Add core Biscuit tools (#1354)

* create files with nf-core command

* update meta.yml files

* starting to work on index main.nf

* prelim test for index

* index test working; not finding all output files

* index passing tests

* index and align passing tests

* prototyping biscuitblaster and pileup

* update containers

* updates to pileup

* pileup passing tests

* template creation for more biscuit tools

* tests passing on blaster,bsconv,pupsom

* epiread passing tests, but need to update SNP bed file path

* vcf2bed working; change test file

* all biscuit commands passing tests

* biscuitblaster rename

* try to fix permissions

* more permission fixes

* trying a couple more permission changes

* hopefully last permission fixes

* really last permission changes

* few more permissions

* add when blocks

* Remove read group meta

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>

* remove read group meta

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>

* changes for first round of review

* update meta.yml with more specific links

* Update modules/biscuit/biscuitblaster/main.nf

Co-authored-by: Sateesh Peri <33637490+sateeshperi@users.noreply.github.com>

* Apply new version reporting

Co-authored-by: Sateesh Peri <33637490+sateeshperi@users.noreply.github.com>

* Update modules/biscuit/pileup/main.nf

Co-authored-by: Sateesh Peri <33637490+sateeshperi@users.noreply.github.com>

* Update main.nf

* Update modules/biscuit/pileupsomatic/main.nf

Co-authored-by: Sateesh Peri <33637490+sateeshperi@users.noreply.github.com>

* update test file path

* Update modules/biscuit/align/main.nf

Co-authored-by: Sateesh Peri <33637490+sateeshperi@users.noreply.github.com>

* Update modules/biscuit/align/main.nf

Co-authored-by: Sateesh Peri <33637490+sateeshperi@users.noreply.github.com>

* tests passing again

* Update modules/biscuit/align/main.nf

* Update modules/biscuit/bsconv/main.nf

* Update modules/biscuit/epiread/main.nf

* Update modules/biscuit/index/main.nf

* Update test.yml

* Update modules/biscuit/pileupsomatic/main.nf

* remove module-specific extension/prefix

* remove module-specific extension/prefix

* add missing args

* switch pileup strategy

* update test.yml

* remove debug

* whitespace cleanup

* add in newline escapes

* requested changes

* Update modules/biscuit/pileup/meta.yml

Co-authored-by: Spix <nathan.spix@submit.cm.cluster>
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
Co-authored-by: Sateesh Peri <33637490+sateeshperi@users.noreply.github.com>
Co-authored-by: Spix <nathan.spix@node107.cm.cluster>
Co-authored-by: njspix <nathan.spix@vai.org>

modules/biscuit/align/main.nf

@@ -0,0 +1,44 @@
+process BISCUIT_ALIGN {
+    tag "$meta.id"
+    label 'process_high'
+
+    conda (params.enable_conda ? "bioconda::biscuit=1.0.2.20220113 bioconda::samtools=1.15" : null)
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/mulled-v2-db16f1c237a26ea9245cf9924f858974ff321d6e:17fa66297f088a1bc7560b7b90dc273bf23f2d8c-0':
+        'quay.io/biocontainers/mulled-v2-db16f1c237a26ea9245cf9924f858974ff321d6e:17fa66297f088a1bc7560b7b90dc273bf23f2d8c-0' }"
+
+    input:
+    tuple val(meta), path(reads)
+    path index
+
+    output:
+    tuple val(meta), path("*.bam"), emit: bam
+    path "versions.yml"           , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args = task.ext.args ?: ''
+    def args2 = task.ext.args2 ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    def biscuit_cpus = (int) Math.max(Math.floor(task.cpus*0.9),1)
+    def samtools_cpus = task.cpus-biscuit_cpus
+    """
+    INDEX=`find -L ./ -name "*.bis.amb" | sed 's/.bis.amb//'`
+
+    biscuit align \\
+        $args \\
+        -@ $biscuit_cpus \\
+        \$INDEX \\
+        $reads \\
+        | samtools sort $args2 --threads $samtools_cpus -o ${prefix}.bam -
+
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        biscuit: \$( biscuit version |& sed '1!d; s/^.*BISCUIT Version: //' )
+        samtools: \$( samtools --version |& sed '1!d; s/^.*samtools //' )
+    END_VERSIONS
+    """
+}

modules/biscuit/align/meta.yml

@@ -0,0 +1,52 @@
+name: biscuit_align
+description: Aligns single- or paired-end reads from bisulfite-converted libraries to a reference genome using Biscuit.
+keywords:
+  - biscuit
+  - DNA methylation
+  - WGBS
+  - scWGBS
+  - bisulfite sequencing
+  - aligner
+  - bam
+tools:
+  - biscuit:
+      description: A utility for analyzing sodium bisulfite conversion-based DNA methylation/modification data
+      homepage: https://huishenlab.github.io/biscuit/
+      documentation: https://huishenlab.github.io/biscuit/docs/alignment
+      tool_dev_url: https://github.com/huishenlab/biscuit
+      doi: ""
+      licence: ["MIT"]
+
+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: Biscuit genome index directory (generated with 'biscuit index')
+      pattern: "BiscuitIndex"
+
+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}"
+  - versions:
+      type: file
+      description: File containing software versions
+      pattern: "versions.yml"
+
+authors:
+  - "@njspix"

modules/biscuit/biscuitblaster/main.nf

@@ -0,0 +1,52 @@
+process BISCUIT_BLASTER {
+    tag "$meta.id"
+    label 'process_high'
+
+    conda (params.enable_conda ? "bioconda::biscuit=1.0.2.20220113 bioconda::samblaster=0.1.26 bioconda::samtools=1.15" : null)
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/mulled-v2-db16f1c237a26ea9245cf9924f858974ff321d6e:17fa66297f088a1bc7560b7b90dc273bf23f2d8c-0':
+        'quay.io/biocontainers/mulled-v2-db16f1c237a26ea9245cf9924f858974ff321d6e:17fa66297f088a1bc7560b7b90dc273bf23f2d8c-0' }"
+
+    input:
+    tuple val(meta), path(reads)
+    path index
+
+    output:
+    tuple val(meta), path("*.bam"), emit: bam
+    tuple val(meta), path("*.bai"), emit: bai
+    path "versions.yml"           , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    def args = task.ext.args ?: ''
+    def args2 = task.ext.args2 ?: ''
+    def args3 = task.ext.args3 ?: ''
+    def biscuit_cpus = (int) Math.max(Math.floor(task.cpus*0.95),1)
+    def samtools_cpus = task.cpus-biscuit_cpus
+    """
+    INDEX=`find -L ./ -name "*.bis.amb" | sed 's/.bis.amb//'`
+
+    biscuit align \\
+        -@ $biscuit_cpus \\
+        $args \\
+        \$INDEX \\
+        $reads | \\
+    samblaster \\
+        $args2 | \\
+    samtools sort \\
+        -@ $samtools_cpus \\
+        $args3 \\
+        --write-index \\
+        -o ${prefix}.bam##idx##${prefix}.bam.bai
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        biscuit: \$( biscuit version |& sed '1!d; s/^.*BISCUIT Version: //' )
+        samtools: \$( samtools --version |& sed '1!d; s/^.*samtools //' )
+        samblaster: \$( samblaster --version |& sed 's/^.*samblaster: Version //' )
+    END_VERSIONS
+    """
+}

