATTTATCTATAGGCAAATATTTTAATGCCTTCTCACATAGTGCATCAACAGCGGCATGAGAGCAAGCTGTATACACTATGCGAGCAGAAGGGTAGTAGAGAGCTAGGCCAATAGCAA
++
+AAAAAEE/EEEEEEEEEEEEEEEEEAEEEEEEEEEAEEAEEEEEAEEEEEEEEAAEEEEE<EEE<EEEEEAEEAEEEAAE/EEEA/EEA<EEEEEEEEEEEE<EE/AEEAEEAA<AEA/EE/EEAE6E/AE/<E/AAAAEEE<AAE<AAA
+@ERR5069949.2730382 NS500628:121:HK3MMAFX2:4:21605:26351:3903/1
+ACTGAATTTTCTGCACCAAGTGACATAGTGTAGGCAATGATGGATTGACTAGCTACACTACGTGCCCGCCGAGGAGAATTAGTCTGAGTCTGATAACTAGCGCATATACCTGCACCAATGGGTATGTCACACTCATATGAGT
++
+AAAAAE/EEEEEEEAEEEEEEEEEEEEEEEAEEEEEEEEEEEEEEEEEEEEEEAEEAEEEEE<EEEEEEEEEEEEEEE/EEEEEEEEEEEEEEEEEEEEE<EEAAAEEE<AEA<<AAE<AEAEAEA<A/AAAEEE<A<AA<A
+@ERR5069949.2125592 NS500628:121:HK3MMAFX2:1:11307:14726:9430/1
+ATGTGAGAAGGCATTAAAATATTTGCCTATAGATAAATGTAGTAGAATTATACCTGCACGTGCTCGTGTAGAGTGTTTTGATAAATTCAAAGTGAATTCAACATTAGAACAGTATGTCTTTTGTACTGTAAATGCATTGCCTGAGACGAC
++
+AAAAAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAEEEEEEEEE<EEEEEEEEEEEEEEEEEEEEEEEAEEEEEEEEEEEEEEAEEEEEEEAEEEEA<EEEEEEEAEEEEEEAEEEEEEAAEEEEEE<EE/A/EEEA
+@ERR5069949.1062611 NS500628:121:HK3MMAFX2:1:11304:13814:5808/1
+AACTAGCATTATACACTGAAGTGTATTACCAGTTATGAAGAAAATAGGGCAATACTCAACACACATAAAAACAATACCTCTGGCCAAAAACATGACAGTTGTAACTACACCTGAGTAGTTAGAAGTAACAGAGATTATAAGAGCCCACATG
++
+AAAAAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAEAEEEE/AEAEEEEEEEE6AEEAEEEEEEEEEEAEEEEAEEEEEEEEEEEEEEEEEE<AEEEEEEEEEEEEEAEEEEEEAEEEAEAEEEEAAEEEAAEEA
+@ERR5069949.1778133 NS500628:121:HK3MMAFX2:1:11203:21125:7007/1
+CATCTTATTTCTATAGAGACACTCATAAAGTCTGTGTTGTAAATTGCGGACATACTTATCGGCAATTTTGTTACCATCAGTAGATAAAAGTGCATTAACATTGGCCGTGACAGCTTGACAAATGTTAAAAACACTATTAGCATAAGCAGTT
++
+AAAAAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEE<EEEEEEEEEEEEEEEEEEEEEEEAAAEEEEA<EEEEEEEEEEEEAEAEAEEEEAEEEEEEEEEEEEEEAEAEEEEEEEAEEEEEEEEEEEEEEEEEEA<AAAAAAEEEEEAEEA
+@ERR5069949.3057020 NS500628:121:HK3MMAFX2:2:21204:6342:14557/1
+CAATTTGCCTATGCCAACAGGAATAGGTTTTTGTATATAATTAAGTTAATTTTCCTCTGGCTGTTATGGCCAGTAACTTTAGCTTGGTTGTACGC
++
+AAAAAEEEEEEEEEEEEEEEEEAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAE
+@ERR5069949.2972968 NS500628:121:HK3MMAFX2:4:21405:4877:14897/1
+AGTAAACTGTTACAAACAACAACAGCAAGTTGCAAACAAAGTGAACACCCTTGGAGAGTGCTAGTTGCCATCTCTTTTTGAGGGTTATGATTTTGGAATCGCTCTGAAAAACAGCAAGAAGTGCAACGCCAACAATAAGAC
++
+AAAAAEEEE//EEEE6AE/AE/E6EEEEEEEE//E/EEEEE//EEA/A<EAEEEEEEEAEEEE/<E</EE/E<E<EE/E/E/E<///A/AE//EEEE//EA/EEAEE//EAA66EEEEEE/E/6//A/EE/EE/A//A//6
+@ERR5069949.2734474 NS500628:121:HK3MMAFX2:4:11507:10751:13427/1
+TGGCAATAGAGTTATTAGAGTAAGCAACTGAATTTTCTGCACCAAGTGACATAGTGTAGGCAATGATGGATTGACTAGCTACACTACGTGCCCGCCGAGGAGAATTAGTCTGAGTCTGATAACTAGCGCATATACCTGCACCAATGGGT
++
+AA/AAAEEEEEEEAEEEE//EEEEEEEEEEEEEEEEEAEEEEE/EEEE/EEAEEEEEEEE/EEEEEEEEE/E/EEE/AEA/EEEAAEE/EEAAEAAEAEEEEAEEEEEEEEA<EEAEE/A<EEEEEEEAAEEEEAA<AAAAE/AEE/AA
+@ERR5069949.856527 NS500628:121:HK3MMAFX2:2:11301:22893:2784/1
+CAACTACACTTAACGGTCTTTGGCTTGATGACGTAGTTTACTGTCCAAGACATGTGATCTGCACCTCTGAAGACATGCTTAACCCTAATTATGAAGATTACTCATTCGTAAGTCTAATCATAATTTCTTGGTACAGGCTGGTAATGTTCAA
++
+AAAAAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAEEAAEEEEEEEAEEEE<AAAEEAEEEAEEEE/EEEEEAEEEAEAEE//<//AE//E<E//<//EA/A<EA6EE//E/AA/6A//6/AEE<EE6AE/AE
+@ERR5069949.2098070 NS500628:121:HK3MMAFX2:3:11406:20552:1667/1
+GCTCTCTACTACCCTTCTGCTCGCATAGTGTATACAGCTTGCTCTCATGCCGCTGTTGATGCACTATGTGAGAAGGCATTAAAATATTTGCCTATAGATAAATGTAGTAGAATTATACCTGCACGTGCTCGTGTAGAGTGTTTTGATAAAT
++
+AAAAAEEEEEEE/EE/EA/EEA/EEEEA/<6EEEEEEA<AE/EAEEEE/AAA<A<E<EEA<EEA/EEAEEEEAEEAEE/EAEEEEE//6/6AEEA</EEAEEEEA<EE/AE66AEAEAAAA/<AA<<<<EAAEAEAEE/EA6EEEEEAEEE
+@ERR5069949.1552198 NS500628:121:HK3MMAFX2:1:11108:11797:17621/1
+ATATTACGCGTATACGCCAACTTAGGTGAACGTGTACGCCAAGCTTTGTTAAAAACAGTACAATTCTGTGATGCCATGCGAAATGCTGGTATTGTTGGTGTACTGACATTAGATAATCAAGATCTCAATGGTAACTGGTATGATTTCGGT
++
+AAAAAEEEEEEEE6EEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEE<EEAEAEEEEEEEEEEEAEEEEEEEEEAEEEEEEEEEEEEEEA
+@ERR5069949.2385514 NS500628:121:HK3MMAFX2:3:21611:13560:16508/1
+GAGTTGACATCTATGAAGTATTTTGTGAAAATAGGACCTGAGCGCACCTGTTGTCTATGTGATAGACGTGCCACATGCTTTTCCACTGCTTCAGACACTTATGCCTGTTGGCATCATTCTATTGGATTTGATTACGTCTATAATCCGTTT
++
+A/AAAE6EEEEEAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEE/EE<EEEEE/A/AE6EEA/E/EEEEEA/AEEEEEEE<EEEAAEEEEEEE/EAEEEEEE/EEAAAEEE/<<AEEEEEEAEAEA<E/AAAAAAAA/<EE/EEAEEAE
+@ERR5069949.2270078 NS500628:121:HK3MMAFX2:4:21510:16801:19554/1
+ATAAACATGTTAGGGTAACCATTAACTTGATAATTCATTTTAAAACCCATCATAGAGATGAGTCTTCTATAGGTCATGTCCTTAGGTATGCCAGGTATGTCAACACATAAACCTTCAGTTTTGAATTTAGTGTCAACACTGAGGTGTGTAG
++
+AAAAAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEE<EEEEEEEEEEEEEEEEEEEEEEEEE/EEEAEEEEEE<EEEEEAEEEEE/<<EEA<EEEA<A<A<6AEE<AEEEEEEEEEAEEEE//AEEAEEEEEEA
+@ERR5069949.114870 NS500628:121:HK3MMAFX2:4:11410:23953:14505/1
+AAAGGAGCTGGTGGCCATAGTTACGGCGCCGATCTAAAGTCATTTGACTTAGGCGACGAGCTTGGCACTGATCCTTATGAAGATTTTCAAGAAAACTGGAACACTAAACATAGCAGTGGTGTTACCCGTGAACTCATGCGTGAGCTTAAC
++
+AAAAA/EAEEEEEEAEEEEEEEEE/EEEAEEEEEEEEEEEEEEEEAEAEAEEAEEEEEEEEEEEEEEEEAEAA<EE</AAEEEEEEEAEEEAEEEEEEEEEEEEEEEEEEEEEAEEA<AEEEEEEA<<AAE<EEEEEAE<AAEAAAEAEE
+@ERR5069949.2668880 NS500628:121:HK3MMAFX2:1:21104:5191:15623/1
+GTTTGTGGACCTAAAAAGTCTACTAATTTGGTTAAAAACAAATGTGTCAATTTCAACTTCAATGGTTTAACAGGCACAGGTGTTCTTACTGAGTCTAACAAAAAGTTTCTGCCTTTCCAACAATTTGGCAGAGACATTGCTGACACT
++
+AAAAAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAAE<EEAEEEEA<EAA<AAAEEEEEE<AEA<EAAEE
+@ERR5069949.257821 NS500628:121:HK3MMAFX2:2:21307:14790:19018/1
+TATGTAGCCATACTCCACTCATCTAAATCAATGCCCAGTGGTGTAAGTAATTCAGATACTGGTTGCAAAGTTTTTATGACAGCATCTGCCACAACACAGGCGAACTCATTTACTTCTGTACCGAGTTCAACTGTATAGG
++
+AAAAAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAEE6EEEAE/EE/EEEE<EEEE/EEEEEEEEEEEA/EEEEEEEAEEE/E<EE/EAAEEE/<E/<E<<E/A/EEAEEA<AAAEAE/<AE<EE<EA/A
+@ERR5069949.2243023 NS500628:121:HK3MMAFX2:2:21301:7521:3094/1
+TTTCAAGACTTGTAAATTGCAACTTGTCATAAAGGTCTCTATCAGACATTATGCAAAGTATGCCTACTTTTGCTCTGGTAATAGCAACATTAAATCTGTTTACATTACAAGAGTGAGCTGTTTCAGTGGTTTGAGTGAATATGACATAGT