modules/biscuit/biscuitblaster/meta.yml

@@ -0,0 +1,78 @@
+name: biscuit_blaster
+
+description: A fast, compact one-liner to produce duplicate-marked, sorted, and indexed BAM files using Biscuit
+keywords:
+  - biscuit
+  - DNA methylation
+  - WGBS
+  - scWGBS
+  - bisulfite sequencing
+  - aligner
+  - bam
+
+tools:
+  - biscuit:
+      description: A utility for analyzing sodium bisulfite conversion-based DNA methylation/modification data
+      homepage: https://huishenlab.github.io/biscuit/
+      documentation: https://huishenlab.github.io/biscuit/biscuitblaster/
+      tool_dev_url: https://github.com/huishenlab/biscuit
+      doi: ""
+      licence: ["MIT"]
+  - samblaster:
+      description: |
+        samblaster is a fast and flexible program for marking duplicates in read-id grouped paired-end SAM files.
+        It can also optionally output discordant read pairs and/or split read mappings to separate SAM files,
+        and/or unmapped/clipped reads to a separate FASTQ file.
+        By default, samblaster reads SAM input from stdin and writes SAM to stdout.
+      homepage: None
+      documentation: https://github.com/GregoryFaust/samblaster
+      tool_dev_url: https://github.com/GregoryFaust/samblaster
+      doi: "10.1093/bioinformatics/btu314"
+      licence: ["MIT"]
+  - 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: hhttp://www.htslib.org/doc/samtools.html
+      doi: 10.1093/bioinformatics/btp352
+      licence: ["MIT"]
+
+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: Biscuit genome index directory (generated with 'biscuit index')
+      pattern: "BiscuitIndex"
+
+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}"
+  - bai:
+      type: file
+      description: Output BAM index
+      pattern: "*.{bai}"
+  - versions:
+      type: file
+      description: File containing software versions
+      pattern: "versions.yml"
+
+authors:
+  - "@njspix"

modules/biscuit/bsconv/main.nf

@@ -0,0 +1,39 @@
+process BISCUIT_BSCONV {
+    tag "$meta.id"
+    label 'process_long'
+
+    conda (params.enable_conda ? "bioconda::biscuit=1.0.2.20220113" : null)
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/biscuit:1.0.2.20220113--h81a5ba2_0':
+        'quay.io/biocontainers/biscuit:1.0.2.20220113--h81a5ba2_0' }"
+
+    input:
+    tuple val(meta), path(bam), path(bai)
+    path(index)
+
+    output:
+    tuple val(meta), path("*.bam"), emit: bsconv_bam
+    path "versions.yml"           , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    if ("$bam" == "${prefix}.bam") error "Input and output names are the same, set prefix in module configuration to disambiguate!"
+    """
+    INDEX=`find -L ./ -name "*.bis.amb" | sed 's/.bis.amb//'`
+
+    biscuit bsconv \\
+        $args \\
+        \$INDEX \\
+        $bam \\
+        ${prefix}.bam
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        biscuit: \$( biscuit version |& sed '1!d; s/^.*BISCUIT Version: //' )
+    END_VERSIONS
+    """
+}

modules/biscuit/bsconv/meta.yml

@@ -0,0 +1,55 @@
+name: biscuit_bsconv
+description: Summarize and/or filter reads based on bisulfite conversion rate
+keywords:
+  - biscuit
+  - DNA methylation
+  - WGBS
+  - scWGBS
+  - bisulfite sequencing
+  - aligner
+  - bam
+  - filter
+
+tools:
+  - biscuit:
+      description: A utility for analyzing sodium bisulfite conversion-based DNA methylation/modification data
+      homepage: https://huishenlab.github.io/biscuit/
+      documentation: https://huishenlab.github.io/biscuit/docs/subcommand_help.html#biscuit-bsconv
+      tool_dev_url: https://github.com/huishenlab/biscuit
+      doi: ""
+      licence: ["MIT"]
+
+input:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  - bam:
+      type: file
+      description: BAM file contained mapped reads
+  - bai:
+      type: file
+      description: BAM file index
+  - index:
+      type: dir
+      description: Biscuit genome index directory (generated with 'biscuit index')
+      pattern: "BiscuitIndex"
+
+output:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  - bsconv_bam:
+      type: file
+      description: Output BAM file containing filtered read alignments
+      pattern: "*.{bam}"
+  - versions:
+      type: file
+      description: File containing software versions
+      pattern: "versions.yml"
+
+authors:
+  - "@njspix"

modules/biscuit/epiread/main.nf

@@ -0,0 +1,57 @@
+process BISCUIT_EPIREAD {
+    tag "$meta.id"
+    label 'process_long'
+
+    conda (params.enable_conda ? "bioconda::biscuit=1.0.2.20220113 bioconda::samtools=1.15" : null)
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/mulled-v2-db16f1c237a26ea9245cf9924f858974ff321d6e:17fa66297f088a1bc7560b7b90dc273bf23f2d8c-0':
+        'quay.io/biocontainers/mulled-v2-db16f1c237a26ea9245cf9924f858974ff321d6e:17fa66297f088a1bc7560b7b90dc273bf23f2d8c-0' }"
+
+    input:
+    tuple val(meta), path(bam), path(bai), path(snp_bed)
+    path(index)
+
+    output:
+    tuple val(meta), path("*.bed.gz"), emit: epiread_bed
+    path "versions.yml"              , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args = task.ext.args ?: ''
+    def args2 = task.ext.args2 ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    def biscuit_cpus = (int) Math.max(Math.floor(task.cpus*0.9),1)
+    def samtools_cpus = task.cpus-biscuit_cpus
+    // As of 2/25/22, epiread does not support reading a gzipped SNP BED file.
+    // This is a bit hacky but allows the user to supply a gzipped OR uncompressed bed file
+    def unzip_snp_bed = snp_bed && (snp_bed.toString() =~ /\.gz$/) ? "bgzip -d ${snp_bed}" : ""
+    def unzipped_snp_bed = snp_bed ? snp_bed.toString() - ~/\.gz$/: ""
+    // SNP BED input is optional
+    def options_snp_bed = snp_bed ? "-B ${unzipped_snp_bed}" : ""
+    if ("$options_snp_bed" == "${prefix}.bed.gz") error "Input and output names are the same, set prefix in module configuration to disambiguate!"
+    """
+    INDEX=`find -L ./ -name "*.bis.amb" | sed 's/.bis.amb//'`
+
+    $unzip_snp_bed
+
+    biscuit epiread \\
+        -@ $biscuit_cpus \\
+        $args \\
+        $options_snp_bed \\
+        \$INDEX \\
+        $bam | \\
+    LC_ALL=C sort -k1,1 -k2,2n | \\
+    bgzip \\
+        -@ $samtools_cpus \\
+        $args2 \\
+        -c > ${prefix}.bed.gz
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        biscuit: \$( biscuit version |& sed '1!d; s/^.*BISCUIT Version: //' )
+        samtools: \$( samtools --version |& sed '1!d; s/^.*samtools //' )
+    END_VERSIONS
+    """
+}

modules/biscuit/epiread/meta.yml

@@ -0,0 +1,58 @@
+name: biscuit_epiread
+description: |
+  Summarizes read-level methylation (and optionally SNV) information from a
+  Biscuit BAM file in a standard-compliant BED format.
+keywords:
+  - biscuit
+  - DNA methylation
+  - WGBS
+  - scWGBS
+  - bisulfite sequencing
+  - aligner
+  - bam
+tools:
+  - biscuit:
+      description: A utility for analyzing sodium bisulfite conversion-based DNA methylation/modification data
+      homepage: https://huishenlab.github.io/biscuit/
+      documentation: https://huishenlab.github.io/biscuit/epiread_format/
+      tool_dev_url: https://github.com/huishenlab/biscuit
+      doi: ""
+      licence: ["MIT"]
+
+input:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  - bam:
+      type: file
+      description: Biscuit BAM file
+  - bai:
+      type: file
+      description: BAM index
+  - snp_bed:
+      type: file
+      description: BED file containing SNP information (optional)
+  - index:
+      type: dir
+      description: Biscuit genome index directory (generated with 'biscuit index')
+      pattern: "BiscuitIndex"
+
+output:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  - epiread_bed:
+      type: file
+      description: Gzipped BED file with methylation (and optionally SNV) information
+      pattern: "*.{epiread.bed.gz}"
+  - versions:
+      type: file
+      description: File containing software versions
+      pattern: "versions.yml"
+
+authors:
+  - "@njspix"

modules/biscuit/index/main.nf

@@ -0,0 +1,33 @@
+process BISCUIT_INDEX {
+    tag "$fasta"
+    label 'process_long'
+
+    conda (params.enable_conda ? "bioconda::biscuit=1.0.2.20220113" : null)
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/biscuit:1.0.2.20220113--h81a5ba2_0':
+        'quay.io/biocontainers/biscuit:1.0.2.20220113--h81a5ba2_0' }"
+
+    input:
+    path fasta, stageAs: "BiscuitIndex/*"
+
+    output:
+    path "BiscuitIndex/*.fa*", emit: index, includeInputs: true
+    path "versions.yml"      , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args = task.ext.args ?: ''
+    """
+    biscuit \\
+        index \\
+        $args \\
+        $fasta
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        biscuit: \$( biscuit version |& sed '1!d; s/^.*BISCUIT Version: //' )
+    END_VERSIONS
+    """
+}

modules/biscuit/index/meta.yml

@@ -0,0 +1,38 @@
+name: biscuit_index
+description: Indexes a reference genome for use with Biscuit
+keywords:
+  - biscuit
+  - DNA methylation
+  - WGBS
+  - scWGBS
+  - bisulfite sequencing
+  - index
+  - reference
+  - fasta
+
+tools:
+  - biscuit:
+      description: A utility for analyzing sodium bisulfite conversion-based DNA methylation/modification data
+      homepage: https://huishenlab.github.io/biscuit/
+      documentation: https://huishenlab.github.io/biscuit/docs/alignment
+      tool_dev_url: https://github.com/huishenlab/biscuit
+      doi: ""
+      licence: ["MIT"]
+
+input:
+  - fasta:
+      type: file
+      description: Input genome fasta file
+
+output:
+  - index:
+      type: dir
+      description: Biscuit genome index directory
+      pattern: "BiscuitIndex"
+  - versions:
+      type: file
+      description: File containing software versions
+      pattern: "versions.yml"
+
+authors:
+  - "@njspix"

modules/biscuit/mergecg/main.nf

@@ -0,0 +1,43 @@
+process BISCUIT_MERGECG {
+    tag "$meta.id"
+    label 'process_long'
+
+    conda (params.enable_conda ? "bioconda::biscuit=1.0.2.20220113 bioconda::samtools=1.15" : null)
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/mulled-v2-db16f1c237a26ea9245cf9924f858974ff321d6e:17fa66297f088a1bc7560b7b90dc273bf23f2d8c-0':
+        'quay.io/biocontainers/mulled-v2-db16f1c237a26ea9245cf9924f858974ff321d6e:17fa66297f088a1bc7560b7b90dc273bf23f2d8c-0' }"
+
+    input:
+    tuple val(meta), path(bed)
+    path index
+
+    output:
+    tuple val(meta), path("*.bed.gz"), emit: mergecg_bed
+    path "versions.yml"              , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args = task.ext.args ?: ''
+    def args2 = task.ext.args2 ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    INDEX=`find -L ./ -name "*.bis.amb" | sed 's/.bis.amb//'`
+
+    biscuit mergecg \\
+        $args \\
+        \$INDEX \\
+        $bed | \\
+    LC_ALL=C sort -k1,1 -k2,2n | \\
+    bgzip \\
+        $args2 \\
+        -c > ${prefix}.bed.gz
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        biscuit: \$( biscuit version |& sed '1!d; s/^.*BISCUIT Version: //' )
+        samtools: \$( samtools --version |& sed '1!d; s/^.*samtools //' )
+    END_VERSIONS
+    """
+}

modules/biscuit/mergecg/meta.yml

@@ -0,0 +1,51 @@
+name: biscuit_mergecg
+description: Merges methylation information for opposite-strand C's in a CpG context
+keywords:
+  - biscuit
+  - DNA methylation
+  - WGBS
+  - scWGBS
+  - bisulfite sequencing
+  - aligner
+  - bed
+tools:
+  - biscuit:
+      description: A utility for analyzing sodium bisulfite conversion-based DNA methylation/modification data
+      homepage: https://huishenlab.github.io/biscuit/
+      documentation: https://huishenlab.github.io/biscuit/docs/methylextraction.html
+      tool_dev_url: https://github.com/huishenlab/biscuit
+      doi: ""
+      licence: ["MIT"]
+
+input:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  - bed:
+      type: file
+      description: |
+        Biscuit BED file (output of biscuit vcf2bed)
+  - index:
+      type: dir
+      description: Biscuit genome index directory (generated with 'biscuit index')
+      pattern: "BiscuitIndex"
+
+output:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  - mergecg_bed:
+      type: file
+      description: Gzipped BED file with merged methylation information
+      pattern: "*.bed.gz"
+  - versions:
+      type: file
+      description: File containing software versions
+      pattern: "versions.yml"
+
+authors:
+  - "@njspix"

modules/biscuit/pileup/main.nf

@@ -0,0 +1,45 @@
+process BISCUIT_PILEUP {
+    tag "$meta.id"
+    label 'process_high'
+
+    conda (params.enable_conda ? "bioconda::biscuit=1.0.2.20220113 bioconda::samtools=1.15" : null)
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/mulled-v2-db16f1c237a26ea9245cf9924f858974ff321d6e:17fa66297f088a1bc7560b7b90dc273bf23f2d8c-0':
+        'quay.io/biocontainers/mulled-v2-db16f1c237a26ea9245cf9924f858974ff321d6e:17fa66297f088a1bc7560b7b90dc273bf23f2d8c-0' }"
+
+    input:
+    tuple val(meta), path(normal_bams), path(normal_bais), path(tumor_bam), path(tumor_bai)
+    path index
+
+    output:
+    tuple val(meta), path("*.vcf.gz"), emit: vcf
+    path "versions.yml"              , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args = task.ext.args ?: ''
+    def args2 = task.ext.args2 ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    def biscuit_cpus = (int) Math.max(Math.floor(task.cpus*0.9),1)
+    def bgzip_cpus = task.cpus-biscuit_cpus
+    if ( tumor_bam != [] && normal_bams.toList().size() > 1 ) error "[BISCUIT_PILEUP] error: Tumor BAM provided with more than one normal BAM"
+    if ( tumor_bam.toList().size() > 1 ) error "[BISCUIT_PILEUP] error: more than one tumor BAM provided"
+    input = ( tumor_bam==[] ) ? "${normal_bams}" : "-S -T ${tumor_bam} -I ${normal_bams}"
+    """
+    INDEX=`find -L ./ -name "*.bis.amb" | sed 's/.bis.amb//'`
+
+    biscuit pileup \\
+        -@ $biscuit_cpus \\
+        $args \\
+        \$INDEX \\
+        $input \\
+        | bgzip -@ $bgzip_cpus $args2 > ${prefix}.vcf.gz
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        biscuit: \$( biscuit version |& sed '1!d; s/^.*BISCUIT Version: //' )
+    END_VERSIONS
+    """
+}

modules/biscuit/pileup/meta.yml

@@ -0,0 +1,70 @@
+name: biscuit_pileup
+description: Computes cytosine methylation and callable SNV mutations, optionally in reference to a germline BAM to call somatic variants
+keywords:
+  - bisulfite
+  - DNA methylation
+  - pileup
+  - variant calling
+  - WGBS
+  - scWGBS
+  - bam
+  - vcf
+tools:
+  - biscuit:
+      description: A utility for analyzing sodium bisulfite conversion-based DNA methylation/modification data
+      homepage: https://huishenlab.github.io/biscuit/
+      documentation: https://huishenlab.github.io/biscuit/docs/pileup.html
+      tool_dev_url: https://github.com/huishenlab/biscuit
+      doi: ""
+      licence: ["MIT"]
+
+input:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  - normal_bams:
+      type: file(s)
+      description: |
+              BAM files to be analyzed. If no tumor_bam file is provided, any number of "normal" BAMs may be provided
+              ("normal" here is just a semantic issue, these BAMs could be from tumor or any other kind of tissue). If a
+              tumor BAM file is provided, exactly one normal (germline) BAM must be provided.
+      pattern: "*.{bam}"
+  - normal_bais:
+      type: file(s)
+      description: BAM index file or files corresponding to the provided normal_bams
+      pattern: "*.{bai}"
+  - tumor_bam:
+      type: file(s)
+      description: |
+              Optional. If a tumor BAM file is provided, pileup will run in "somatic" mode and will annotate variants with
+              their somatic state (present in tumor only, present in normal only, present in both, etc). Note that if a
+              tumor BAM file is provided, exactly one normal BAM must be provided.
+      pattern: "*.{bam}"
+  - tumor_bai:
+      type: file(s)
+      description: Optional. BAM index file corresponding to provided tumor_bam
+      pattern: "*.{bai}"
+  - index:
+      type: dir
+      description: Biscuit genome index directory (generated with 'biscuit index')
+      pattern: "BiscuitIndex"
+
+output:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  - versions:
+      type: file
+      description: File containing software versions
+      pattern: "versions.yml"
+  - vcf:
+      type: file
+      description: vcf file with methylation information
+      pattern: "*.{vcf.gz}"
+
+authors:
+  - "@njspix"