++
+AAAAAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAEEEEEEAEEEEEEAEEEEEEEEEEEEEEEEEAEEEE<EEEAEAAEEEEEEEEEA<AAEEEE<EEEEAEAEE/E<AE<EAEEAE<EE
+@ERR5069949.2605155 NS500628:121:HK3MMAFX2:1:21311:18812:15592/1
+GTTCTTACCTTTCTTTTCCAATGTTACTTGGTTCCATGCTATACATGTCTCTGGGACCAATGGTACTAAGAGGTTTGATAACCCTGTCCTACCATTTAATGATGGTGTTTATTTTGCTTCCACTGAGAAGTCTAACATAATAAGAG
++
+AAAAAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAEEEEEEEEE/EEEEEEEEEEEEEE<EEAEEEAEAEAEEEEEEEEAAEEEEE<EEAEAEEEAA<E<EAAE</E/AA
+@ERR5069949.1340552 NS500628:121:HK3MMAFX2:2:11309:7320:9079/1
+TGCCTGACCAGTACCAGTGTGTGTACACAACATCTTAACACAATTAGTGATTGGTTGTCCCCCACTAGCTAGATAATCTTTGTAAGCTTTAGCAGCATCTACAGCAAAAGCACAGAAAGATAATACAGTTGAATTGGCAGGCACTTCTGTT
++
+AAAAAEEEEEEEEEAEEEEEEEEEEEEEEEEEEEEEAEEEEEEEEEEEEEEEEEEEEEE<EEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAEEEAEEE<EEEEEEEEEAAEEEEEEEEAAEEEEEEEEEE/EEEAAEE<A/EEAAAAEA
+@ERR5069949.1561137 NS500628:121:HK3MMAFX2:2:11303:23159:8428/1
+ATGTAAGGCTTTGTTAAGTCAGTGTCAACATGTGACTCTGCAGTTAAAGCCCTGGTCAAGGTTAATATAGGCATTAACAATGAATAATAAGAATCTACAACAGGAACTCCACTACCTGGCGTGGTTTGTATGAAATCACCGAAATCATAC
++
+AAAAAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAEEEEEEEEEEEEEEEEEAEEEEEEEEEE/EEEEEEEEEEEEEEEEEEAEEAEEAEEEEEEEEEEEEEEEE/EEEEEEEAEEEEEAAAEE/EE<EEAA/A<A<EEAEE/AAAE<EA
+@ERR5069949.2361683 NS500628:121:HK3MMAFX2:2:21103:8659:7427/1
+GATTTTTCCAGAGTTAGTGCTAAACCACCGCCTGGAGATCAATTTAAACACCTCATACCACTTATGTACAAAGGACTTCCTTGGAATGTAGTGCGTATAAAGATTGTACAAATGTTAAGTGACACACTTAAAAATCTCTCTGACAGAGT
++
+AAAAA/AA/EAEEAAEEEEAEE/EAEAAA<EEAAEEEEEE/EEEEEEEEEAAEEE/AEEE/EEEA<EEEAEEEEE<AAA<EEEEEEEEEAAEEA<AEEEEEEEEE<EEE/<AEEEEEAEEA<//A<EEAAEE6EAEEAAAEEAA6AEEA
+@ERR5069949.2521353 NS500628:121:HK3MMAFX2:3:11508:26680:5334/1
+CTTTTACAAGACTTCAGAGTTTAGAAATTGTGGCTTATAATGTTGTAATTAAGGGACACTTTGATGGACAACAGGGTGAAGTACCAGTTTCTATCATTAATAACTCTGTTTACACAAAAGTTGATGGTGTTGATGTAGAATTGTTTGAAA
++
+AAA/AE/6E6EEEEAEE/EE/EEE/EE/EA/EAEA//EEEEE6EAEAE/EEEEEE/EAE////EEA/EEEEEEEEEEEEEE///A/EEAEEEEEEEE<AEAEEE/AE/E<E/EEEEEA/E///AE/66AEEAEEE<E//E/EA/A<6AEE
+@ERR5069949.1261808 NS500628:121:HK3MMAFX2:3:11601:6846:14627/1
+GTGAAATTAGTATGGACAAATCACCTAATTTAGCATGGCCTCTTATTGTAACAGCTTTAAGGGCCAATTCTGCTGTCAAATAACAGAATAATGAGCTTAGTCCTGTTGCACTACGACAGATGTCTTGTGCTGCCGGAACTACACAAACT
++
+AAAA/AAA/EEEE/AE<EE//EE/EEEEEA<EAEEE66//EE/E/A6EEEA/E<<E/E//A/EE/AEEE6/E6EA<EEE/E//EAAEEEA/E//EEE/EA/A/A</<<E/AA<EEE<E<EEEE<A6</<A//A/AA/<<<AA<<A<AEA
+@ERR5069949.2734873 NS500628:121:HK3MMAFX2:4:21611:11682:9300/1
+ACATAGTGTAGGCAATGATGGATTGACTAGCTACACTACGTGCCCGCCGAGGAGAATTAGTCTGAGTCTGATAACTAGCGCATATACCTGCACCAATG
++
+AAAAAEEEEEEEEEEEEEEEEEEEE/EEEEEEEEAEEEEEEEEEEEEEEEEEEEEEEEAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEE
+@ERR5069949.3017828 NS500628:121:HK3MMAFX2:1:21111:18284:17510/1
+ATGATGAACCGACGACGACTACTAGCGTGCCTTTGTAAGCACAAGCTGATGAGTACGAACTTATGTACTCATTCGTTTCGGAAGAGACAGGTACGTTAATAGTTAAT
++
+AAAAAE6EEEEAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAEEEEAEEEEEEEEEEEEEEEEEEEEEEEEAEEEEE
+@ERR5069949.573706 NS500628:121:HK3MMAFX2:3:21407:23793:9689/1
+GTACGAACTTAAGCATGGTACATTTACTTGTGCTAGTGAGTACACTGGTAATTACCAGTGTGGTCACTATAAACATATATCTTCTAAAGAAACTTTGTATTGCATAGACGGTGCTTTACTTACAAAGTCCTCAGAATACAAAGGTCCTAT
++
+AAAAA6EEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEE/EEEEEEEEEEEEEEEEEEEEEEAEEEEEEEEEEAEEEEEEEEEEEEEEEEEEEAAEEEAEEEEEEEEEEE
+@ERR5069949.1980512 NS500628:121:HK3MMAFX2:1:21303:8321:13259/1
+ATATTGAGTGTTGGGTATAAGCCAGTAATTCTAACATAGTGCTCTTGTGGCACTAGTGTAGGTGCACTTAATGGCATTACTGTATGTGATGTCAGCACAAAATAATCACCAACATTTAATTTGTAAGTTGTTGTACCTCGGTAAACAACAG
++
+AAAAAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAEAEEEEEEEEEEEAEEEEEEEAEAEEEEAAEAEEEEEAEEEAEEEAEAEEEAEAAAEAEAAEEEEEAAEEEEEEAEEEEEEEEEE
+@ERR5069949.1014693 NS500628:121:HK3MMAFX2:1:11109:13494:20222/1
+GTCTATATGCCTGCTAGTTGGGTGATGCGTATTATGACATGGTTGGATATGGTTGATACTAGTTTGTCTGGTTTTAAGCTAAAAGACTGTGTTATGTATGCATCAGCTGTAGTGTTACTAATCCTTATGACAGCAAGAACTGTGTATGAT
++
+AAAAAAEEAEEE6EAE//E/EEE6AEAA/EAEAEE6/E//EAE/EEEEAEE/EEE/EAEEEEEAE/EEEEEAEEEEEAAEEAEEE/AE/EAEAEEEEEEEEEEEEEE/AE/E/E/<<<AA<E<AEE</EEEEA6<AEEAAAA//A//EEE
+@ERR5069949.3184655 NS500628:121:HK3MMAFX2:3:21606:7576:13093/1
+TTCCAGAAGAGCAAGGTTCTTTTAAAAGTACTGTTGTACCTCTAACACACTCTTGGTAGTGATAAAGCTCACAAGTAGCGAGTGTTATCAGTGCCAAGAAAAGAATAATTTTCATGTTCGTTTAATCAATCTCCATTGGTTGCTCTTCAT
++
+AAAAAEEEEEE/EEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAEEEEA/EEEEEEEEEEEEEAEEEEEEE/EAEAEEA<A/EE/E<E/EEEEEEEEEE<E<EEEEA/<<<A/E///AEE<EEE/<A6E/A/6A<6AE/<E6EAAA
+@ERR5069949.29668 NS500628:121:HK3MMAFX2:2:21202:17958:8710/1
+CTCCAAAGCCACGTACGAGCACGTCGCGAACCTGTAAAACAGGCAAACTGAGTTGGACGTGTGGTTTCTAGTTGTAACCAGGGACAAGG
++
+AA/AAEE6////EEEAEEE<EAEA/AEEEEEAEEEAEEEAE/A6EA/E/EA6A<A<AAA</////EEE6///<</EE/EE/E/6////E
+@ERR5069949.3258358 NS500628:121:HK3MMAFX2:3:21508:15641:1056/1
+GTTCCTAGGTAGTAGAAATACCATCTAGGACTGAGATCTTTCATTTTACAGTCACCACCACGAATTCGTCTTGTAGCTCTTCGGTAGTAGCCAATTTGGTCATCTGGACTGCTATTGGTGTTAATTGGAACGCCTTCTCCTCGAGGGAATT
++
+AAA/AAEAEEAEEEEEEA/EEEEEEE//EE/EAEE/EE/A6EEEAEAEE/EE//EEEE/AE/AAAE/AAEE/A/E//AEE/AA/EE/EE6EE<///E//AEE<EEA<EE//EE<<</<EAEEEEEE//</A<EE<</<EA/A/<A<A/EEE
+@ERR5069949.1476386 NS500628:121:HK3MMAFX2:2:21303:26270:9400/1
+TAATGACCCTGTGGGTTTTACACTTAAAAACACAGTCTGTACCGTCTGCGGTATGTGGAAAGGTTATGGCTGTAGTTGTGATCAACTCCGCGAACCCATGCTTCAGTCAGCTGATGCACAATCGTTTTTAAACGGGTTTGCGGTGTAAGTG
++
+AAAAA/EEEEEEEEEEEEEEEEEEEEEEEEEEEEEAEEEEEEEEEEEEEAEAEEEEEEEEEEEEEEEEEEEEEEAEEEEEAEEEAEEEEEEE/AEEE/EEEEEE/AEE/EEAE/EEE<EA/<EEA/EEEEE/EEEEAAEEEAAAAEEAEEE
+@ERR5069949.2415814 NS500628:121:HK3MMAFX2:1:11107:11754:7444/1
+GCTTTGAGTTGACATCTATGAAGTATTTTGTGAAAATAGGACCTGAGCGCACCTGTTGTCTATGTGATAGACGTGCCACATGCTTTTCCACTGCTTCAGACACTTATGCCTGTTGGCATCATTCTATTGGATTTGATTACGTCTATAATC
++
+AAAAAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAEEEEEEEEEEEEEEEEEEEEEEEEE<EEEEEEEEEEEEEEEEEEEEE<EEEEEEEEEAEEEEEEAEEEEEEEAEEEAEEEEEAEEEEEAEAAAE<AEA

tests/data/fastq/dna/sarscov2_2.fastq.gz

@@ -0,0 +1,400 @@
+@ERR5069949.2151832 NS500628:121:HK3MMAFX2:2:21208:10793:15304/2
+ATGTGTACATTGGCGACCCTGCTCAATTACCTGCACCACGCACATTGCTAACTAAGGGCACACTAGAACCAGAATATTTCAATTCAGTGTGTAGACTTATGAAAACTATAGGTCCAGACATGTTCCTCGGAACTTGTCGGCGTTGTCCTG
++
+AAAAAEEEEEEEEEE/EEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAEEEEEEEEEE/EEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAAEEEEEEEAEEEEEAAEEEEEEEEEAAEAAA<<EAAEEEEEEEAAA<<<AE
+@ERR5069949.576388 NS500628:121:HK3MMAFX2:4:11501:11167:14939/2
+GCATAGACGGTGCTTTACTTACAAAGTCCTCAGAATACAAAGGTCCTATTACGGATGTTTTCTACAAAGAAAACAGT
++
+AAAAA6EEAEEEEEAEEAEEAEEEEEEA6EEEEAEEAEEEEE6EEEEEEAEEEEA///A<<EEEEEEEEEAEEEEEE
+@ERR5069949.501486 NS500628:121:HK3MMAFX2:1:21305:3080:7962/2
+TTACAGAGCAAGGGCTGGTGAAGCTGCTAACTTTTGTGCACTTATCTTAGCCTACTGTAATAAGACAGTAGGTGAGTTAGGTGATGTTAGAGAAACAATGAGTTACTTGTTTCAACATGCCAATTTAGATTCTTGCAAAAGAGTCTTGAA
++
+AAAAAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAEEEEEEEEEEEEEEEEEEAAAAEEEEEEEEEEEEEEEEEEEEEEEEEEEAA/EEE/<AEEAAEAEA</EEEAEAAAAAEE
+@ERR5069949.1331889 NS500628:121:HK3MMAFX2:3:11605:17658:18222/2
+CACAATTAGTGATTGGTTGTCCCCCACTAGCTAGATAATCTTTGTAAGCTTTAGCAGCATCTACAGCAAAAGCACAGAAAGATAATACAGTTGAATTGGCAGGCACTTCTGTTGCATTACCAGCTTGTAGAC
++
+AAAAAEEEEEEEEAEEEEEEEEEEAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAEEEE/EEEEEEAAEE/EEEEEEEEEEEEEEEEEEEEEEEEEEEEEE<AEEEEEEEEEAEEEEEEEEAEEEEE/A
+@ERR5069949.2161340 NS500628:121:HK3MMAFX2:2:21107:15810:18317/2
+GGACAACGCCGACAAGTTCCGAGGAACATGTCTGGACCTATAGTTTTCATAAGTCTACACACTGAATTGAAATATTCTGGTT
++
+AA6AAAE6/EA/<E/E/<//EE///EAEAEEEE////6EEE//EEE/EAEEE/AEA/EA<EA</AEEE/EE/AEAE</E//A
+@ERR5069949.973930 NS500628:121:HK3MMAFX2:2:21105:5548:5659/2
+CCTTTTGATGTTGTTAGACAATGCTCAGGTGTTACTTTCCAAAGTGCAGTGAAAAGAACAATCAAGGGTACACACCACTGGTTGTTACTCACAATTTTGACTTCACTTTTAG
++
+AAAAAEEAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEE/EEEEEEEEEEEEEEEEEEEEEEEAE<EAEEEEEEAEEAEE
+@ERR5069949.2417063 NS500628:121:HK3MMAFX2:1:11310:4428:10115/2
+CAATAGTCCAGTCAACACGCTTAACAAAGCACTCGTGGACAGCTAGACACCTAGTCATGATTGCATCACAACTAGCTACATGTGCATTACCATGGACTTGACAATACGGATCATGGTTGCTTTGTAGGTTACCTGTAAAACCCCATTGTT
++
+AAAAAEEEEEEEEE/E6EEEEEEEEEEEEEEEEEEEEEAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAEEAEEEEEEAEEEEEEEAEEEEEAEEEEEAAEAEE/EEAE/EEEAAAA6A<E/EAEAE/EEAEAE<//EEEEE<AEEA
+@ERR5069949.376959 NS500628:121:HK3MMAFX2:1:21205:12113:10369/2
+AGATAATAGATGGTAGAATGTAAAAGGCACTTTTACACTTTTTAAGCACTGTCTTTGCCTCCTCTACAGTGTAACCATTTAAACCCTGACCCGGGTAAGTGGTTATATAATTGTCTGTTGGCACTTTTCTCAAAGCTTTCGCTAGCATTT
++
+AAAAAEEEEEEEEEAEEEEEEEEEEEEEEEEEEEEEEEEAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAEEEEEEEEEEE<EEEEEA<A<AAAAAAA<<<EAEEEE<AEEEAAAAA<AAAEAAAEE
+@ERR5069949.1088785 NS500628:121:HK3MMAFX2:1:21109:26270:17779/2
+GCATTTCTTCACAAAGCTTGTTTATGTCTACAGCACCCTGCATGGAAAGCAAAACAGAAAGTAGTGAAACCATTTTTTCAAAGGCTTCAGTAGTATCTTTAGCTAAGAGAATGTCATTGTGTAACTGGACACATTGAGCCCACAATTTAG
++
+AAAAAEEEEAEEEEEEEEEE/EEEEEEEEEEEEEEEEAEE/EEAEEE/AAEEEEEEEEEEEEEEEEEEEE/EEEEEEEAEEEEEEEEEAEEEE</EEE/EA/<EAEAEEEEEEAEEA<EEEEEAEEEA<AAAA/EEAE<E//E<EEEEEA
+@ERR5069949.1066259 NS500628:121:HK3MMAFX2:1:11312:18369:8333/2
+GTACAAAAATAGCCTAAGAAACAATAAACTAGCATTATACACTGAAGTGTATTACCAGTTATGAAGAAAATAGGGCAATACTCAACACACATAAAAACAATACCTCTGGCCAAAAACATGACAGTTGTAACTACACCTGAGTAGTTAGAAG
++
+AAAAAEEEEEEEEAEEEEEEEEEEEEEEEEEEEEEEEEAEAEEEEEEEEEEEEEEEEEEEEEEEEEEEEAEEEEEEEEA/EAA</EEEEEEEEEE/AE//A/E<AE<AA<AEEE/AAEAAAEEAEEA<A6AEEA<EEAEEEEEEEAA//EE
+@ERR5069949.2832676 NS500628:121:HK3MMAFX2:4:11602:20035:16369/2
+TGATCAACCTATCAATTTGCACTTCAGCCTCAACTTTGTCAAGACGTGAAAGGATATCATTTAAAACACTTGAAATTGCACCAAAATTGGAGCTAAGTTGTTTAACAAGCGTGTTTAAAGCTTGTGCATTTTGGTTGAC
++
+AA6AAEEEEEEEEEEEAEEEEEEEEEEEEEEEEEEEEEE<EEEEEEEEEEEEEEEEEAEEE<AEEEEEEE<AAEEAEEAEEEEEEEE/EEEAAEEEEAAA<A<EEAEE/EAAEEEAEEEEA/<AEE6AEAE/<EEEE<A
+@ERR5069949.2953930 NS500628:121:HK3MMAFX2:3:21504:10316:13537/2
+CCCTTGGAGAGTGCTAGTTGCCATCTCTTTTTGAGGGTTATGATTTTGGAAGCGCTCTGAAAAACAGCAAGAAGTGCAACGCCAACAATAAGCCATCCGAAAGGGAGTGAGGCTTGTATCGGTATCGTTGCAGTAGCGCGAACAAAAT
++
+AAAAAEEEEEEEEEEEEEEEEEEEEEEE/EEEEEEEEEEEEEEEEEEEEE/EEEEAEEEEEEAAEEEEEEEEEEAEE/EEEEAEEEEEEEEEAEEEEEEEAEEEEAAEEEEEE/EEEEEEAAAAAEEEEAAEEEEEEEEEE/EEEEEE
+@ERR5069949.324865 NS500628:121:HK3MMAFX2:1:11102:17526:14721/2
+ATGAATCTGATGAATACATAGCTACTAATGGACCTCTTAAAGTGCGTGGTAGTTGTGATTAAAGCGGACACATACTTGCTAAACACTCTCTTCATGATGTC
++
+A/AAAEEEEA6AA6EE//EEA/EEEAE/EA/A////E</EEAA//EEA////EAE<///E/AEA</AAE/EA//E<EAAAE/AA//AEE//A/AE//</EE
+@ERR5069949.2185111 NS500628:121:HK3MMAFX2:2:11210:1473:2754/2
+GCTAAGCACTATGTGTACATTGGCGACCCTGCTCAATTACCTGCACCACGCACATTGCTAACTAAGGGCACACTAGAACAAGAATATATCAATTCAGTGTGTAGACTTATGAAAACTATAGGTCCAGACATGTTCCTCGGAACTTGT
++
+AAAAA6/E//AEEAEEEEE/EEE/E/EEEE/E/E6E///E<E/<EE</A/<EEE//E6/<EEEAE<//<E/E/6EEE/EAAA<//EE//<EEE/AEEAA/A<EAE/EEA<//AEAEEE/<A/E</AA<EEA<<EAAEA<<</E/EEE
+@ERR5069949.937422 NS500628:121:HK3MMAFX2:2:11104:8644:10925/2
+GGTTAAAGTCATTAAGAGTTGTGGTAAATCGATTGAGAAACCACCTGTCTCCATTTATAACAGCAGCGTACAACCAAGCTAAAACATTAACTGTAATAGTTGTGTCCGTACCAGCTGCTTGTGCTGTTTGCCTGTCAACAAAAGGTCCATA
++
+AAAAAEEEAEEEEAEEEEEEEEEEEEEEEEEEEEEEEE6/EE/EEEEEEAAAAAEEEEEEAEEE<EEEAEE//EEEEEEEEEEAEEEEEEEAEAAEEAEA<EA<AEEEA/EEEAEAAAA<AAAAAAAAA6EA/AAE<EAAEEE/EE<A/AA
+@ERR5069949.2431709 NS500628:121:HK3MMAFX2:3:21609:20858:5879/2
+ATTATAGGATATTCAATAGTCCAGTCAACACGCTTAACAAAGCACTCGTGGACAGCTAGACACCTAGTCATGATTGCATCACAACTAGCTACATGTGCATTACCATGACTTGACAATACAGATCATGGTTGCTTTGTAGGTTACCTGTAAA
++
+AAAAAEEEEEEEEEEEEEEEEEEEEEE/EEEEEEEEEEEEEEEEEEEAEEEEEEEEEEE/EEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAEEEEEEEEEEEAEEEAEEEEEEEEEEEEEEEEEEAEEAAAEAEEEEAAAA<EAAAAAAA
+@ERR5069949.1246538 NS500628:121:HK3MMAFX2:4:11505:20131:7933/2
+GTTGTAGTAAGCTAACGCATTGTCATCAGTGCAAGCAGTTTGTGTAGTACCGGCAGCACAAGACATCTGTCGTAGTGCAACAGGACTAAGCTCATTATTCTGTAATTTGACAGCAGAATTGGCCCTTAAAGCTGTTACAATAAGAGGCCAT
++
+AAAAAEEEEEEEEEAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAEEEEEEEEEEEEEAAEEEAEEAAA<AEEAAAEAAEEEEAAEEEAAAAAA
+@ERR5069949.1189252 NS500628:121:HK3MMAFX2:2:21308:10087:1427/2
+CAATTTTACTATCTGCATCTACAACCTGTTGGATTTCCCACAATGCTGATGCATAAGTAAATGTTGTACCATCACACGTATTTTTATATGTGTTATAG
++
+AAAAAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAEEE
+@ERR5069949.2216307 NS500628:121:HK3MMAFX2:1:21302:10479:19538/2
+GTGTAGACTTATGAAAACTATAGGTCCAGACATGTTCCTCGGAACTTGTCGGCGTTGTCCTGCTGAAATTGATGACACTGTGAGTGCTTTGGTTTATGATAATAAGCTTAAAGCACATAAAGACAAATCAGCTCAATGCTTTAAA
++
+A//AA6EEE/EEEEAEEEEE/EE/A/6E/EAE</EE/AEE/AEEAEAE/E//AA<6AA6<E/EE/EEE/AE/6/EEE<//E/E6A/<E/////EAE<E<</AAAEE//AAEE/6AAA6/AEA/AAEEAAAA////AA/6E<6AAE
+@ERR5069949.3273002 NS500628:121:HK3MMAFX2:4:11506:23944:16676/2
+TGGCAAGGAAGACCTTAAATTCCCTCGAGGACAAGGCGTTCCAATTAACACCAATAGCAGTCCAGATGACCAAATTGGCTACTACCGAAGAGCTACCAGACGAATTCGTGGTGGTGACGGTAAAATGAAAGATCTCAGTCCAAGATGGTA
++
+AAAAAEEEEEEEEEEEEEEEEEEAEEAEEEEEEEAEEE/EEA/EEEEEE6EEEAEEEEEEEEEAEEEEAEEEEE<EEEE<EEE/EE//AE/EEAEAEAE/EAAEEA6AEEE/<E<</EEE/E</AEA//A/EA6<AAEEEA/AEE6AE/E
+@ERR5069949.3277445 NS500628:121:HK3MMAFX2:4:11601:26589:14031/2
+CTCAGTTGCAACCCATATGATGCCGTCTTTGTTAGCACCATAGGGAAGTCCCGCTTCTGGCCCCGTTCCTAGGTAGTAGAAATACCATCTTGGACTGAGAT
++
+AAAAAEEEEE6EEEEEEEEEEEEEEE//6EEAE//A/AEE<EAAE/A/E/E//E/E///E/EE///</A/E/<//E<EA/AE/EA</<//<AE///A/</<
+@ERR5069949.3022231 NS500628:121:HK3MMAFX2:1:21102:10897:17190/2
+ATATTGCAGCAGTACGCACACAATCGAAGCGCAGTAAGGATGGCTAGTGTAACTAGCAAGAATACCACGAAAGCAAGAAAAAGAAGTACGCTATTAACTATTAACGTACCTGTCTCTTCCGAAACGAATGAGTACATAAGTTCGTAC
++
+AAAAAEEEEEEEEEEEEEEEEEEEEE6EEEEEEEEEEEEEAEEEEAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAEEEEEEAEEEEEEEEEEEEEEEEAAEAAEE<EAEEEE<EEEEEAEEEEEEAAAE
+@ERR5069949.184542 NS500628:121:HK3MMAFX2:2:21205:8408:1786/2
+GGCACCTTCTTTAGTCAAATTCTCAGTGCCACAAAATTCGCAAGTGGCTTTAACAAAATCGCACGT
++
+AAA/AAEAEE/AAAE6/A/EE6AAAAEEE/E//AA6EEE/6/A/A///EEA<EEEAE6A/E////E
+@ERR5069949.540529 NS500628:121:HK3MMAFX2:3:21609:5345:11242/2
+TGGGCACACTTTCTTATGAACAATTTAAGAAAGGTGTTCAGATACCTTGTACGTGTGGTAAACAAGCTACAAAATATCTAGTACAACAGGAGTCACCTTTTGTTATGATGTCAGCACCACCTGCTCAGTATGAACTTAAGCATGGTACAT
++
+AAAAAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAEEAEEEEAEAEEEEEEEEEEAAEEEEEEEEEEAEEEEEEE<EA<AEEEAEEEAEEEEAEEAEEEAEEEEEEEAAAEEE
+@ERR5069949.686090 NS500628:121:HK3MMAFX2:1:11212:8601:4499/2
+GATCAGGCATTAGTGTCTGATGTTGGTGATAGTGCGGAAGTTGCAGTTAAAATGTTTGATGCTTACGTTAATACGTTTTCATCAACTTTTAACGTACCAATGGAAAAACTCAAAACACTAGTTGCAACTGCAGAAGCTGAACTTGCAAAGA
++
+AAAAAEEEEEEAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAEEEEEEEEEEAEEEEEAEEEEEEEE/EEEEEEEEEEEEEEAEEEEEAEEEE<AEE/EEEEEEEAAAAEEEEEEEEEEEAEAEEEEEAEEEEA
+@ERR5069949.2787556 NS500628:121:HK3MMAFX2:4:11609:10602:17177/2
+CCGCTAACAGTGCAGAAGTGTATTGAGCAATCATTTCATCTGTGAGCAAAGGTGGCAAAACAGTAAGGCCGTTAAACTTTTGTGCACAAACGAGGTCTCTAGCAGC
++
+AAAAAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAEEEEEEEEEEEAEEEEEEAEEEEE<AAA<EEEE<AEEEEEEEEAAEE
+@ERR5069949.2650879 NS500628:121:HK3MMAFX2:1:21111:16524:5801/2
+ATATAATTCCGCATCATTTTCCACTTTTAAGTGTTATGGAGTGTCTCCTACTAAATTAAATGATCTCTGCTTTACTAATGTCTATGCAGATTCATTTGTAATTAGAGGTGATGAAGTCAGACAAATCGCTCCAGGGCAAACTGGAAAGATT
++
+AAAAAEEEEEEEEEEEEEEEEEEEEAEEEEEEEEEEEEEEEEEEEEEEAEE<EEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAEEEEEEAEEEEEEEEEEEEAEEE<A<EEEEAAAAEEEEEEEEEEEE
+@ERR5069949.2064910 NS500628:121:HK3MMAFX2:3:21608:24504:13289/2
+ACATACTGTTCTAATGTTGAAGTCACTTTGAATTTATCAAAACACTCTACACGAGCACGTGCAGGTATAATTCTACTACATTTATCTATAGGCAAATATTTTAATGCCTACTCACAT
++
+A//AAE/EEEA/EEE/A/EEE6EE/EEEEAE6AA<EAE<EEEEEE/E</<EA/6EEA<EAAEEEEEAEAE/AEAEE/EA<E//EEEEEEEE/EAAE<AA///AE<EAAA/A////<<
+@ERR5069949.2328704 NS500628:121:HK3MMAFX2:4:21612:9379:15958/2
+CATGGATTGGCTTCGATGTCGAGGGGTGTCATGCTACTAGAGAAGCTGTTGGTACCAATTTACCTTTACAGCTAGGTTTTTCTACAGGTGTTAACCTAGTTGCTGTACCTACAGGTTATGTTGATACACCTAATAATACAGATTTTTCCA
++
+AAAAAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEE<EEEEEEEEAEEEEEEEEEEEEAEEEEEEAEEEEEEEEEEEAEEEAEAEEEA<AEEEEEEEE/EEEEEEEAEEEEEEE/EEEEAEE
+@ERR5069949.1067032 NS500628:121:HK3MMAFX2:4:21403:19263:10183/2
+GCTTTAGATCAAGCCATTTCCATGTGGGCTCTTATAATCTCTGTTACTTCTAACTACTCAGGTGTAGTTACAACTGTCATGTTTTTGGCCAGAGGTATTGTTTTTATGTGTGTTGAGTATTGCCCTATTTTCTTCATAACTGGTAATACA
++
+AAAAAAEEEE666<EEEE/E/EEEAEAEEEE/EEEEEEEE/AEEEAEE/<AAEE<EAEEEA/AEEE/EAEEEE<E<AEEAEEEE<<//EEE/EEE<EEE<A/A/A<EEE///A/6<A<AE<//<EEEE6</<AAAAAAE<A//<</<A/E
+@ERR5069949.3338256 NS500628:121:HK3MMAFX2:1:11108:15722:2450/2
+CAGCAAACTGTGACTCTTCTTCCTGCTGCAGATTTGGATGATTTCTCCAAACAATTGCAACAATCCATGAGCAGTGCTGACTCAACTCAGGCCTAAACTCATGCAGACCACACAAGGCAGATGGGCTATATAAACGTTTTCGCTTTTCCG
++
+AAAAAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAEEEEEEEAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEE/EEEEAEEEEEEEEAAAAAEA<AAAEA<AA
+@ERR5069949.1412839 NS500628:121:HK3MMAFX2:3:11609:15519:12102/2
+GTACACACACTGGTACTGGTCAGGCAATAACAGTTACACCGGAAGCCAATATGGATCAAGAATCCTTTGGTGGTGCATCGTGTTGTCTGTACTGCCGTTGCCACATAGATCATCCAAATCCTAAAGGATTTTGTGACTTAAAAGGTAAGT
++
+AAAA6EEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAEEEEEEE6EEEEEEEEEEEEEEEEEEEEEEEEEAEEEAAAAEEEEEEEEEEAAEEAEAE<EEEAEAEEE/<AAAEAEAA/EAEEEEAEEAAE/AEA/EEEAEEAEAA
+@ERR5069949.1538968 NS500628:121:HK3MMAFX2:2:11304:14669:15804/2
+CACGATGGCAGACCTCGTCTATGCTTTAAGGCATTTTGATGAAGGTAATTGTGACACATTAAAAGAAATACTTGTCACATACAATTGTTGTGATGATGATTATTTCAATAAAAAGGACTGGTATGATTTTGTAGAAAACCCAGATATATTA
++
+AAAAAEEEAEEAEEEAEEEAEEEAE<EEE6EAEA<EAAAEEEEEEEEEEEEEA/</EEEEEEEEEEEEEEEEEEEEEEAEEEEE/AEEEEEEEEAEEEEEEEEEEEEEEEEAEEEAA<AEAEE<AAE<A<AEEEEE/EA6AAA/EE/EEEA
+@ERR5069949.147998 NS500628:121:HK3MMAFX2:3:21611:12530:12698/2
+ATCTAAAGTCATTTGACTTAGGCCACGAGCTTGGCACTGATCCTTATGAAGATTTTCAAGAAAACTGGAACACTAAACATAGCAGTGGTGTTACCCGTGAACTCATGCGTGAGCTTAACGGAGGGGCATACACTCGCTATGTCGATAACAA
++
+AAAAAAE6EEE/EEE/E/EEA6E/EEE/AE/E//EEEEAA/E/E/EAEEEE/EEEEEEE<EE/E/A/A</<E</<AE<///A<AA<//E/AE/E/EEE/EEEEA//E/A</<AE/////E<AAE<EE//EA/<6/A</A//<AAAA<EE/A
+@ERR5069949.366975 NS500628:121:HK3MMAFX2:1:11105:12446:15727/2
+CTAAAAAGGCTGGTGGCACTACTGAAATGCTAGCGAAAGCTTTGAGAAAAGTGCCAACAGACAATTATATAACCACTTACCCGGGTCAGGGTTTAAATGGTTACAC
++
+AAAAAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAEEEEEEEEEEEEEEEEEEEEEEEEEAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEE
+@ERR5069949.1372331 NS500628:121:HK3MMAFX2:3:11601:26764:8562/2
+TCTACAAGCTGGTAATGCAACAGAAGTGCCTGCCAATTCAACTGTATTATCTTTCTGTGCTTTTGCTGTAGATGCTGCTAAAGCTTACAAAGATTATCTAGCTAGTGGGGGACAACCAATCACTAATTGTGTTAAGATGTTGTGTACACA
++
+AAAAAEEEEEEEEEEEEEEEEEEAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAAEEEEEEEEEEEEE/EEEEEEE<EEAEEEEEEA/EEA<EAEEEEEEAEAAAEEAAAEEEEEAAA<AAAEEEA
+@ERR5069949.1709367 NS500628:121:HK3MMAFX2:1:11301:9990:2022/2
+GGTGGCTGTATTAATGCTAACCAAGTCATCGTCAACAACCTAGACAAATCAGCTGGTTTTCCATTTAATAAATGGGGTAAGGCTAGACTTTATTATGATTCAATGAGTTATGAGGATCAAGATACACTT
++
+AAAAAEEEEEEEEEEEEEE6EEEEEEEEEEEEEEEEE6EEEEEEEEEEEEEEEEEEEEEEEEEEEEEEE/EEEEEEEEEEEEEEEEEEEEEAEEEEEEAEEEEEEEEEEEEEEAEEEEEEEEEEEEEEE
+@ERR5069949.2388984 NS500628:121:HK3MMAFX2:2:21306:17580:3896/2
+AGCTACATGTGCATTACCATGGACTTGACAATACAGATCATGGTTGCTTTGTAGGTTACCTGTAAAACCCCATTGTTGAACATCAATCATAAACGGATTATAGACGTAATCAAATCCAATAGAATGATGCCAACAGGCATAAGTGTCTG
++
+AAAAAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAEEEEEEEEAEEEEEEEEEEEEEEEAEEEEE/<EE<EE<AEEEAEEEEAAAEEEEEE<<AAEAEEEEEEEEAEEEEEAAEEEAEAAAA<EA/EEAAAAEEEAEE<EEE6AAAAE
+@ERR5069949.1132353 NS500628:121:HK3MMAFX2:2:21111:21744:6806/2
+CAACAGGGCAACCTTACAAGCTATAGCCTCAGAGTTTAGTTCCCTTCCATCATATGCAGCTTTTGCTACTGCTCAAGAAGCTTATGAGCAGGCTGTTGCTAATGGTGATTCTGAAGTTGTTCTTAAAAAGTTGAAGAAGTCTTTGAATGTG
++
+AAAAAEEEE/EEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAAEEEEEEEEEEEEEEEEEEE<EEEEEEEEAAEEAAEEEEEEEEEEEEEAE<AAAAAAE/AEEAEEEEEEEEEEEEEAAAEAAEEA
+@ERR5069949.1151736 NS500628:121:HK3MMAFX2:4:21406:11928:13664/2
+TTTTGCTACTGCTCAAGAAGCTTATGAGCAGGCTGTTGCTAATGGTGATTCTGAAGTTGTTCTTAAAAAGTTGAAGAAGTCTTTGAATGTGGCTAAATCTGAATTTGACCGTGATGCAGCCATGCAACGTAAGTTGGAAAAGATGGCTGAT
++
+AAAAAEEEEEEEEEEEEEEEEEEEEAEEEEEEEEEEEEEEEAAEEEEEEEEEEEEEEEEEEE<EEEEAEEEEEEEEEEEEEEEEAEEEEEAEEAAEEE<AEAEEE<A/AAEEEEEEEAAAAA<AAAE<EEEEAEEEAEEEEEEAEEAEA/A
+@ERR5069949.479807 NS500628:121:HK3MMAFX2:3:11402:16906:16736/2
+GTTTACAACAGTAGACAACATTAACCTCCACACGCAAGTTGTGGACATGTCAATGACATATGGACAACAGTTTGGTCCAACTTATTTGGATGGAGCTGATGTTACTAAAATAAAACCTCATAATTCACATGAAGGTAAAACATTTTATGT
++
+AAAAAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEE<AEEEEEEEEEE<EEE<AEE/EEEEEEEEEAEEE<AA/EAA<AEEEEEEEAEEAAA
+@ERR5069949.2176303 NS500628:121:HK3MMAFX2:4:11608:21150:1680/2
+ATAACACCCTTATAAAACATTTTAAAGCATTGAGCTGATTTGTCTTTATGTGCTTTAAGCTTATTATCATAAACCAAAGCACTCACAGTGTCAACAATTTCAGCAGGACAACGCCGACAAGTTCCGAGGAACATGTCTGGACCTATAGTT
++
+AAAAAEEEEEEEEEEEEEEEEEAEEEEEEEEEEEEEEEAAEEEEEAEAEEAEAEAEEEEEEEEEEEEEEEEEEEAEEEEEEEEEEEEEAEEEEEEAEEEEEEEAAEEAAE/<A/EEAEE/A<AAAA<AAAEEEEEEAAAEAEAEEEAEAE
+@ERR5069949.2772897 NS500628:121:HK3MMAFX2:1:11106:12629:15009/2
+CTTTCGTTGCAATATGGCAGTTTTTGTACACAATTAAACCGTGCTTTAACTGGAATAGCTGTTGAACAAGACAAAAACACCCAAGAAGTTTTTGCACAAGTCAAACAAATTTACAAAACACCACCAATTAAAGATTTTGGTGGTTTTAAT
++
+AAAAAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEE6EEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAEEEEEEEEEEEEEEEEEA<EAEEEE<EEEEAEEAAEEEEEEEEEEE
+@ERR5069949.1020777 NS500628:121:HK3MMAFX2:3:11408:13234:17983/2
+CTATATGCCTGCTAGTTGGGTGATGCGTATTATGACATGGTTGGATATGGTTGATACTAGTTTGTCTGGTTTTAAGCTAAAAGACTGTGTTATGTATGCATCAGCTGTAGTGTTACTAATCC
++
+AAAAAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAEEEEEEEEEEEEEEEEAEEEEEEAEEEAAEEEEEEEEEAEEEEA
+@ERR5069949.465452 NS500628:121:HK3MMAFX2:3:11503:20241:8941/2
+GTTGTAAACACCTTAATAGTCCTCACTTCTCTCAAAGAAAGAAGTGTCTTAAGATTGTCAAAGGTGATAACTTCACCATCTAGGTGGAATGTGGTAGGATTACTAGTGTAATATACACTTTTATCACCTCTCTTAAGAAATTCTATACCT
++
+AAAAAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAEEEEEE/AEE/EEEEEEEAEEEEEEEEEEEEEEEEEEEEEEAEEEEEEEEEEEAE/AA<AE</AAEEEEEEEEEEEEAAA
+@ERR5069949.1704586 NS500628:121:HK3MMAFX2:3:11408:18502:19140/2
+CTTGGTTAGCATTAATACAGCCACCATCGTAACAATCAAAGTACTTATCAACAACTTCAACTACAAATAGTAGTTGTCTGATATCACACATTGTTGGTAGATTATAACGATAGTAGTCATAATCGCTGATAGCAGCATTACCATCCTGAG
++
+AAA/AEEE<EEEEE/EEEEEE/EEEEEEEEEEEAEEEEEE/EEEEEEEEEEEEEE<EAEEEEEE/EEEAEEAEAEEEAEEAEEEE/EA<AEA<AAEAEEEE<EEEEEA//E<EA<<A<A//EE6AAA</<EEE6AAEA<AAA<EAEE//A
+@ERR5069949.1258508 NS500628:121:HK3MMAFX2:2:21106:23201:10887/2
+GTGTTCCCTTGAACATAATACCTCTTACAACAGCAGCCAAACTAATGGTTGTCATACCAGACTATAACACATATAAAAATACGTGTGATGGTACAACATTTACTTATGCATCAGCATTGTGGGAAATCCAACAGGTTGTAGATGCAGATAG
++
+AAAAAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEE<EEEEEEEEEEEEEAEEEEEEEEEEEEEEEEEEEEEEEEAAEEEEE/EEEEEEEEEAEEEEEEEEA/AEAEAAAEAEEEEEAEEEEE<<EEEEEEE<AEAEAAA<EEE
+@ERR5069949.986441 NS500628:121:HK3MMAFX2:2:11310:5407:13956/2
+TGTCATAATACGCATCACCCAACTAGCAGGCATATAGACCATATTAAAATAAGCTACAGTGGCAAGAGAAGGTAACAAAAACAAACAGAGAAATGCATGCTTATGTTTGACAAACATCATTGCAAAAGCAGACATAGCAATAATACCCAT
++
+AAAAAEEEEEEEEAEEEEEEEEAEEEEEAEEEEEEAE/EEEEEAEAEEEEEEEAEAEEEEEEAE/AAAEA/EAEAE/EEEAEEEEEEE/EEEAEAAAE</AAEAEEEE/E/E/E<AEEAE/<AEAEEAA<AEAAEAE<E<EEEEEA<A6A
+@ERR5069949.2674295 NS500628:121:HK3MMAFX2:1:21303:10381:8722/2
+CCTAAAAAGTCTACTAATTTGGTTAAAAACAAATGTGTCAATTTCAACTTCAATGGTTTAACAGGCACAGGTGTTCTTACTGAGTCTAACAAAAAGTTTCTGCCTTTCCAACAATTTGGCAGAGACATTGCTGACACTACTGATGCTGTC
++
+AAAAAEEEEEEEEEEAEEEEEEEEEEEE6EEEEEEEEEEEEEEEEEEEEEEEEEEEEAEEEEEEEEEEEEE<EEEEEEAEEE/EEEEEEE<EEAEEAEEEEEAEEAEE<EEAEE<E/AAAAAAE<AEAAAEEEEAEEAEAEE/EEAAAEE
+@ERR5069949.885966 NS500628:121:HK3MMAFX2:4:11610:19682:20132/2
+CTTAGGTCTTAGGATTGGCTGTATCAACCTTAAGCTTAAGTACACAATTTTGCATAGAATGTCCAATAA
++
+A//AA6EEAEEEEE6EEE/EEA/EA///AAE/EAEEEAE6AE/E/E/EEAAE/EAA/E/E/<EA//E/6