modules/biscuit/qc/main.nf

@@ -0,0 +1,40 @@
+process BISCUIT_QC {
+    tag "$meta.id"
+    label 'process_long'
+
+    conda (params.enable_conda ? "bioconda::biscuit=1.0.2.20220113" : null)
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/biscuit:1.0.2.20220113--h81a5ba2_0':
+        'quay.io/biocontainers/biscuit:1.0.2.20220113--h81a5ba2_0' }"
+
+    input:
+    tuple val(meta), path(bam)
+    path(index)
+
+    output:
+    tuple val(meta), path("*.txt"), emit: biscuit_qc_reports
+    path "versions.yml"           , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    def se = meta.single_end ? "-s" : ""
+    """
+    INDEX=`find -L ./ -name "*.bis.amb" | sed 's/.bis.amb//'`
+
+    biscuit qc \\
+        $args \\
+        $se \\
+        \$INDEX \\
+        $bam \\
+        $prefix
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        biscuit: \$( biscuit version |& sed '1!d; s/^.*BISCUIT Version: //' )
+    END_VERSIONS
+    """
+}

modules/biscuit/qc/meta.yml

@@ -0,0 +1,51 @@
+name: biscuit_qc
+description: Perform basic quality control on a BAM file generated with Biscuit
+keywords:
+  - biscuit
+  - DNA methylation
+  - WGBS
+  - scWGBS
+  - bisulfite sequencing
+  - index
+  - BAM
+  - quality control
+
+tools:
+  - biscuit:
+      description: A utility for analyzing sodium bisulfite conversion-based DNA methylation/modification data
+      homepage: https://huishenlab.github.io/biscuit/
+      documentation: https://huishenlab.github.io/biscuit/docs/subcommand_help.html#biscuit-qc
+      tool_dev_url: https://github.com/huishenlab/biscuit
+      doi: ""
+      licence: ["MIT"]
+
+input:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  - bam:
+      type: file
+      description: BAM file produced using Biscuit
+
+output:
+  - biscuit_qc_reports:
+      type: file
+      description: |
+        Summary files containing the following information:
+          - CpG retention by position in read
+          - CpH retention by position in read
+          - Read duplication statistics
+          - Insert size distribution
+          - Distribution of mapping qualities
+          - Proportion of reads mapping to each strand
+          - Read-averaged cytosine conversion rate for CpA, CpC, CpG, and CpT
+      pattern: "*.txt"
+  - versions:
+      type: file
+      description: File containing software versions
+      pattern: "versions.yml"
+
+authors:
+  - "@njspix"

modules/biscuit/vcf2bed/main.nf

@@ -0,0 +1,39 @@
+process BISCUIT_VCF2BED {
+    tag "$meta.id"
+    label 'process_long'
+
+    conda (params.enable_conda ? "bioconda::biscuit=1.0.2.20220113 bioconda::samtools=1.15" : null)
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/mulled-v2-db16f1c237a26ea9245cf9924f858974ff321d6e:17fa66297f088a1bc7560b7b90dc273bf23f2d8c-0':
+        'quay.io/biocontainers/mulled-v2-db16f1c237a26ea9245cf9924f858974ff321d6e:17fa66297f088a1bc7560b7b90dc273bf23f2d8c-0' }"
+
+    input:
+    tuple val(meta), path(vcf)
+
+    output:
+    tuple val(meta), path("*.bed.gz"), emit: bed
+    path "versions.yml"              , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args = task.ext.args ?: ''
+    def args2 = task.ext.args2 ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    biscuit vcf2bed \\
+        $args \\
+        $vcf | \\
+    LC_ALL=C sort -k1,1 -k2,2n | \\
+    bgzip \\
+        $args2 \\
+        -c > ${prefix}.bed.gz
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        biscuit: \$(echo \$(biscuit version 2>&1) | sed 's/^.*BISCUIT Version: //; s/Using.*\$//')
+        samtools: \$( samtools --version |& sed '1!d; s/^.*samtools //' )
+    END_VERSIONS
+    """
+}

modules/biscuit/vcf2bed/meta.yml

@@ -0,0 +1,48 @@
+name: biscuit_vcf2bed
+description: |
+  Summarizes methylation or SNV information from a Biscuit VCF in a
+  standard-compliant BED file.
+keywords:
+  - biscuit
+  - DNA methylation
+  - WGBS
+  - scWGBS
+  - bisulfite sequencing
+  - aligner
+  - vcf
+tools:
+  - biscuit:
+      description: A utility for analyzing sodium bisulfite conversion-based DNA methylation/modification data
+      homepage: https://huishenlab.github.io/biscuit/
+      documentation: https://huishenlab.github.io/biscuit/docs/methylextraction.html
+      tool_dev_url: https://github.com/huishenlab/biscuit
+      doi: ""
+      licence: ["MIT"]
+
+input:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  - vcf:
+      type: file
+      description: Biscuit vcf file (output of biscuit pileup)
+
+output:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  - bed:
+      type: file
+      description: Gzipped BED file with methylation or SNV information
+      pattern: "*.{bed.gz}"
+  - versions:
+      type: file
+      description: File containing software versions
+      pattern: "versions.yml"
+
+authors:
+  - "@njspix"

tests/config/nextflow.config

@@ -28,5 +28,5 @@ conda { createTimeout = "120 min" }
 includeConfig 'test_data.config'
 
 manifest {
-    nextflowVersion = '!>=21.10.3'
+    nextflowVersion = '!>=21.10.0'
 }

tests/config/pytest_modules.yml

@@ -198,6 +198,49 @@ bedtools/subtract:
   - modules/bedtools/subtract/**
   - tests/modules/bedtools/subtract/**
 
+biscuit/align:
+  - modules/biscuit/index/**
+  - modules/biscuit/align/**
+  - tests/modules/biscuit/align/**
+
+biscuit/biscuitblaster:
+  - modules/biscuit/index/**
+  - modules/biscuit/biscuitblaster/**
+  - tests/modules/biscuit/biscuitblaster/**
+
+biscuit/bsconv:
+  - modules/biscuit/index/**
+  - modules/biscuit/bsconv/**
+  - tests/modules/biscuit/bsconv/**
+
+biscuit/epiread:
+  - modules/biscuit/index/**
+  - modules/biscuit/epiread/**
+  - tests/modules/biscuit/epiread/**
+
+biscuit/index:
+  - modules/biscuit/index/**
+  - tests/modules/biscuit/index/**
+
+biscuit/mergecg:
+  - modules/biscuit/index/**
+  - modules/biscuit/mergecg/**
+  - tests/modules/biscuit/mergecg/**
+
+biscuit/pileup:
+  - modules/biscuit/index/**
+  - modules/biscuit/pileup/**
+  - tests/modules/biscuit/pileup/**
+
+biscuit/qc:
+  - modules/biscuit/index/**
+  - modules/biscuit/qc/**
+  - tests/modules/biscuit/qc/**
+
+biscuit/vcf2bed:
+  - modules/biscuit/vcf2bed/**
+  - tests/modules/biscuit/vcf2bed/**
+
 biobambam/bammarkduplicates2:
   - modules/biobambam/bammarkduplicates2/**
   - tests/modules/biobambam/bammarkduplicates2/**