+@ERR5069949.2342766 NS500628:121:HK3MMAFX2:4:21501:7762:9816/2
+TCATAGATGTCAACTCAAAGCCATGTGCCCATAAGACAAATACGACTCTGTCAGAGAGATTTTTAAGTGTGTCACTTAACATTTGTACAATCTTTATACGCACTACATTCCAAGGAAGTCCTTTGTACATAAGTGGTATGAGGTGTTTAA
++
+AAAAAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAEEEEEEEEEEEEEEEAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAEEEEEEEEAAAEEEEEEEEEEEAEEEEEAEEEAAAA<<AEEEEAEAEAE
+@ERR5069949.3122970 NS500628:121:HK3MMAFX2:2:21304:20157:2460/2
+ATCAAGGACCTGCCTAAAGAAATCACTGTTGCTACATCACGAACGCTTTCTTATTACAAATTGGGAGCTTCGCAGCGTGTAGCAGGTGACTCAGGTTTTGCTGCATACAGTCGCTACAGGATTGGC
++
+AAAAAEE6EEEEEEEAEEEEEEEEEEEAEEEEEEEEEEEEEE/EEEEEAE<EEAEAEEEEEEEEEAAEEEEAEAEEE/AEEE<A<A/AAAAAE/E<A66AEEEEEEEEEEEAE<</6AA<A/6/EA
+@ERR5069949.3279513 NS500628:121:HK3MMAFX2:1:21110:4328:5711/2
+TCTTTGTTAGCACCATAGGGAAGTCCAGATTCTGGCCCAGGTCCTAGGTAGTATAAATACCATCTTTG
++
+AAAA/AEEEEEE/EEAEEEEE/EEEEAE/EEEEAA/<EAE6EA//AEEA/A/</EE6<E//EE//E/E
+@ERR5069949.309410 NS500628:121:HK3MMAFX2:1:11107:4644:2079/2
+TTAGTAGCCGTATTTAAGGCTCCTGCAACACCTCCTCCATGTTTAAGGTAAACATTGGCTGCATTAACAACCACTGTTGGTTTTACCTTTTTAGCTTCTTCCACAATGTCTGCATTTTTAATGTATACATTGTCAGTAAGTTTTAAATAA
++
+AAA/AEE/E/EE66E//EEEEEEEE/AE///EEEEEAEEEE/AAE/EEAAEE/EE/</<E//EE</EAEE6EEE/E</EEEEEEAEE/EEAEEEEEEAEEE<EAAEE/EA//<A</E/6</A/<AEAAAAEAAAA/EAAE<<AEAEE//E
+@ERR5069949.532979 NS500628:121:HK3MMAFX2:2:21104:15575:19089/2
+TGTTTATAGTGACCACACTGGTAATTACCAGTGTACTCACTAGCACAAGTAAATGTACCATGCTTAAGTTCATACTGAGCAGGTGGTGCTGACATCATAACAAAAGGTGACTCCTGTTGTACTAGATATTTTGTAGCTTGTTTACCACACG
++
+AAAAAEEEEEEEEEEEEEEEEAEEEEAEEEEEEE/EEE6EAEEE/EEEEEEEEEEEAEE/EEEEEEEEEEE/EAEEEEEE/EEEEEEEE<EA<AEA/EE/EEEAEEA<EEEE</<AAAEA/EEAEA<AEAEEEE<AE<AE/AA/E</E/EA
+@ERR5069949.2888794 NS500628:121:HK3MMAFX2:3:11604:17798:16811/2
+TCCCTGCACAAGAAAAGAACTTCACAACTGCTCCTGCCATTTGTCATGATGGAAAAGCACACTTTCCTCGTGAAGGTGTCTTTGTTTCAAATGGCACACACTGGTTTGTAACACAAAGGAATTTTTATGAACCACAAATCATTACTACAG
++
+AAAAAEEEEEEEEEEEEE/EEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEE<EEEEEEEEEEEEEAEE<<<6AEE</AAAEEEEEEEAA<EEAAEA
+@ERR5069949.2205229 NS500628:121:HK3MMAFX2:1:11212:26331:4199/2
+CGTGTAAGGAATTCTCTTACCACGCCTATTTGTGGCCTGTTAATTGCAGATGAAACATCATGCGTGATAACACCCTTATAAAACATTTTAAAGCATTGAGCTGATTTGTCTTTATGTGCTTAAGCTTATTATCATAAACCAAAGCACTC
++
+AAAAAEEEEAEEEEEEEAEEA/EEEEEEEEEE<EEEEEEA/EEEEEEE/EEEAEEEAEEEEEEEEAEEE/E/E/EAEEEAEEEEEEEEEEE/EEE/E<EEEAEE<<E<//<AAEEE<AEEAEEEAAAA/AEAEEAEE/EEE/EE<<A<A
+@ERR5069949.786562 NS500628:121:HK3MMAFX2:2:11109:4461:9003/2
+GCATTTCTTACCTAGAGTTTTTAGTGCAGTTGGTAACATCTGTTACACACCATCAAAACTTATAGAGTACACTGACTTTGCAACATCAGCTTGTGTTTTGGCTGCTGAATGTACAATTTTTAAAGATGCTTCTGGTAAGCCAGTACCATA
++
+AAAAAEEEEEEEEAEEEAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEE/EEEEEEEEEEAEEEEEEEEEEEEEEEAEEEEEEE<EEAEEEEE<EEEEEEEEEAEEEAEEEAEEAA6A<EEEEAAEEEEAA/AEEEEEE/EEEEEEE
+@ERR5069949.919671 NS500628:121:HK3MMAFX2:4:21608:23884:15511/2
+CCTTAATGGTTCATGTGGTAGTGTTGGTTTTAACATAGATTATGACTGTGTCTCTTTTTGTTACATGCACCATATGGAATTACCAACTGGAGTTCATGCTGGCACAGACTTAGAAGGTAACTTTTATGGACCTTTTGTTGACAGGCAAAC
++
+AAAAAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAAE/EEEEEEAEEEEEEEEAEEEEEEEEEEEAEEEEEEEAEEEEAEEEEAEEEEE6EEEEEEEAAEAEEEEEEE<EEEEEEE6AAEEAEEEAA6AEEAAAAAEEAAEEEAEAEEE
+@ERR5069949.1328186 NS500628:121:HK3MMAFX2:3:21510:25432:14327/2
+GTACTATCTATACAGAACTGGAACCACCTTGTAGGTTTGTTACAGACACACCTAAAGGTCCTAAAGTGAAGTATTTATACTTTATTAAAGGATTAAACAACCTAAATAGAGGTATGGTACTTGGTAGTTTAGCTGCCACAGTACGTCTACA
++
+AAAAAEEEEEEE/EEAEEEEAEEEEEAEEEEEEEEAEEEEEEEEEEEEEAE/EEEEEEAEE/EEEEEEEEEEEEEEEEEAAAEA/EEEEEEEAAEEEEE/EEEEAEEEEEAAEEEE/AAAE<A<EEEE6AEEAAA<<<<AA<AE/EEAEEA
+@ERR5069949.870926 NS500628:121:HK3MMAFX2:4:11510:4100:9432/2
+AGCTAACACTGAAAAAGTCTGTCCTGGTTGAATGCGAACAAACTTATACTTAGGTGTCTTAGGATTGGCTGTATCAACCTTAAGCTTAAGTACACAATTTTGCATAGAATGTCCAATAACCCTGAGTTGAACATTACCAGCCTGTACCAAG
++
+AAAA6/EEEE6EEEEEEEEEEEE/EEEEEEEE/A/E/EEEEEEEEEEAEEEAEEEEEEE/AAE/AE<AE/<AEEE//AEEEEEEE<EEEE<<E<EEAEEE/E/<EEE/</</</<AAE/EA<AAAAEEEE/EE/</6AE/6<////EAAAA
+@ERR5069949.2257580 NS500628:121:HK3MMAFX2:3:11512:13762:8305/2
+TCTATAGGTCATGTCCTTAGGTATGCCAGGTATGTCAACACATAAACCTTCAGTTTTGAATTTAGTGTCAACACTGAGGTGTGTAGGTGCCTGTGTAGGATGTAACCCAGTGATTACCTTACTACAATCTTTAAAGAGTCCTGTTACATT
++
+AAAAAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAEEEEEEEEEEEEEEEEEEEAEEEAEAEEEEAEEEEEEAAAAEEEEAAEEAEEEEEE
+@ERR5069949.3249622 NS500628:121:HK3MMAFX2:2:21101:6979:17698/2
+ATCATGACGTTCGTGTTGTTTTAGATTTCATCGAAACGAACAAACAAAAATGTCTGATAATGGACCCCAAAATCATCGAAATGCACCCCGCATTACGGTTGGTGGACCCTCCGATT
++
+AAA/AE//EEE/EE6AE/A</EE//6AE6EE//EE/AE//A/EE//EEEE<EAA/EE//<E/A/E/EE//E/A/E/E//EE/<A/A<EE/A//</EE//E/E//A/EEE///A//6
+@ERR5069949.611123 NS500628:121:HK3MMAFX2:4:21402:10868:14846/2
+ATTATACTTAAACCAGCAAATAATAGTTTAAAAATTACAGAAGAGGTTGGCCACACAGATCTAATGGCTGCTTATGTAGACAATTCTAGTCTTACTATTAAGAAACCTAATGAATTATCTAGAGT
++
+AAAAAEEEEEA6EEEEEEEEEEEEAEEEEEEEEEEEEEEEEEEEEEEEEEEE<EEEEEEEEEEEEEEEEEE<EEEEEEEAEEEEEEEEEEEEAEEEEEEEEEEE/EEEEEEEA/AAEAAEAAEAE
+@ERR5069949.651338 NS500628:121:HK3MMAFX2:2:11307:9572:4021/2
+ATTCTGTGCTGGTAGTACATTTATTAGTGATGAAGATGCGAGAGACTTGTCACTACAGTTTAAAAGACCAATAAATCCTACTGACCAGTCTTCTTACATCGTTGATAGTGTTACAGTGAAGAATGGTTCCATCCATCTTTACTTTGATA
++
+AAAAAE/EAEEE/AEAEEE/EEEAAEEEEAEEEEE/EEEEAEEEEEEAEE/EEEE/EEE</EE/AEAE/<E/EEAEE<EEEE//AEEEEEE<EEAEE/EEE//E/<EE<A<A/EAA<AA/AEEA//A<A/A<A<6A6/AEE/AEEA<AE
+@ERR5069949.169513 NS500628:121:HK3MMAFX2:2:21303:6012:2171/2
+CATTTGGTGACGCAACTGGATAGACAGATCGAATTCTACCCATAAAGCCATCAAGCTTTTTCTTTTCAACCCTTGGTTGAATAGTCTTGATT
++
+AAAAAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAEE/EEEEEEEEEEEEEEEEEEEEEEE
+@ERR5069949.155944 NS500628:121:HK3MMAFX2:2:21111:24075:19469/2
+GTACACGGAACGTTCTGAAAAGAGCTATGAATTGCAGACACCTTTTGAAATTAAATTGGCAAAGAAATTTGACACCTTCAATGGGGAATGTCCAAATTTTGTATTTCCCTTAAATTCCATAATCAAGACTATTCAACCAAGGGTTGAAAA
++
+AAAA/EEEEEEAEEEEEEEEEEEE/EEEEEEEEEE/EAEEEEEEEEEEEEEEEAEEEAEE/AEEEEEEAAEEEEEEAEAEEEE/AEE/<EAE/E<EEA<<<AAEEAEEE<AA<EE/EAAEEEE<<<EEEA/AEAEE6</EEA<AEEE<<E
+@ERR5069949.2033605 NS500628:121:HK3MMAFX2:4:21508:23814:9228/2
+GTACTGGTAAGAGTCATTTTGCTATTGGCCTAGCTCTCTACTACCCTTCTGCTCGCATAGTGTATACAGCTTGCTCTCATGCCGCTGTTGATGCACTATGTGAGAAGGCATTAAAATATTTGCCTATAGATAAATGTAGTAGAATTATA
++
+AAAAAEAEEEEEEEEEEEEAEEEEEEEEEEEEE<EEEEEEEEEEE<EEEEEEEEAAEAEEEEEEEEEEEE/EAAEEEA/EEEEEEAE<EEEEEEEEE<AEEEEAAAEAE<EAEEEEEE//</A/AEAAAEA/<E<AEEEAEE<EEEEEE
+@ERR5069949.2730382 NS500628:121:HK3MMAFX2:4:21605:26351:3903/2
+ACTCATATGAGTGTGACATACCCATTGGTGCAGGTATATGCGCTAGTTATCAGACTCAGACTAATTCTCCTCGGCGGGCACGTAGTGTAGCTAGTCAATCCATCATTGCCTACACTATGTCACTTGGTGCAGAAAATTCAGT
++
+AAAAAEEEEEEEEEEEEEEEEEEE/EEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAE<EE/EEEEEEE/EEAEEEEEEEEEEEEEEEEEEAEEEEA<AEA<<EA<A<AEEEEEA<EAE<66A/AEEEEEEEAE<AAEA
+@ERR5069949.2125592 NS500628:121:HK3MMAFX2:1:11307:14726:9430/2
+TGTACACATAGTGCTTAGCACGTAATCTGGCATTGACAACACTCAAATCATAATTTGTGGCCATTGAAATTTCATCAAAGACAACTATATCTGCTGTCGTCTCAGGCAATGCATTTACAGTACAAAAGACATACTG
++
+AAAAAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAAEEEEEEEEEEEEEEAEEEEEEEEEEEEEEEEEEEEEEEEEEAEE/EEE<EEEEEEEEEEEE//E<EE//A/<//6AA//</</</<EE//E//<//A
+@ERR5069949.1062611 NS500628:121:HK3MMAFX2:1:11304:13814:5808/2
+TGGTAATGCTTTAGATCAAGCCATTTCCATGTGGGCTCTTATAATCTCTGTTACTTCTAACTACTCAGGTGTAGTTACAACTGTCATGTTTTTGGCCAGAGGTATTGTTTTTATGTGTGTTGAGTATTGCCCTATTTTCTTCATAACTGGT
++
+AAAAAAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAAAAAEEE<AAEEEEEEEEAAEEAAA6AEEEEEEEEEEEEEEEEEA
+@ERR5069949.1778133 NS500628:121:HK3MMAFX2:1:11203:21125:7007/2
+TGCCACAACTGCTTATGCTAATAGTGTTTTTAACATTTGTCAAGCTGTCACGGCCAATGTTAATGCACTTTTATCTACTGATGGTAACAAAATTGCCGATAAGTATGTCCGCAATTTACAACACAGACTTTATGAGTGTCTCTATAGAAA
++
+AAAAAEEEEEEEEEEEEEEAEEAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAEEEEEEEEEEAAEEEEEE<AEEEEEEE/AAAE<AAEEAAEEEA<EAAEEEA<AAEEEEEE/EEAAAEE/EAAAAEEEEEAEAEE
+@ERR5069949.3057020 NS500628:121:HK3MMAFX2:2:21204:6342:14557/2
+GCGTACAACCAAGCTAAAGTTACTGGCCATAACAGCCAGAGGAAAATTAACTTAATTATATACAAAAACCTATTCCTGTTGGCATAGGCAAATTG
++
+AAAAAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEE
+@ERR5069949.2972968 NS500628:121:HK3MMAFX2:4:21405:4877:14897/2
+CTTTGAAGCAAGGTGAAATCAAGGATGCTACTCCTTCAGATTTTCTTCGCGCTACTGCAACGATACCGATACAAGCCTCACTCCCTTACGGATGGCTTATTGTAGGCGTTGCACTTCTAGCTGTTTTTCAGAGCGCTTCCAAAAACA
++
+AAAAAEEEEEEA/E/EEEEEEE/EEEEEEEAEEEEE/EEE/E/E/<66<6/EEEE///EEE<<E/<AEAEEEE/EEEEE6A/EEA/E//AE<EEE</6E/E/E/A<AAEA/A//AE<A/E<EE//6A/A<AAA6<E<<A66</E/AA
+@ERR5069949.2734474 NS500628:121:HK3MMAFX2:4:11507:10751:13427/2
+CCCATTGGTGCAGGTATATGCGCTAGTTATCAGACTCAGACTAATTCTCCTCGGCGGGCACGTAGTGTAGCTAGTCAATCCATCATTGCCTACACTATGTCACTTGGTGCAGAAAATTCAGTTGCTTACTCTAATAACTCTATTGCCA
++
+AAAA/EEEEEEEEE/E/EE6EEEEAEEEEEEAEEEEE/EEEEEEEEEEEAE/EAEE/EEEEEAE/EE<EAEEEEEEA/E<EEEEAE/EA<EEEEAEE/E/EE<EEEEE</EE/E//<<<AA6A<A<A/<AE/AE/EEEA6<A6A/</A
+@ERR5069949.856527 NS500628:121:HK3MMAFX2:2:11301:22893:2784/2
+ATACTTAGGTGTCTTAGGATTGGCTGTATCAACCTTAAGCTTAAGTACACAATTTTGCATAGAATGTCCAATAACACTTAGTTGAACATTACCAGCCTGTACCAAGAAATTATGATTAGACTTACGAATGAGTAATCTTCATAATTAGGGT
++
+AAAAAAAE/EEEEAEEEEEEEEAEEEEEE<E/<<EEEEEEAEEAAAEEEAE</EA<<EE/EAEEE6E//EE/EEE/6A/EEEEEEEEEAE<E/E<AAA/EEEEA/A<EEEEE<6EE<A/A<A<</6A<A<E<EEEE/AE//<6A/A6///A
+@ERR5069949.2098070 NS500628:121:HK3MMAFX2:3:11406:20552:1667/2
+CATAGTGCTTAGCACGTAATCTGGCATTGACAACACTCAAATCATAATTTGTGGCCATTGAAATTTCATCAAAGACAACTATATCTGCTGTCGTCTCAGGCAATGCATTTACAGTACAAAAGACATACTGTTCTAATGTTGAATTCACT
++
+AAAAA/EEEEEEEEEEEEEEEEEEEEE/EEEEEEEAAEEEEAAEEEEA/E/E<<EEEEEEAEEEE<AE/AEEEEAA<EEEE/EE6A<AEAEEAEA/<E/AEEA/AAA6A/E<A/AEAAEEE/EE/AE<<//EAAEE6/</6EEE6/A6A
+@ERR5069949.1552198 NS500628:121:HK3MMAFX2:1:11108:11797:17621/2
+GGTCAAGGTTAATATAGGCATTAACAATGAATAATAAGAATCTACAACAGGAACTCCACTACCTGGCGTGGTTTGTATGAAATCACCGAAATCATACCAGTTACCATTGAGATCTTGATTATCTAATGTCAGTACACCAACAATACCAGCA
++
+AAAAAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEE/EEEA<AA/<EE//AEA/EEE</E/AEA/EE/EEAEEEEE/</EEA<AE/E/E<EAAA6AA<///<A/AAAEA<EAA/EA
+@ERR5069949.2385514 NS500628:121:HK3MMAFX2:3:21611:13560:16508/2
+GTGCATTACCATGGACTTGACAATACAGATCATGGTTGCTTTGTAGGTTACCTGTAAAACCCCATTGTTGAACATCAATCATAAACGGATTATAGACGTAATCAAATCCAATAGAATGATGCCAACAGGCATAAGTGTCTGAAGCAGTGG
++
+A/AAAEEEEEEEEEEEEEEEEEEEEEEE6EEEEEEEEEEEEEEEEAEEEEEEEAEEEEEEEEEAAEEEEAAEEEEEEEEEEAAEEEEAEAE/EEEEEAAEEEEAEEEEAEEEAEAEAEEEAA<<EEAAEEAA/EEAAEE<AA<EAAE<AA
+@ERR5069949.2270078 NS500628:121:HK3MMAFX2:4:21510:16801:19554/2
+CTTTATGACAAGTTGCAATTTACAAGTCTTGAAATTCCACGTAGGAATGTGGCAACTTTACAAGCTGAAAATGTAACAGGACTCTTTAAAGATTGTAGTAAGGTAATCACTGGGTTACATCCTACACAGGCACCTACACACCTCAGTGTTG
++
+AAAAAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEE<EEEEAEEEEEEEEEEEAEEAAEEEEAEEEEEAEEAEEEAAEAEEEEEAEAEEAEA<EAA
+@ERR5069949.114870 NS500628:121:HK3MMAFX2:4:11410:23953:14505/2
+GCATGAAGCTTTACCAGCACGTGCTAGAAGGTCTTTAATGCACTCAAGAGGGTAGCCATCAGGGCCACAGAAGTTGTTATCGACATAGCGAGTGTATGCCCCTCCGTTAAGCTCACGCATGAGTTCACGGGTAACACCACTGCTATGTTT
++
+AAAAAAEEEEEEEAEAEE/EEEEEEEEEEEEEEEEAEEEAAEEEEEEAAEAAEAEEEEEEEAEE<EEEEEEEEAE/EEEEAEAEEAEE/A/AEEEE<A<E/EEEA<AEE<EEAA<E/A<EA<EA/<<<<<<<<AA/E/EAAA<<<AAEEA
+@ERR5069949.2668880 NS500628:121:HK3MMAFX2:1:21104:5191:15623/2
+CTGTGGATCACGGACAGCATCAGTAGTGTCAGCAATGTCTCTGCCAAATTGTTGGAAAGGCAGAAACTTTTTGTTAGACTCAGTAAGAACACCTGTGCCTGTTAAACCATTGAAGTTGAAATTGACACATTTGTTTTTAACCAAATTAGT
++
+AAAAAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAEAEEEEEEEEEAEEAEEEEEEEEEEEEAEEEEEAEEEEEEEAEEEAAE<EEEEEE6A<AEEEEEEAEAEAE/EA
+@ERR5069949.257821 NS500628:121:HK3MMAFX2:2:21307:14790:19018/2
+GCCTATACAGTTGAACTCGGTACAGAAGTAAATGAGTTCGCCTGTGTTGTGGCAGATGCTGTCATAAAAACTTTGCAACCAGTATCTGAATTACTTACACCACTGGGCATTGATTTAGATGAGTGGAGTATGGCTACATA
++
+AAAAAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAAEEEEEEEEEEEEEEEAEEEEEE
+@ERR5069949.2243023 NS500628:121:HK3MMAFX2:2:21301:7521:3094/2
+TGGTAAGAGAATTCCTTACACGTAACCCTGCTTGGAGAAAAGCTGTCTTTATTTCACCTTATAATTCACAGAATGCTGTAGCCTCAAAGATTTTGGGACTACCAACTCAAACTGTTGATTCATCACAGGGCTCAGAATATGACTATGTCAT
++
+AAAAAEEEEEEEEEEEEEEEEEEE6EEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAEEEEEEEEAEEEEEEEEEEEEEE/EEEEAAEEAEEA<EEEEEEEEEEEEEEAEEEEE<<AA6AAEEEAEE
+@ERR5069949.2605155 NS500628:121:HK3MMAFX2:1:21311:18812:15592/2
+CCAAAAATCCAGCCTCTTATTATGTTAGACTTCTCAGTGGAAGCAAAATAAACACCATCATTAAATGGTAGGACAGGGTTATCAAACCTCTTAGTACCATTGGTCCCAGAGACATGTATAGCATGGAACCAAGTAACATTGGAAAAGAAA
++
+AAAAAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAEEEEEEEEEEEEEEEEEEEEEEAEEEEEAEEAEEEEEEAEAEAEEE/EEAEEEEEEAEEEAAAEEEAEEAEEEEEAEAEE/EEEE/A
+@ERR5069949.1340552 NS500628:121:HK3MMAFX2:2:11309:7320:9079/2
+GGTAATGCAACAGAAGTGCCTGCCAATTCAACTGTATTATCTTTCTGTGCTTTTGCTGTAGATGCTGCTAAAGCTTACAAAGATTATCTAGCTAGTGGGGGACAACCAATCACTAATTGTGTTAAGATGTTGTGTACACACACTGGTA
++
+AAAAAEEEEEEEEEEEEEEEEEEEEEEEEE/EEEEEEEEEEEEEEEEEEAEEEEEEEEEAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAEEAEEEEEEEAEAEEEEEEEEEE<EEEEEEEEEEEEEEAAA<AEEEEEEEEEEEEEE
+@ERR5069949.1561137 NS500628:121:HK3MMAFX2:2:11303:23159:8428/2
+GTTAAAAACAGTACAATTCTGTGATGCCATGCGAAATGCTGGTATTGTTGGTGTACTGACATTAGATAATCAAGATCTCAATGGTAACTGGTATGATTTCGGTGATTTCATACAAACCACGCCAGGTAGTGGAGTTCCTGTTGTAGATT
++
+AAAAAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAAEEEEEEEEEEEEEEEE<EAEEEAEEEEEEEEEEEEEEEAEEEEEEEEEEEEEEEEEEEEE<EEEEAEEEE/EEEEAAAEEEA<AEEEAEEEEEAEAEEA/AA<A
+@ERR5069949.2361683 NS500628:121:HK3MMAFX2:2:21103:8659:7427/2
+ATAGACAACAGGTGCGCTCAGGTCCTATTTTCACAAAATACTTCATAGATGTCAACTCAAAGCCATGTGCCCATAAGACAAATACGACTCTGTCAGAGAGATTTTTAAGTGTGTCACTTAACATTTGTACAATCTTTATACGCACTAC
++
+AAAAAAEEAEE/EEAEEEEEE/AEEEEEEAE<EEEEEEEEEEE/E/<EEEE<EEE/EEAA/EA/E<E/<<6AE<EE/EEE6/EAE/EEEEA/EEEEEEAE/</E/AA/AAE6EEAE/A<E//AAAAEEEE<EEA</AAEEA/<AE6<A
+@ERR5069949.2521353 NS500628:121:HK3MMAFX2:3:11508:26680:5334/2
+GTCCACACCCAAATTATTGAGTATTTTCACCTCTGGTACTGGTTTAATGTTGCGCTTAGCCCAAAGCACAAAAGCTACATTAACAGGTAATGTTGTTTTATTTTCAAACAATTCTACATCAACACCATCAACTTTTGTGAAAACAGTGAT
++
+AAAAAEEEEEE/EEEE6EEEEEAE/EE<EEE<EEA/EEE/AAE/E//EEEE/A/AEEE/EAEEA/<//EEA//AEE/<EAEE6AA/<//AEE/AE<<//A/<AAA/EEEEEAE6<///A<</A<E/EEE<E//AEEA<A/EE/</<A//A
+@ERR5069949.1261808 NS500628:121:HK3MMAFX2:3:11601:6846:14627/2
+TTGTCATCAGTGCAAGCAGTTTGTGTAGTACCGGCAGCACAAGACATCTGTCGTAGTGCAACAGGACTAAGCTCATTATTCTGTAATTTGACAGCAGAATTGGCC
++
+AA//AEEEA6EAE/EAEE/EAEEEEEEEA//E/EE/EEEEEE/EAEE/A/AEEEEAEA//EEEE/E<EAE/E/EE////6E</EAEA<A/E<EE<</EEE/<//<
+@ERR5069949.2734873 NS500628:121:HK3MMAFX2:4:21611:11682:9300/2
+CATTGGTGCAGGTATATGCGCTAGTTATCAGACTCAGACTAATTCTCCTCGGCGGGCACGTAGTGTAGCTAGTCAATCCATCATTGCCTACACTATGT
++
+AAAAAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEE
+@ERR5069949.3017828 NS500628:121:HK3MMAFX2:1:21111:18284:17510/2
+ATTAACTATTAACGTACCTGTCTCTTCCGAAACGAATGAGTACATAAGTTCGTACTCATCAGCTTGTGCTTACAAAGGCACGCTAGTAGTCGTCGTCGGTTCATCA
++
+AAAAAEEEAEEEEEEEEEEEEEEEEEEEEEEEEEEEAEEEEEEEEEEAEE<EEEEEEEEEEEE<E/EE<EAEEEEEE<EAEEEEEEEEE/<E<EAEEAEEEAAE/A
+@ERR5069949.573706 NS500628:121:HK3MMAFX2:3:21407:23793:9689/2
+TTTCTGTACAAACAACACCATCCAATTTATAAGTAACTGGTTTTATGGTTGTTGTGTAACTGTTTTCTTTGTAGAAAACATCCGTAATAGGACCTTTGTATTCTGAGGACTTTGTAAGTAAAGCACCGTCTATGCAATACAAAGTTTCT
++
+AAAAAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAEEEEEEEEEEEEEEEEEEEEEAEEEEEEEEEEEEAEEEEEEAEAEAAAAEAEEEEEEA<EEE<<AAEEAEEEA<AEEEEEEEE<E<AA
+@ERR5069949.1980512 NS500628:121:HK3MMAFX2:1:21303:8321:13259/2
+GTAAAGTACAAATAGGAGAGTACACCTTTGAAAAAGGTGACTATGGTGATGCTGTTGTTTACCGAGGTACAACAACTTACAAATTAAATGTTGGTGATTATTTTGTGCTGACATCACATACAGTAATGCCATTAAGTGCACCTACACTAG
++
+AAAAAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAEEEEEEEEEEEEEEAEEEEEEEEEA<EEEEEEAEEEEAAAEEAAE<EEEAAAA<AA<EEEE/AE
+@ERR5069949.1014693 NS500628:121:HK3MMAFX2:1:11109:13494:20222/2
+ATCATACACAGTTCTTGCTGTCATAAGGATTAGTAACACTACAGCTGATGCATACATAACACAGTCTTTTAGCTTAAAACCAGACAAACTAGTATCAACCATATCCAACCATGTCATAATACGCATCACCCAACTAGCAGGCATATAGCC
++
+AAAAAEEEEAE/EEAEEEEEEEE/EEEEEEEEE/EEEEEEEEEEAAEEEAEAEAAEEEEEEAEEE<EEEEEAA<6EEEEEEEA<EEEAEAEA/EE/E/EEEEE/6AE/AAEAA<EEEAE///<AE<AA<A<6<EAEA<AA<<AAEEE</A
+@ERR5069949.3184655 NS500628:121:HK3MMAFX2:3:21606:7576:13093/2
+TTTATCTAAGTCACTAACTGAGAATAAATATTCTCAATTAGATGAAGAGCAACCAATGGAGATTGATTAAACGAACATGAAAATTATTCTTTTCTTGGCACTGATAACACTCGCTACTTGTGAGCTTTATCACTACCAAGAGTGTGTTAG
++
+AAAAAEEEEEEEEEEEEEEEEAEEAEEEEEEEEEEEEEEEEEEEEEEEEEE/EEEEEEEEEEEE<EEEEE/EEEEEAEAEEEEE/EEEAEEE<EEEEEE<EEAAEEAEEEEEAAAEEE/E<AAEEAAAE6A/A<<A<AAAEE/AA6AE/A
+@ERR5069949.29668 NS500628:121:HK3MMAFX2:2:21202:17958:8710/2
+TATAATTAATAACTAATTACTGTCGTTGACAGGACACGAGTAACTCGTCTATCTTCTGCAGGCTGCTTACGGTTTCTTCCGTGTTGCAGCCGATCATCAGCACATCTAGGTTTTGTCCGGGTGTGACCGAAAGGTAAGATGGAGAGCCTT
++
+AAA/E/EEEEEEEEEAEEEEEEEEE/</E/E/EE<E/EEAAEA/E/EE//EA/EEEEEA/AEEE/EEEEE/E/EA/EE/EEE<E/E///E<AEE<<EEE/<EEEAA///AE/6A///A/AE/EAEE</EAEAE///AA/EEAEE/AAEAA
+@ERR5069949.3258358 NS500628:121:HK3MMAFX2:3:21508:15641:1056/2
+ATACTGCGTCAAGGTTCACCGCACTCACTCAACATGCCAAGGAAGACATAAAA
++
+AAAAAA/A/////EE/EEE/A</EEEEEE/EAEEE//AEEEAEEEEA///6E6
+@ERR5069949.1476386 NS500628:121:HK3MMAFX2:2:21303:26270:9400/2
+GTATACGACATCAGTACTAGTGCCTGTGCCGCACGGTGTAAGACGGGCTGCACTTACACCGCAAACCCGTTTAAAAACGATTGTGCATCAGCTGACTGAAGCATGGGTTCGCGGAGTTGATCACAACTACAGCCATAACCTTTCCACA
++
+AA6AAEE6EEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAEEAEEAE//AAEEEEE/AEEEEEEEEEEEEEEEEEEEEE<<EEAAEEEEEEEEAEEE<EEE/EAE/EA6E/EEA/E/EEEAAA/AEA<AEEEAA
+@ERR5069949.2415814 NS500628:121:HK3MMAFX2:1:11107:11754:7444/2
+CAATAGTCCAGTCAACACGCTTAACAAAGCACTCGTGGACAGCTAGACACCTAGTCATGATTGCATCACAACTAGCTACATGTGCATTACCATGGACTTGACAATACAGATCATGGTTGCTTTGTAGGTTACCTGTAAAACCCCATTGTTG
++
+AAAAAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAEEEEEEEEEEAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAEEAAEAEAEEEEEEEEEEEEAEEEE/EEEEE<AEEEA