tests/modules/biscuit/align/main.nf

@@ -0,0 +1,33 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { BISCUIT_INDEX }                     from '../../../../modules/biscuit/index/main.nf'
+include { BISCUIT_ALIGN as BISCUIT_ALIGN_SE } from '../../../../modules/biscuit/align/main.nf'
+include { BISCUIT_ALIGN as BISCUIT_ALIGN_PE } from '../../../../modules/biscuit/align/main.nf'
+
+
+// Single-end test
+workflow test_biscuit_align_single {
+
+    input = [ [ id:'test' ], // meta map
+              [ file(params.test_data['sarscov2']['illumina']['test_methylated_1_fastq_gz'], checkIfExists: true) ]
+            ]
+    fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
+
+    BISCUIT_INDEX ( fasta )
+    BISCUIT_ALIGN_SE (input, BISCUIT_INDEX.out.index )
+}
+
+// paired-end test
+workflow test_biscuit_align_paired {
+
+    input = [ [ id:'test' ], // meta map
+              [ file(params.test_data['sarscov2']['illumina']['test_methylated_1_fastq_gz'], checkIfExists: true),
+                file(params.test_data['sarscov2']['illumina']['test_methylated_2_fastq_gz'], checkIfExists: true) ]
+            ]
+    fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
+
+    BISCUIT_INDEX ( fasta )
+    BISCUIT_ALIGN_SE (input, BISCUIT_INDEX.out.index )
+}

tests/modules/biscuit/align/nextflow.config

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

tests/modules/biscuit/align/test.yml

@@ -0,0 +1,53 @@
+- name: biscuit align test_biscuit_align_single
+  command: nextflow run tests/modules/biscuit/align -entry test_biscuit_align_single -c tests/config/nextflow.config
+  tags:
+    - biscuit
+    - biscuit/align
+  files:
+    - path: output/biscuit/BiscuitIndex/genome.fasta
+      md5sum: 6e9fe4042a72f2345f644f239272b7e6
+    - path: output/biscuit/BiscuitIndex/genome.fasta.bis.amb
+      md5sum: 3a68b8b2287e07dd3f5f95f4344ba76e
+    - path: output/biscuit/BiscuitIndex/genome.fasta.bis.ann
+      md5sum: c32e11f6c859f166c7525a9c1d583567
+    - path: output/biscuit/BiscuitIndex/genome.fasta.bis.pac
+      md5sum: 983e3d2cd6f36e2546e6d25a0da78d66
+    - path: output/biscuit/BiscuitIndex/genome.fasta.dau.bwt
+      md5sum: a11bc31775f7b7a4f9cd3bc4f981661a
+    - path: output/biscuit/BiscuitIndex/genome.fasta.dau.sa
+      md5sum: 9c9e07fa1c75ef32d764274579c89b08
+    - path: output/biscuit/BiscuitIndex/genome.fasta.par.bwt
+      md5sum: 62eb83cd557a47b59589713d98024fc2
+    - path: output/biscuit/BiscuitIndex/genome.fasta.par.sa
+      md5sum: 55bcd97d7059bf73dc0d221e36e8e901
+    - path: output/biscuit/test.bam
+      md5sum: eb36532425cb9b259410d6464a9e523a
+    - path: output/biscuit/versions.yml
+      md5sum: a86c4170bbf90cc75b93eb59ea124acd
+
+- name: biscuit align test_biscuit_align_paired
+  command: nextflow run tests/modules/biscuit/align -entry test_biscuit_align_paired -c tests/config/nextflow.config
+  tags:
+    - biscuit
+    - biscuit/align
+  files:
+    - path: output/biscuit/BiscuitIndex/genome.fasta
+      md5sum: 6e9fe4042a72f2345f644f239272b7e6
+    - path: output/biscuit/BiscuitIndex/genome.fasta.bis.amb
+      md5sum: 3a68b8b2287e07dd3f5f95f4344ba76e
+    - path: output/biscuit/BiscuitIndex/genome.fasta.bis.ann
+      md5sum: c32e11f6c859f166c7525a9c1d583567
+    - path: output/biscuit/BiscuitIndex/genome.fasta.bis.pac
+      md5sum: 983e3d2cd6f36e2546e6d25a0da78d66
+    - path: output/biscuit/BiscuitIndex/genome.fasta.dau.bwt
+      md5sum: a11bc31775f7b7a4f9cd3bc4f981661a
+    - path: output/biscuit/BiscuitIndex/genome.fasta.dau.sa
+      md5sum: 9c9e07fa1c75ef32d764274579c89b08
+    - path: output/biscuit/BiscuitIndex/genome.fasta.par.bwt
+      md5sum: 62eb83cd557a47b59589713d98024fc2
+    - path: output/biscuit/BiscuitIndex/genome.fasta.par.sa
+      md5sum: 55bcd97d7059bf73dc0d221e36e8e901
+    - path: output/biscuit/test.bam
+      md5sum: be3f6aa86c499d6a6b2996e5936e4f50
+    - path: output/biscuit/versions.yml
+      md5sum: f0b7dffd28f5e6bb1466fce6661d133f

tests/modules/biscuit/biscuitblaster/main.nf

@@ -0,0 +1,32 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { BISCUIT_INDEX                         } from '../../../../modules/biscuit/index/main.nf'
+include { BISCUIT_BLASTER as BISCUIT_BLASTER_SE } from '../../../../modules/biscuit/biscuitblaster/main.nf'
+include { BISCUIT_BLASTER as BISCUIT_BLASTER_PE } from '../../../../modules/biscuit/biscuitblaster/main.nf'
+
+// Single-end test
+workflow test_biscuit_blaster_single {
+
+    input = [ [ id:'test' ], // meta map
+              [ file(params.test_data['sarscov2']['illumina']['test_methylated_1_fastq_gz'], checkIfExists: true) ]
+            ]
+    fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
+
+    BISCUIT_INDEX ( fasta )
+    BISCUIT_BLASTER_SE (input, BISCUIT_INDEX.out.index )
+}
+
+// paired-end test
+workflow test_biscuit_blaster_paired {
+
+    input = [ [ id:'test' ], // meta map
+              [ file(params.test_data['sarscov2']['illumina']['test_methylated_1_fastq_gz'], checkIfExists: true),
+                file(params.test_data['sarscov2']['illumina']['test_methylated_2_fastq_gz'], checkIfExists: true) ]
+            ]
+    fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
+
+    BISCUIT_INDEX ( fasta )
+    BISCUIT_BLASTER_PE (input, BISCUIT_INDEX.out.index )
+}