tests/data/index/E_coli/bwameth/genome.fa.bwameth.c2t.amb

@@ -0,0 +1,5 @@
+9372274 2 4
+20895 1 Y
+142347 1 R
+4707032 1 Y
+4828484 1 R

tests/data/index/E_coli/bwameth/genome.fa.bwameth.c2t.ann

@@ -0,0 +1,5 @@
+9372274 2 11
+0 rgi|170079663|ref|NC_010473.1| Escherichia coli str. K-12 substr. DH10B, complete genome
+0 4686137 2
+0 fgi|170079663|ref|NC_010473.1| Escherichia coli str. K-12 substr. DH10B, complete genome
+4686137 4686137 2

tests/data/paf/GCA_011545545.1_ASM1154554v1_cds_from_genomic.paf

@@ -0,0 +1,11 @@
+lcl|MT192765.1_cds_QIK50426.1_1	21291	1	21289	+	lcl|MT192765.1_cds_QIK50426.1_1	21291	1	21289	21288	21288	60	tp:A:P	cm:i:3984	s1:i:21288	s2:i:0	dv:f:0	rl:i:0
+lcl|MT192765.1_cds_QIK50427.1_2	3822	8	3821	+	lcl|MT192765.1_cds_QIK50427.1_2	3822	8	3821	3813	3813	60	tp:A:P	cm:i:722	s1:i:3813	s2:i:0	dv:f:0	rl:i:0
+lcl|MT192765.1_cds_QIK50428.1_3	828	4	819	+	lcl|MT192765.1_cds_QIK50428.1_3	828	4	819	815	815	60	tp:A:P	cm:i:148	s1:i:815	s2:i:0	dv:f:0	rl:i:0
+lcl|MT192765.1_cds_QIK50429.1_4	228	6	226	+	lcl|MT192765.1_cds_QIK50429.1_4	228	6	226	220	220	60	tp:A:P	cm:i:42	s1:i:220	s2:i:0	dv:f:0	rl:i:0
+lcl|MT192765.1_cds_QIK50430.1_5	669	6	663	+	lcl|MT192765.1_cds_QIK50430.1_5	669	6	663	657	657	60	tp:A:P	cm:i:115	s1:i:657	s2:i:0	dv:f:0	rl:i:0
+lcl|MT192765.1_cds_QIK50431.1_6	186	0	185	+	lcl|MT192765.1_cds_QIK50431.1_6	186	0	185	185	185	60	tp:A:P	cm:i:33	s1:i:185	s2:i:0	dv:f:0	rl:i:0
+lcl|MT192765.1_cds_QIK50432.1_7	366	1	358	+	lcl|MT192765.1_cds_QIK50432.1_7	366	1	358	357	357	60	tp:A:P	cm:i:64	s1:i:357	s2:i:0	dv:f:0	rl:i:0
+lcl|MT192765.1_cds_QIK50433.1_8	132	6	124	+	lcl|MT192765.1_cds_QIK50433.1_8	132	6	124	118	118	60	tp:A:P	cm:i:20	s1:i:118	s2:i:0	dv:f:0	rl:i:0
+lcl|MT192765.1_cds_QIK50434.1_9	366	6	357	+	lcl|MT192765.1_cds_QIK50434.1_9	366	6	357	351	351	60	tp:A:P	cm:i:68	s1:i:351	s2:i:0	dv:f:0	rl:i:0
+lcl|MT192765.1_cds_QIK50435.1_10	1260	4	1255	+	lcl|MT192765.1_cds_QIK50435.1_10	1260	4	1255	1251	1251	60	tp:A:P	cm:i:231	s1:i:1251	s2:i:0	dv:f:0	rl:i:0
+lcl|MT192765.1_cds_QIK50436.1_11	117	0	116	+	lcl|MT192765.1_cds_QIK50436.1_11	117	0	116	116	116	60	tp:A:P	cm:i:19	s1:i:116	s2:i:0	dv:f:0	rl:i:0

tests/software/TOOL/SUBTOOL/test.yml

@@ -5,4 +5,4 @@
     - tool_subtool
   files:
     - path: output/tool/test.bam
-      md5sum: a41bfadacd2eeef1d31e05c135cc4f4e
+      md5sum: e667c7caad0bc4b7ac383fd023c654fc

tests/software/bcftools/mpileup/main.nf

@@ -0,0 +1,17 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { BCFTOOLS_MPILEUP } from '../../../../software/bcftools/mpileup/main.nf' addParams( options: ['args2': '--no-version --ploidy 1 --multiallelic-caller',
+                                                                                                       'args3': '--no-version' ] )
+
+workflow test_bcftools_mpileup {
+
+    def input = []
+    input = [ [ id:'test' ], // meta map
+              [ file("${launchDir}/tests/data/bam/test-sc2-artic-v3.bam", checkIfExists: true) ]]
+    fasta = [ file("${launchDir}/tests/data/fasta/sarscov2/MN908947.3.fa", checkIfExists: true) ]
+
+    BCFTOOLS_MPILEUP ( input, fasta )
+
+}

tests/software/bcftools/mpileup/test.yml

@@ -0,0 +1,13 @@
+- name: bcftools mpileup
+  command: nextflow run ./tests/software/bcftools/mpileup -entry test_bcftools_mpileup -c tests/config/nextflow.config
+  tags:
+    - bcftools
+    - bcftools_mpileup
+  files:
+    - path: output/bcftools/test.vcf.gz
+      md5sum: f25141161cb935ef7719cfb41563ffb0
+    - path: output/bcftools/test.vcf.gz.tbi
+      md5sum: 4423be9f13fa07e5eadb13b1cbe8baf7
+    - path: output/bcftools/test.bcftools_stats.txt
+      md5sum: b8d6b6927f7bf024acf11ba438b54fa0
+

tests/software/bismark/deduplicate/main.nf

@@ -0,0 +1,14 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { BISMARK_DEDUPLICATE } from '../../../../software/bismark/deduplicate/main.nf' addParams( options: [:] )
+
+workflow test_bismark_deduplicate {
+
+    def input = []
+    input = [ [ id:'test', single_end:false ], // meta map
+              [ file("${launchDir}/tests/data/bismark/Ecoli_10K_methylated_R1_bismark_bt2_pe.bam", checkIfExists: true) ] ]
+
+    BISMARK_DEDUPLICATE ( input )
+}

tests/software/bismark/deduplicate/test.yml

@@ -0,0 +1,10 @@
+- name: Run bismark deduplicate test workflow
+  command: nextflow run ./tests/software/bismark/deduplicate -entry test_bismark_deduplicate -c tests/config/nextflow.config
+  tags:
+    - bismark
+    - bismark_deduplicate
+  files:
+    - path: output/bismark/Ecoli_10K_methylated_R1_bismark_bt2_pe.deduplicated.bam
+      md5sum: 35794f413740d9097010e8411f03b785
+    - path: output/bismark/Ecoli_10K_methylated_R1_bismark_bt2_pe.deduplication_report.txt
+      md5sum: 125b01ad4f1784a77b7802667d4bfee7

tests/software/bismark/genome_preparation/main.nf

@@ -0,0 +1,10 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { BISMARK_GENOME_PREPARATION } from '../../../../software/bismark/genome_preparation/main.nf' addParams( options: [:] )
+
+workflow test_bismark_genome_preparation {
+
+    BISMARK_GENOME_PREPARATION ( file("${launchDir}/tests/data/fasta/E_coli/NC_010473.fa", checkIfExists: true) )
+}

tests/software/bismark/genome_preparation/test.yml

@@ -0,0 +1,36 @@
+- name: Run bismark_genome_preparation test workflow
+  command: nextflow run ./tests/software/bismark/genome_preparation -entry test_bismark_genome_preparation -c tests/config/nextflow.config
+  tags:
+    - bismark
+    - bismark_genome_preparation
+  files:
+    - path: output/bismark/BismarkIndex/NC_010473.fa
+      md5sum: ad277e6b3da5dcf9fccfcd3a55fcec8e
+    - path: output/bismark/BismarkIndex/Bisulfite_Genome/CT_conversion/genome_mfa.CT_conversion.fa
+      md5sum: f878bc2c1d6d1404157ebf931e971f02
+    - path: output/bismark/BismarkIndex/Bisulfite_Genome/CT_conversion/BS_CT.1.bt2
+      md5sum: d865be3bfe02a3d5e277128fe7902b47
+    - path: output/bismark/BismarkIndex/Bisulfite_Genome/CT_conversion/BS_CT.2.bt2
+      md5sum: 486dfea5dde17f126cf498ead0e91421
+    - path: output/bismark/BismarkIndex/Bisulfite_Genome/CT_conversion/BS_CT.3.bt2
+      md5sum: cd201e81724f3099131aec16ef2cc53b
+    - path: output/bismark/BismarkIndex/Bisulfite_Genome/CT_conversion/BS_CT.4.bt2
+      md5sum: 4c81a7364a80bf3151a5464108593497
+    - path: output/bismark/BismarkIndex/Bisulfite_Genome/GA_conversion/genome_mfa.GA_conversion.fa
+      md5sum: 8cb16ceaf0543061151d8c1b7d1f85b4
+    - path: output/bismark/BismarkIndex/Bisulfite_Genome/GA_conversion/BS_GA.1.bt2
+      md5sum: fe77e5d17a7aa30c3a788bb90b396842
+    - path: output/bismark/BismarkIndex/Bisulfite_Genome/GA_conversion/BS_GA.2.bt2
+      md5sum: 3c6e4a48ad05f8af5f4015db7571d253
+    - path: output/bismark/BismarkIndex/Bisulfite_Genome/GA_conversion/BS_GA.3.bt2
+      md5sum: cd201e81724f3099131aec16ef2cc53b
+    - path: output/bismark/BismarkIndex/Bisulfite_Genome/GA_conversion/BS_GA.4.bt2
+      md5sum: f651bcfb9713f6ee1ce648b7c244b50e
+    - path: output/bismark/BismarkIndex/Bisulfite_Genome/CT_conversion/BS_CT.rev.1.bt2
+      md5sum: 2261afbed214da6f59f1bf648c20fb6b
+    - path: output/bismark/BismarkIndex/Bisulfite_Genome/CT_conversion/BS_CT.rev.2.bt2
+      md5sum: 622991847ea56f3c4f8583bb23ceee7a
+    - path: output/bismark/BismarkIndex/Bisulfite_Genome/GA_conversion/BS_GA.rev.1.bt2
+      md5sum: 32220350073a71a9cd69677f3aa4e577
+    - path: output/bismark/BismarkIndex/Bisulfite_Genome/GA_conversion/BS_GA.rev.2.bt2
+      md5sum: f7467830c4f33497c54c9e7e502a5def

tests/software/bwa/mem/test.yml

@@ -6,7 +6,7 @@
     - bwa_mem_single_end
   files:
     - path: output/bwa/test.bam
-      md5sum: 52e81e5bd523d0b27fe533b21a0d80f5
+      md5sum: 2bea94a4458cd1216214874b11c2e394
 
 - name: bwa mem paired-end
   command: nextflow run ./tests/software/bwa/mem -entry test_bwa_mem_paired_end -c tests/config/nextflow.config
@@ -16,4 +16,4 @@
     - bwa_mem_paired_end
   files:
     - path: output/bwa/test.bam
-      md5sum: 86d82fdb68ed384c656cfc62a253052f
+      md5sum: 2d952be81c7d2856712391b5d8556039

tests/software/bwamem2/mem/test.yml

@@ -6,7 +6,7 @@
     - bwamem2_mem_single_end
   files:
     - path: output/bwamem2/test.bam
-      md5sum: 354acd3b7033a2d4ee69452df18c0a4d
+      md5sum: b8fceee111b3e23372c95ed765ac4401
 
 - name: bwamem2 mem paired-end
   command: nextflow run ./tests/software/bwamem2/mem -entry test_bwamem2_mem_paired_end -c tests/config/nextflow.config
@@ -16,4 +16,4 @@
     - bwamem2_mem_paired_end
   files:
     - path: output/bwamem2/test.bam
-      md5sum: 26187528a7bde13a2a9e9dd549b9bcd0
+      md5sum: 4b05c7e1b28e0835c647e890854897e4

tests/software/bwameth/align/main.nf

@@ -0,0 +1,37 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { BWAMETH_ALIGN as BWAMETH_ALIGN_SE } from '../../../../software/bwameth/align/main.nf' addParams( options: [ publish_dir:'test_single_end' ] )
+include { BWAMETH_ALIGN as BWAMETH_ALIGN_PE } from '../../../../software/bwameth/align/main.nf' addParams( options: [ publish_dir:'test_paired_end' ] )
+
+/*
+ * Test with single-end data
+ */
+workflow test_bwameth_align_single_end {
+
+    def input = []
+    input = [ [ id:'test', single_end:true ], // meta map
+              [ file("${launchDir}/tests/data/fastq/methylated_dna/Ecoli_10K_methylated_R1.fastq.gz", checkIfExists: true) ] ]
+
+    BWAMETH_ALIGN_SE (
+        input,
+        file("${launchDir}/tests/data/index/E_coli/bwameth", checkIfExists: true)
+    )
+}
+
+/*
+ * Test with paired-end data
+ */
+workflow test_bwameth_align_paired_end {
+
+    def input = []
+    input = [ [ id:'test', single_end:false ], // meta map
+              [ file("${launchDir}/tests/data/fastq/methylated_dna/Ecoli_10K_methylated_R1.fastq.gz", checkIfExists: true),
+                file("${launchDir}/tests/data/fastq/methylated_dna/Ecoli_10K_methylated_R2.fastq.gz", checkIfExists: true) ] ]
+
+    BWAMETH_ALIGN_PE (
+        input,
+        file("${launchDir}/tests/data/index/E_coli/bwameth", checkIfExists: true)
+    )
+}

tests/software/bwameth/align/test.yml

@@ -0,0 +1,17 @@
+- name: Run bwameth single-end test workflow
+  command: nextflow run ./tests/software/bwameth/align -entry test_bwameth_align_single_end -c tests/config/nextflow.config
+  tags:
+    - bwameth
+    - bwameth_align
+  files:
+    - path: output/test_single_end/test.bam
+      md5sum: 48dde56f7b74de3a3e0b1914c45150de
+
+- name: Run bwameth paired-end test workflow
+  command: nextflow run ./tests/software/bwameth/align -entry test_bwameth_align_paired_end -c tests/config/nextflow.config
+  tags:
+    - bwameth
+    - bwameth_align
+  files:
+    - path: output/test_paired_end/test.bam
+      md5sum: b473343b32b7cfc677bfad1ab0e6bb5a

tests/software/bwameth/index/main.nf

@@ -0,0 +1,10 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { BWAMETH_INDEX } from '../../../../software/bwameth/index/main.nf' addParams( options: [:] )
+
+workflow test_bwameth_index {
+
+    BWAMETH_INDEX ( file("${launchDir}/tests/data/fasta/E_coli/NC_010473.fa", checkIfExists: true) )
+}

tests/software/bwameth/index/test.yml

@@ -0,0 +1,18 @@
+- name: Run bwameth index test workflow
+  command: nextflow run ./tests/software/bwameth/index -entry test_bwameth_index -c tests/config/nextflow.config
+  tags:
+    - bwameth
+    - bwameth_index
+  files:
+    - path: ./output/bwameth/bwameth/NC_010473.fa.bwameth.c2t.pac
+      md5sum: 7586c6a3be45c4dea15376a5c7bb9bf0
+    - path: ./output/bwameth/bwameth/NC_010473.fa.bwameth.c2t.amb
+      md5sum: 87e019665cbb66bdee2bacccb26845c9
+    - path: ./output/bwameth/bwameth/NC_010473.fa.bwameth.c2t.ann
+      md5sum: a4659a63572b6998c67457bd8e95790d
+    - path: ./output/bwameth/bwameth/NC_010473.fa.bwameth.c2t.bwt
+      md5sum: 582854008bcbe99d5b51290773a7db5f
+    - path: ./output/bwameth/bwameth/NC_010473.fa.bwameth.c2t
+      md5sum: db670853725f4a31080c991e9df6b330
+    - path: ./output/bwameth/bwameth/NC_010473.fa.bwameth.c2t.sa
+      md5sum: 020db07e7e1544dc961c30c9936f3213

tests/software/fastp/test.yml

@@ -5,9 +5,9 @@
     - fastp_single_end
   files:
     - path: ./output/fastp/test.fastp.json
-      md5sum: b81d53bfa5c1553bed89f6475edcf437
+      md5sum: 8740a96898a850a3c2ce0081d9a259fb
     - path: ./output/fastp/test.trim.fastq.gz
-      md5sum: 2f5516df477b123e3f78adb67effa3bc
+      md5sum: 63fea84c6907d2716aeb53fe890b288d
     - path: ./output/fastp/test.fastp.log
     - path: ./output/fastp/test.fastp.html
 