tests/modules/biscuit/biscuitblaster/nextflow.config

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

tests/modules/biscuit/biscuitblaster/test.yml

@@ -0,0 +1,57 @@
+- name: biscuit biscuitblaster test_biscuit_blaster_single
+  command: nextflow run tests/modules/biscuit/biscuitblaster -entry test_biscuit_blaster_single -c tests/config/nextflow.config
+  tags:
+    - biscuit/biscuitblaster
+    - biscuit
+  files:
+    - path: output/biscuit/BiscuitIndex/genome.fasta
+      md5sum: 6e9fe4042a72f2345f644f239272b7e6
+    - path: output/biscuit/BiscuitIndex/genome.fasta.bis.amb
+      md5sum: 3a68b8b2287e07dd3f5f95f4344ba76e
+    - path: output/biscuit/BiscuitIndex/genome.fasta.bis.ann
+      md5sum: c32e11f6c859f166c7525a9c1d583567
+    - path: output/biscuit/BiscuitIndex/genome.fasta.bis.pac
+      md5sum: 983e3d2cd6f36e2546e6d25a0da78d66
+    - path: output/biscuit/BiscuitIndex/genome.fasta.dau.bwt
+      md5sum: a11bc31775f7b7a4f9cd3bc4f981661a
+    - path: output/biscuit/BiscuitIndex/genome.fasta.dau.sa
+      md5sum: 9c9e07fa1c75ef32d764274579c89b08
+    - path: output/biscuit/BiscuitIndex/genome.fasta.par.bwt
+      md5sum: 62eb83cd557a47b59589713d98024fc2
+    - path: output/biscuit/BiscuitIndex/genome.fasta.par.sa
+      md5sum: 55bcd97d7059bf73dc0d221e36e8e901
+    - path: output/biscuit/test.bam
+      md5sum: 9ece50b67349382d38b20c2702e65675
+    - path: output/biscuit/test.bam.bai
+      md5sum: 8f14bb42fd38cc7ce4a3c3a9d7133ea4
+    - path: output/biscuit/versions.yml
+      md5sum: bfb660b5b0d92dde6817a1c6a2a302bb
+
+- name: biscuit biscuitblaster test_biscuit_blaster_paired
+  command: nextflow run tests/modules/biscuit/biscuitblaster -entry test_biscuit_blaster_paired -c tests/config/nextflow.config
+  tags:
+    - biscuit/biscuitblaster
+    - biscuit
+  files:
+    - path: output/biscuit/BiscuitIndex/genome.fasta
+      md5sum: 6e9fe4042a72f2345f644f239272b7e6
+    - path: output/biscuit/BiscuitIndex/genome.fasta.bis.amb
+      md5sum: 3a68b8b2287e07dd3f5f95f4344ba76e
+    - path: output/biscuit/BiscuitIndex/genome.fasta.bis.ann
+      md5sum: c32e11f6c859f166c7525a9c1d583567
+    - path: output/biscuit/BiscuitIndex/genome.fasta.bis.pac
+      md5sum: 983e3d2cd6f36e2546e6d25a0da78d66
+    - path: output/biscuit/BiscuitIndex/genome.fasta.dau.bwt
+      md5sum: a11bc31775f7b7a4f9cd3bc4f981661a
+    - path: output/biscuit/BiscuitIndex/genome.fasta.dau.sa
+      md5sum: 9c9e07fa1c75ef32d764274579c89b08
+    - path: output/biscuit/BiscuitIndex/genome.fasta.par.bwt
+      md5sum: 62eb83cd557a47b59589713d98024fc2
+    - path: output/biscuit/BiscuitIndex/genome.fasta.par.sa
+      md5sum: 55bcd97d7059bf73dc0d221e36e8e901
+    - path: output/biscuit/test.bam
+      md5sum: 0c6de35f38003df6ea5dd036170df91b
+    - path: output/biscuit/test.bam.bai
+      md5sum: 0d76977b2e36046cc176112776c5fa4e
+    - path: output/biscuit/versions.yml
+      md5sum: 82160a7ad29ccc3a21e59b1869399c04

tests/modules/biscuit/bsconv/main.nf

@@ -0,0 +1,19 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { BISCUIT_INDEX  } from '../../../../modules/biscuit/index/main.nf'
+include { BISCUIT_BSCONV } from '../../../../modules/biscuit/bsconv/main.nf'
+
+workflow test_biscuit_bsconv {
+
+    input = [
+        [ id:'test', single_end:false ], // meta map
+        file(params.test_data['sarscov2']['illumina']['test_paired_end_methylated_sorted_bam'], checkIfExists: true),
+        file(params.test_data['sarscov2']['illumina']['test_paired_end_methylated_sorted_bam_bai'], checkIfExists: true)
+    ]
+    fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
+
+    BISCUIT_INDEX( fasta )
+    BISCUIT_BSCONV ( input, BISCUIT_INDEX.out.index )
+}

tests/modules/biscuit/bsconv/nextflow.config

@@ -0,0 +1,10 @@
+process {
+
+    publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+    withName: '.*BISCUIT_BSCONV' {
+        ext.args = '-f 0.1'
+    }
+
+}
+

tests/modules/biscuit/bsconv/test.yml

@@ -0,0 +1,26 @@
+- name: biscuit bsconv test_biscuit_bsconv
+  command: nextflow run tests/modules/biscuit/bsconv -entry test_biscuit_bsconv -c tests/config/nextflow.config
+  tags:
+    - biscuit
+    - biscuit/bsconv
+  files:
+    - path: output/biscuit/BiscuitIndex/genome.fasta
+      md5sum: 6e9fe4042a72f2345f644f239272b7e6
+    - path: output/biscuit/BiscuitIndex/genome.fasta.bis.amb
+      md5sum: 3a68b8b2287e07dd3f5f95f4344ba76e
+    - path: output/biscuit/BiscuitIndex/genome.fasta.bis.ann
+      md5sum: c32e11f6c859f166c7525a9c1d583567
+    - path: output/biscuit/BiscuitIndex/genome.fasta.bis.pac
+      md5sum: 983e3d2cd6f36e2546e6d25a0da78d66
+    - path: output/biscuit/BiscuitIndex/genome.fasta.dau.bwt
+      md5sum: a11bc31775f7b7a4f9cd3bc4f981661a
+    - path: output/biscuit/BiscuitIndex/genome.fasta.dau.sa
+      md5sum: 9c9e07fa1c75ef32d764274579c89b08
+    - path: output/biscuit/BiscuitIndex/genome.fasta.par.bwt
+      md5sum: 62eb83cd557a47b59589713d98024fc2
+    - path: output/biscuit/BiscuitIndex/genome.fasta.par.sa
+      md5sum: 55bcd97d7059bf73dc0d221e36e8e901
+    - path: output/biscuit/test.bam
+      md5sum: e33e9498d00dd32222b90a6bd981226f
+    - path: output/biscuit/versions.yml
+      md5sum: 7deec1f096203542bbb72ac4fa05f9ba

tests/modules/biscuit/epiread/main.nf

@@ -0,0 +1,48 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { BISCUIT_INDEX   } from '../../../../modules/biscuit/index/main.nf'
+include { BISCUIT_EPIREAD } from '../../../../modules/biscuit/epiread/main.nf'
+
+workflow test_biscuit_epiread_nosnp {
+
+    input = [
+        [ id:'test', single_end:false ], // meta map
+        file(params.test_data['sarscov2']['illumina']['test_paired_end_methylated_sorted_bam'], checkIfExists: true),
+        file(params.test_data['sarscov2']['illumina']['test_paired_end_methylated_sorted_bam_bai'], checkIfExists: true),
+        [] //SNP BED file
+    ]
+    fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
+
+    BISCUIT_INDEX( fasta )
+    BISCUIT_EPIREAD ( input, BISCUIT_INDEX.out.index )
+}
+
+workflow test_biscuit_epiread_snp {
+
+    input = [
+        [ id:'test', single_end:false ], // meta map
+        file(params.test_data['sarscov2']['illumina']['test_paired_end_methylated_sorted_bam'], checkIfExists: true),
+        file(params.test_data['sarscov2']['illumina']['test_paired_end_methylated_sorted_bam_bai'], checkIfExists: true),
+        file('https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/biscuit/test-snp.bed')
+    ]
+    fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
+
+    BISCUIT_INDEX( fasta )
+    BISCUIT_EPIREAD ( input, BISCUIT_INDEX.out.index )
+}
+
+workflow test_biscuit_epiread_snp_decompress {
+
+    input = [
+        [ id:'test', single_end:false ], // meta map
+        file(params.test_data['sarscov2']['illumina']['test_paired_end_methylated_sorted_bam'], checkIfExists: true),
+        file(params.test_data['sarscov2']['illumina']['test_paired_end_methylated_sorted_bam_bai'], checkIfExists: true),
+        file('https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/biscuit/test-snp.bed.gz')
+    ]
+    fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
+
+    BISCUIT_INDEX( fasta )
+    BISCUIT_EPIREAD ( input, BISCUIT_INDEX.out.index )
+}

tests/modules/biscuit/epiread/nextflow.config

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

tests/modules/biscuit/epiread/test.yml

@@ -0,0 +1,80 @@
+- name: biscuit epiread test_biscuit_epiread_nosnp
+  command: nextflow run tests/modules/biscuit/epiread -entry test_biscuit_epiread_nosnp -c tests/config/nextflow.config
+  tags:
+    - biscuit
+    - biscuit/epiread
+  files:
+    - path: output/biscuit/BiscuitIndex/genome.fasta
+      md5sum: 6e9fe4042a72f2345f644f239272b7e6
+    - path: output/biscuit/BiscuitIndex/genome.fasta.bis.amb
+      md5sum: 3a68b8b2287e07dd3f5f95f4344ba76e
+    - path: output/biscuit/BiscuitIndex/genome.fasta.bis.ann
+      md5sum: c32e11f6c859f166c7525a9c1d583567
+    - path: output/biscuit/BiscuitIndex/genome.fasta.bis.pac
+      md5sum: 983e3d2cd6f36e2546e6d25a0da78d66
+    - path: output/biscuit/BiscuitIndex/genome.fasta.dau.bwt
+      md5sum: a11bc31775f7b7a4f9cd3bc4f981661a
+    - path: output/biscuit/BiscuitIndex/genome.fasta.dau.sa
+      md5sum: 9c9e07fa1c75ef32d764274579c89b08
+    - path: output/biscuit/BiscuitIndex/genome.fasta.par.bwt
+      md5sum: 62eb83cd557a47b59589713d98024fc2
+    - path: output/biscuit/BiscuitIndex/genome.fasta.par.sa
+      md5sum: 55bcd97d7059bf73dc0d221e36e8e901
+    - path: output/biscuit/test.bed.gz
+      md5sum: dbb30b59f4ef6fdfdee38630225c0574
+    - path: output/biscuit/versions.yml
+      md5sum: 674a77ac5ca8f4b42d30e58e30c3a9af
+
+- name: biscuit epiread test_biscuit_epiread_snp
+  command: nextflow run tests/modules/biscuit/epiread -entry test_biscuit_epiread_snp -c tests/config/nextflow.config
+  tags:
+    - biscuit
+    - biscuit/epiread
+  files:
+    - path: output/biscuit/BiscuitIndex/genome.fasta
+      md5sum: 6e9fe4042a72f2345f644f239272b7e6
+    - path: output/biscuit/BiscuitIndex/genome.fasta.bis.amb
+      md5sum: 3a68b8b2287e07dd3f5f95f4344ba76e
+    - path: output/biscuit/BiscuitIndex/genome.fasta.bis.ann
+      md5sum: c32e11f6c859f166c7525a9c1d583567
+    - path: output/biscuit/BiscuitIndex/genome.fasta.bis.pac
+      md5sum: 983e3d2cd6f36e2546e6d25a0da78d66
+    - path: output/biscuit/BiscuitIndex/genome.fasta.dau.bwt
+      md5sum: a11bc31775f7b7a4f9cd3bc4f981661a
+    - path: output/biscuit/BiscuitIndex/genome.fasta.dau.sa
+      md5sum: 9c9e07fa1c75ef32d764274579c89b08
+    - path: output/biscuit/BiscuitIndex/genome.fasta.par.bwt
+      md5sum: 62eb83cd557a47b59589713d98024fc2
+    - path: output/biscuit/BiscuitIndex/genome.fasta.par.sa
+      md5sum: 55bcd97d7059bf73dc0d221e36e8e901
+    - path: output/biscuit/test.bed.gz
+      md5sum: a29fea6ad74453ec94f8220747dab906
+    - path: output/biscuit/versions.yml
+      md5sum: f2f7c4ff3c6a135b1c8a3aff24a44d81
+
+- name: biscuit epiread test_biscuit_epiread_snp_decompress
+  command: nextflow run tests/modules/biscuit/epiread -entry test_biscuit_epiread_snp_decompress -c tests/config/nextflow.config
+  tags:
+    - biscuit
+    - biscuit/epiread
+  files:
+    - path: output/biscuit/BiscuitIndex/genome.fasta
+      md5sum: 6e9fe4042a72f2345f644f239272b7e6
+    - path: output/biscuit/BiscuitIndex/genome.fasta.bis.amb
+      md5sum: 3a68b8b2287e07dd3f5f95f4344ba76e
+    - path: output/biscuit/BiscuitIndex/genome.fasta.bis.ann
+      md5sum: c32e11f6c859f166c7525a9c1d583567
+    - path: output/biscuit/BiscuitIndex/genome.fasta.bis.pac
+      md5sum: 983e3d2cd6f36e2546e6d25a0da78d66
+    - path: output/biscuit/BiscuitIndex/genome.fasta.dau.bwt
+      md5sum: a11bc31775f7b7a4f9cd3bc4f981661a
+    - path: output/biscuit/BiscuitIndex/genome.fasta.dau.sa
+      md5sum: 9c9e07fa1c75ef32d764274579c89b08
+    - path: output/biscuit/BiscuitIndex/genome.fasta.par.bwt
+      md5sum: 62eb83cd557a47b59589713d98024fc2
+    - path: output/biscuit/BiscuitIndex/genome.fasta.par.sa
+      md5sum: 55bcd97d7059bf73dc0d221e36e8e901
+    - path: output/biscuit/test.bed.gz
+      md5sum: a29fea6ad74453ec94f8220747dab906
+    - path: output/biscuit/versions.yml
+      md5sum: cb0258ebf4e1a731a4310ec17c3dc442

tests/modules/biscuit/index/main.nf

@@ -0,0 +1,12 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { BISCUIT_INDEX } from '../../../../modules/biscuit/index/main.nf'
+
+workflow test_biscuit_index {
+
+    fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
+
+    BISCUIT_INDEX ( fasta )
+}

tests/modules/biscuit/index/nextflow.config

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

tests/modules/biscuit/index/test.yml

@@ -0,0 +1,24 @@
+- name: biscuit index test_biscuit_index
+  command: nextflow run tests/modules/biscuit/index -entry test_biscuit_index -c tests/config/nextflow.config
+  tags:
+    - biscuit/index
+    - biscuit
+  files:
+    - path: output/biscuit/BiscuitIndex/genome.fasta
+      md5sum: 6e9fe4042a72f2345f644f239272b7e6
+    - path: output/biscuit/BiscuitIndex/genome.fasta.bis.amb
+      md5sum: 3a68b8b2287e07dd3f5f95f4344ba76e
+    - path: output/biscuit/BiscuitIndex/genome.fasta.bis.ann
+      md5sum: c32e11f6c859f166c7525a9c1d583567
+    - path: output/biscuit/BiscuitIndex/genome.fasta.bis.pac
+      md5sum: 983e3d2cd6f36e2546e6d25a0da78d66
+    - path: output/biscuit/BiscuitIndex/genome.fasta.dau.bwt
+      md5sum: a11bc31775f7b7a4f9cd3bc4f981661a
+    - path: output/biscuit/BiscuitIndex/genome.fasta.dau.sa
+      md5sum: 9c9e07fa1c75ef32d764274579c89b08
+    - path: output/biscuit/BiscuitIndex/genome.fasta.par.bwt
+      md5sum: 62eb83cd557a47b59589713d98024fc2
+    - path: output/biscuit/BiscuitIndex/genome.fasta.par.sa
+      md5sum: 55bcd97d7059bf73dc0d221e36e8e901
+    - path: output/biscuit/versions.yml
+      md5sum: 5c5873e482a57966db246648ffddf62f

tests/modules/biscuit/mergecg/main.nf

@@ -0,0 +1,18 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { BISCUIT_INDEX   } from '../../../../modules/biscuit/index/main.nf'
+include { BISCUIT_MERGECG } from '../../../../modules/biscuit/mergecg/main.nf'
+
+workflow test_biscuit_mergecg {
+
+    input = [
+        [ id:'test', single_end:false ], // meta map
+        file('https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/biscuit/test-cg.bed.gz', checkIfExists: true)
+    ]
+    fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
+
+    BISCUIT_INDEX( fasta )
+    BISCUIT_MERGECG ( input, BISCUIT_INDEX.out.index )
+}