@@ -19,7 +19,7 @@
   files:
     - path: ./output/fastp/test.fastp.html
     - path: ./output/fastp/test.fastp.json
-      md5sum: 40db7fcbed478b0a96a1c5c1bb5f737b
+      md5sum: 7afba66526b1dd4cd3b1012809ba0327
     - path: ./output/fastp/test.fastp.log
     - path: ./output/fastp/test_1.trim.fastq.gz
       md5sum: c8844c05194b50ae368e6825e997aa7f

tests/software/gatk4/bedtointervallist/main.nf

@@ -0,0 +1,16 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { GATK4_BEDTOINTERVALLIST } from '../../../../software/gatk4/bedtointervallist/main.nf' addParams( options: [:] )
+
+workflow test_gatk4_bedtointervallist {
+
+    def input = []
+    input = [ [ id:'test' ], // meta map
+              [ file("${launchDir}/tests/data/bed/sarscov2.bed", checkIfExists: true)] ]
+
+    sd = file("${launchDir}/tests/data/fasta/sarscov2/GCA_011545545.1_ASM1154554v1_genomic.dict", checkIfExists: true)
+
+    GATK4_BEDTOINTERVALLIST ( input, sd )
+}

tests/software/gatk4/bedtointervallist/test.yml

@@ -0,0 +1,8 @@
+- name: gatk4 bedtointervallist
+  command: nextflow run ./tests/software/gatk4/bedtointervallist -entry test_gatk4_bedtointervallist -c tests/config/nextflow.config
+  tags:
+    - gatk4
+    - gatk4_bedtointervallist
+  files:
+    - path: output/gatk4/test.interval_list
+      md5sum: e51101c9357fb2d59fd30e370eefa39c

tests/software/gatk4/mergevcfs/main.nf

@@ -0,0 +1,31 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { GATK4_MERGEVCFS } from '../../../../software/gatk4/mergevcfs/main.nf' addParams( options: [:] )
+
+workflow test_gatk4_mergevcfs {
+
+    def input = []
+    input = [ [ id:'test' ], // meta map
+              [ file("${launchDir}/tests/data/vcf/test.vcf", checkIfExists: true),
+                file("${launchDir}/tests/data/vcf/test2.vcf.gz", checkIfExists: true),
+                file("${launchDir}/tests/data/vcf/test3.vcf.gz", checkIfExists: true)  ] ]
+
+    ref_dict = file("tests/data/fasta/test.consensus.for_vcf.dict", checkIfExists: true)
+
+    GATK4_MERGEVCFS ( input, ref_dict, false )
+}
+
+workflow test_gatk4_mergevcfs_refdict {
+
+    def input = []
+    input = [ [ id:'test' ], // meta map
+              [ file("${launchDir}/tests/data/vcf/test.vcf", checkIfExists: true),
+                file("${launchDir}/tests/data/vcf/test2.vcf.gz", checkIfExists: true),
+                file("${launchDir}/tests/data/vcf/test3.vcf.gz", checkIfExists: true)  ] ]
+
+    ref_dict = file("tests/data/fasta/test.consensus.for_vcf.dict", checkIfExists: true)
+
+    GATK4_MERGEVCFS ( input, ref_dict, true )
+}

tests/software/gatk4/mergevcfs/test.yml

@@ -0,0 +1,17 @@
+- name: gatk4 mergevcfs
+  command: nextflow run ./tests/software/gatk4/mergevcfs -entry test_gatk4_mergevcfs -c tests/config/nextflow.config
+  tags:
+    - gatk4
+    - gatk4_mergevcfs
+  files:
+    - path: output/gatk4/test.merged.vcf.gz
+      md5sum: f25850b7bd4d362b5ea67d4453e9df55
+
+- name: gatk4 mergevcfs refdict
+  command: nextflow run ./tests/software/gatk4/mergevcfs -entry test_gatk4_mergevcfs_refdict -c tests/config/nextflow.config
+  tags:
+    - gatk4
+    - gatk4_mergevcfs
+  files:
+    - path: output/gatk4/test.merged.vcf.gz
+      md5sum: f25850b7bd4d362b5ea67d4453e9df55

tests/software/gatk4/revertsam/main.nf

@@ -0,0 +1,14 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { GATK4_REVERTSAM } from '../../../../software/gatk4/revertsam/main.nf' addParams( options: [:] )
+
+workflow test_gatk4_revertsam {
+
+    def input = []
+    input = [ [ id:'test' ], // meta map
+                file("${launchDir}/tests/data/bam/sarscov2_aln.bam", checkIfExists: true) ]
+
+    GATK4_REVERTSAM( input )
+}

tests/software/gatk4/revertsam/test.yml

@@ -0,0 +1,8 @@
+- name: gatk4 revertsam
+  command: nextflow run ./tests/software/gatk4/revertsam -entry test_gatk4_revertsam -c tests/config/nextflow.config
+  tags:
+    - gatk4
+    - gatk4_revertsam
+  files:
+    - path: output/gatk4/test.reverted.bam
+      md5sum: 6de199f7a0577e2a3fe7b3a9cb4ae25d

tests/software/gatk4/samtofastq/main.nf

@@ -0,0 +1,23 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { GATK4_SAMTOFASTQ } from '../../../../software/gatk4/samtofastq/main.nf' addParams( options: [:] )
+
+workflow test_gatk4_samtofastq_single_end {
+
+    def input = []
+    input = [ [ id:'test', single_end: true ], // meta map
+              [ file("${launchDir}/tests/data/bam/test.single_end.sorted.bam", checkIfExists: true)] ]
+
+    GATK4_SAMTOFASTQ ( input )
+}
+
+workflow test_gatk4_samtofastq_paired_end {
+
+    def input = []
+    input = [ [ id:'test', single_end: false ], // meta map
+              [ file("${launchDir}/tests/data/bam/test.single_end.sorted.bam", checkIfExists: true)] ]
+
+    GATK4_SAMTOFASTQ ( input )
+}

tests/software/gatk4/samtofastq/test.yml

@@ -0,0 +1,21 @@
+- name: gatk4 samtofastq single-end
+  command: nextflow run ./tests/software/gatk4/samtofastq -entry test_gatk4_samtofastq_single_end -c tests/config/nextflow.config
+  tags:
+    - gatk4
+    - gatk4_samtofastq
+    - gatk4_samtofastq_single_end
+  files:
+    - path: output/gatk4/test.fastq.gz
+      md5sum: 61c6d3556ac6e0d09d800415b9a48508
+
+- name: gatk4 samtofastq paired-end
+  command: nextflow run ./tests/software/gatk4/samtofastq -entry test_gatk4_samtofastq_paired_end -c tests/config/nextflow.config
+  tags:
+    - gatk4
+    - gatk4_samtofastq
+    - gatk4_samtofastq_paired_end
+  files:
+    - path: output/gatk4/test_1.fastq.gz
+      md5sum: 61c6d3556ac6e0d09d800415b9a48508
+    - path: output/gatk4/test_2.fastq.gz
+      md5sum: d0e74ab8dccca91c0ccd7125e588d5cd

tests/software/gatk4/splitncigarreads/main.nf

@@ -0,0 +1,18 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { GATK4_SPLITNCIGARREADS } from '../../../../software/gatk4/splitncigarreads/main.nf' addParams( options: [:] )
+
+workflow test_gatk4_splitncigarreads {
+
+    def input = []
+    input = [ [ id:'test' ], // meta map
+              [ file("${launchDir}/tests/data/bam/sarscov2_aln.bam", checkIfExists: true)] ]
+
+    fasta = [ file("tests/data/fasta/sarscov2/GCA_011545545.1_ASM1154554v1_genomic.fna", checkIfExists: true),
+              file("tests/data/fasta/sarscov2/GCA_011545545.1_ASM1154554v1_genomic.fna.fai", checkIfExists: true),
+              file("tests/data/fasta/sarscov2/GCA_011545545.1_ASM1154554v1_genomic.dict", checkIfExists: true)]
+
+    GATK4_SPLITNCIGARREADS ( input, fasta )
+}

tests/software/gatk4/splitncigarreads/test.yml

@@ -0,0 +1,8 @@
+- name: gatk4 splitncigarreads
+  command: nextflow run ./tests/software/gatk4/splitncigarreads -entry test_gatk4_splitncigarreads -c tests/config/nextflow.config
+  tags:
+    - gatk4
+    - gatk4_splitncigarreads
+  files:
+    - path: output/gatk4/test.split_cigar.bam
+      md5sum: 9228ac79882a4929c797c891b1bd9f6d

tests/software/methyldackel/extract/main.nf

@@ -0,0 +1,18 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { METHYLDACKEL_EXTRACT } from '../../../../software/methyldackel/extract/main.nf' addParams( options: [:] )
+
+workflow test_methyldackel_extract {
+
+    def input = []
+    def fasta = file("${launchDir}/tests/data/fasta/E_coli/NC_010473.fa", checkIfExists: true)
+    def fai   = file("${launchDir}/tests/data/fasta/E_coli/NC_010473.fa.fai", checkIfExists: true)
+
+    input     = [ [ id:'test', single_end:false ], // meta map
+                  file("${launchDir}/tests/data/bam/test.paired_end_methylated.sorted.bam", checkIfExists: true),
+                  file("${launchDir}/tests/data/bam/test.paired_end_methylated.sorted.bam.bai", checkIfExists: true) ]
+
+    METHYLDACKEL_EXTRACT ( input, fasta, fai )
+}

tests/software/methyldackel/extract/test.yml

@@ -0,0 +1,8 @@
+- name: Run methyldackel extract test workflow
+  command: nextflow run ./tests/software/methyldackel/extract -entry test_methyldackel_extract -c tests/config/nextflow.config
+  tags:
+    - methyldackel
+    - methyldackel_extract
+  files:
+    - path: output/methyldackel/test.paired_end_methylated.sorted_CpG.bedGraph
+      md5sum: a83c1c9abe632e1996402185ddc4d2b6

tests/software/methyldackel/mbias/main.nf

@@ -0,0 +1,18 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { METHYLDACKEL_MBIAS } from '../../../../software/methyldackel/mbias/main.nf' addParams( options: [:] )
+
+workflow test_methyldackel_mbias {
+
+    def input = []
+    def fasta = file("${launchDir}/tests/data/fasta/E_coli/NC_010473.fa", checkIfExists: true)
+    def fai   = file("${launchDir}/tests/data/fasta/E_coli/NC_010473.fa.fai", checkIfExists: true)
+
+    input     = [ [ id:'test', single_end:false ], // meta map
+                  file("${launchDir}/tests/data/bam/test.paired_end_methylated.sorted.bam", checkIfExists: true),
+                  file("${launchDir}/tests/data/bam/test.paired_end_methylated.sorted.bam.bai", checkIfExists: true) ]
+
+    METHYLDACKEL_MBIAS ( input, fasta, fai )
+}

tests/software/methyldackel/mbias/test.yml

@@ -0,0 +1,8 @@
+- name: Run methyldackel mbias test workflow
+  command: nextflow run ./tests/software/methyldackel/mbias -entry test_methyldackel_mbias -c tests/config/nextflow.config
+  tags:
+    - methyldackel
+    - methyldackel_mbias
+  files:
+    - path: ./output/methyldackel/test.txt
+      md5sum: 4a8f76da62eaa169576c8e6d509c5066

tests/software/pangolin/test.yml

@@ -4,4 +4,4 @@
     - pangolin
   files:
     - path: ./output/pangolin/test.pangolin.csv
-      md5sum: 097669de1843e27f4529d6db8bbed97b
+      md5sum: 43edd267815f6408b66961a0abf9ddd6

tests/software/qualimap/bamqc/main.nf

@@ -0,0 +1,16 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { QUALIMAP_BAMQC } from '../../../../software/qualimap/bamqc/main.nf' addParams( options: [:] )
+
+workflow test_qualimap_bamqc {
+
+    def input = []
+    input = [ [ id:'test', single_end:false ], // meta map
+              file("${launchDir}/tests/data/bam/test.paired_end.sorted.bam", checkIfExists: true) ]
+    def gff = file("dummy_file.txt")
+    def use_gff = false
+
+    QUALIMAP_BAMQC ( input, gff, use_gff )
+}

tests/software/qualimap/bamqc/test.yml

@@ -0,0 +1,26 @@
+- name: Run qualimap bamqc test workflow
+  command: nextflow run ./tests/software/qualimap/bamqc -entry test_qualimap_bamqc -c tests/config/nextflow.config
+  tags:
+    - qualimap
+    - qualimap_bamqc
+  files:
+    - path: output/qualimap/test/raw_data_qualimapReport/coverage_across_reference.txt
+      md5sum: 0e2ae3deae8adbe6c66db4dadb260c76
+    - path: output/qualimap/test/raw_data_qualimapReport/coverage_histogram.txt
+      md5sum: 0e9f37aabb761969526f445ed8d3173b
+    - path: output/qualimap/test/raw_data_qualimapReport/duplication_rate_histogram.txt
+      md5sum: 2299c92a3049270b9d7b1f521cafbb86
+    - path: output/qualimap/test/raw_data_qualimapReport/genome_fraction_coverage.txt
+      md5sum: 89c8c882c9423fafe03b4fc98e2bfb5a
+    - path: output/qualimap/test/raw_data_qualimapReport/insert_size_across_reference.txt
+      md5sum: 966230f2bbe796788beac30678597e79
+    - path: output/qualimap/test/raw_data_qualimapReport/insert_size_histogram.txt
+      md5sum: b3049afc6c3c57c3b278abd66a66a690
+    - path: output/qualimap/test/raw_data_qualimapReport/mapped_reads_gc-content_distribution.txt
+      md5sum: e9e0189463430b5565ea6da1d5976e40
+    - path: output/qualimap/test/raw_data_qualimapReport/mapped_reads_nucleotide_content.txt
+      md5sum: fa1566299e1bcd2d65c95b32ae2ca3d1
+    - path: output/qualimap/test/raw_data_qualimapReport/mapping_quality_across_reference.txt
+      md5sum: 40b6951739a602da545e38a00b698fde
+    - path: output/qualimap/test/raw_data_qualimapReport/mapping_quality_histogram.txt
+      md5sum: c66579f0114a9aedc70820fa609fb1ec