tests/modules/biscuit/mergecg/nextflow.config

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

tests/modules/biscuit/mergecg/test.yml

@@ -0,0 +1,26 @@
+- name: biscuit mergecg test_biscuit_mergecg
+  command: nextflow run tests/modules/biscuit/mergecg -entry test_biscuit_mergecg -c tests/config/nextflow.config
+  tags:
+    - biscuit
+    - biscuit/mergecg
+  files:
+    - path: output/biscuit/BiscuitIndex/genome.fasta
+      md5sum: 6e9fe4042a72f2345f644f239272b7e6
+    - path: output/biscuit/BiscuitIndex/genome.fasta.bis.amb
+      md5sum: 3a68b8b2287e07dd3f5f95f4344ba76e
+    - path: output/biscuit/BiscuitIndex/genome.fasta.bis.ann
+      md5sum: c32e11f6c859f166c7525a9c1d583567
+    - path: output/biscuit/BiscuitIndex/genome.fasta.bis.pac
+      md5sum: 983e3d2cd6f36e2546e6d25a0da78d66
+    - path: output/biscuit/BiscuitIndex/genome.fasta.dau.bwt
+      md5sum: a11bc31775f7b7a4f9cd3bc4f981661a
+    - path: output/biscuit/BiscuitIndex/genome.fasta.dau.sa
+      md5sum: 9c9e07fa1c75ef32d764274579c89b08
+    - path: output/biscuit/BiscuitIndex/genome.fasta.par.bwt
+      md5sum: 62eb83cd557a47b59589713d98024fc2
+    - path: output/biscuit/BiscuitIndex/genome.fasta.par.sa
+      md5sum: 55bcd97d7059bf73dc0d221e36e8e901
+    - path: output/biscuit/test.bed.gz
+      md5sum: d693b28ddc81265f388860d391fc7c5b
+    - path: output/biscuit/versions.yml
+      md5sum: f670d63671af06bf8654677bf373b3a1

tests/modules/biscuit/pileup/main.nf

@@ -0,0 +1,38 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { BISCUIT_INDEX  } from '../../../../modules/biscuit/index/main.nf'
+include { BISCUIT_PILEUP } from '../../../../modules/biscuit/pileup/main.nf'
+
+workflow test_biscuit_pileup {
+
+    input = [ [ id:'test' ], // meta map
+        [file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true),
+        file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_sorted_bam'], checkIfExists: true)],
+        [file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true),
+        file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_sorted_bam_bai'], checkIfExists: true)],    
+	[], //tumor bam 
+	[] //tumor bai
+        ]
+    fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
+
+    BISCUIT_INDEX ( fasta )
+    BISCUIT_PILEUP ( input, BISCUIT_INDEX.out.index )
+
+}
+
+workflow test_biscuit_pileup_somatic {
+
+    input = [ [ id:'test' ], // meta map
+        file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true),
+        file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true),
+        file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_sorted_bam'], checkIfExists: true),
+        file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_sorted_bam_bai'], checkIfExists: true)    
+        ]
+    fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
+
+    BISCUIT_INDEX ( fasta )
+    BISCUIT_PILEUP ( input, BISCUIT_INDEX.out.index )
+
+}

tests/modules/biscuit/pileup/nextflow.config

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

tests/modules/biscuit/pileup/test.yml

@@ -0,0 +1,53 @@
+- name: biscuit pileup test_biscuit_pileup
+  command: nextflow run tests/modules/biscuit/pileup -entry test_biscuit_pileup -c tests/config/nextflow.config
+  tags:
+    - biscuit
+    - biscuit/pileup
+  files:
+    - path: output/biscuit/BiscuitIndex/genome.fasta
+      md5sum: f315020d899597c1b57e5fe9f60f4c3e
+    - path: output/biscuit/BiscuitIndex/genome.fasta.bis.amb
+      md5sum: 1891c1de381b3a96d4e72f590fde20c1
+    - path: output/biscuit/BiscuitIndex/genome.fasta.bis.ann
+      md5sum: 2df4aa2d7580639fa0fcdbcad5e2e969
+    - path: output/biscuit/BiscuitIndex/genome.fasta.bis.pac
+      md5sum: 8569fbdb2c98c6fb16dfa73d8eacb070
+    - path: output/biscuit/BiscuitIndex/genome.fasta.dau.bwt
+      md5sum: 668799eea40aefb8013cbf8ed6c47cfe
+    - path: output/biscuit/BiscuitIndex/genome.fasta.dau.sa
+      md5sum: 10541b05bbea44d0344b0345a6522ba8
+    - path: output/biscuit/BiscuitIndex/genome.fasta.par.bwt
+      md5sum: 2c38edd64234420add133f5fe1ff975d
+    - path: output/biscuit/BiscuitIndex/genome.fasta.par.sa
+      md5sum: 7deee1aac3395d93bef1df11ab38379e
+    - path: output/biscuit/test.vcf.gz
+      md5sum: ef9798c318ead0f8a79ee7fdeb1ffbf9
+    - path: output/biscuit/versions.yml
+      md5sum: ae38b891fdbf9f7ff5c486408f949dc5
+
+- name: biscuit pileup test_biscuit_pileup_somatic
+  command: nextflow run tests/modules/biscuit/pileup -entry test_biscuit_pileup_somatic -c tests/config/nextflow.config
+  tags:
+    - biscuit
+    - biscuit/pileup
+  files:
+    - path: output/biscuit/BiscuitIndex/genome.fasta
+      md5sum: f315020d899597c1b57e5fe9f60f4c3e
+    - path: output/biscuit/BiscuitIndex/genome.fasta.bis.amb
+      md5sum: 1891c1de381b3a96d4e72f590fde20c1
+    - path: output/biscuit/BiscuitIndex/genome.fasta.bis.ann
+      md5sum: 2df4aa2d7580639fa0fcdbcad5e2e969
+    - path: output/biscuit/BiscuitIndex/genome.fasta.bis.pac
+      md5sum: 8569fbdb2c98c6fb16dfa73d8eacb070
+    - path: output/biscuit/BiscuitIndex/genome.fasta.dau.bwt
+      md5sum: 668799eea40aefb8013cbf8ed6c47cfe
+    - path: output/biscuit/BiscuitIndex/genome.fasta.dau.sa
+      md5sum: 10541b05bbea44d0344b0345a6522ba8
+    - path: output/biscuit/BiscuitIndex/genome.fasta.par.bwt
+      md5sum: 2c38edd64234420add133f5fe1ff975d
+    - path: output/biscuit/BiscuitIndex/genome.fasta.par.sa
+      md5sum: 7deee1aac3395d93bef1df11ab38379e
+    - path: output/biscuit/test.vcf.gz
+      md5sum: 692b4a6191b08fabe5efa5abe00da420
+    - path: output/biscuit/versions.yml
+      md5sum: cc51fd498d67fdc7cc067686eb855b93

tests/modules/biscuit/qc/main.nf

@@ -0,0 +1,18 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { BISCUIT_INDEX  } from '../../../../modules/biscuit/index/main.nf'
+include { BISCUIT_QC } from '../../../../modules/biscuit/qc/main.nf'
+
+workflow test_biscuit_qc {
+
+    input = [
+        [ id:'test', single_end:false ], // meta map
+        file(params.test_data['sarscov2']['illumina']['test_paired_end_methylated_sorted_bam'], checkIfExists: true)
+    ]
+    fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
+
+    BISCUIT_INDEX( fasta )
+    BISCUIT_QC ( input, BISCUIT_INDEX.out.index )
+}

tests/modules/biscuit/qc/nextflow.config

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

tests/modules/biscuit/qc/test.yml

@@ -0,0 +1,38 @@
+- name: biscuit qc test_biscuit_qc
+  command: nextflow run tests/modules/biscuit/qc -entry test_biscuit_qc -c tests/config/nextflow.config
+  tags:
+    - biscuit/qc
+    - biscuit
+  files:
+    - path: output/biscuit/BiscuitIndex/genome.fasta
+      md5sum: 6e9fe4042a72f2345f644f239272b7e6
+    - path: output/biscuit/BiscuitIndex/genome.fasta.bis.amb
+      md5sum: 3a68b8b2287e07dd3f5f95f4344ba76e
+    - path: output/biscuit/BiscuitIndex/genome.fasta.bis.ann
+      md5sum: c32e11f6c859f166c7525a9c1d583567
+    - path: output/biscuit/BiscuitIndex/genome.fasta.bis.pac
+      md5sum: 983e3d2cd6f36e2546e6d25a0da78d66
+    - path: output/biscuit/BiscuitIndex/genome.fasta.dau.bwt
+      md5sum: a11bc31775f7b7a4f9cd3bc4f981661a
+    - path: output/biscuit/BiscuitIndex/genome.fasta.dau.sa
+      md5sum: 9c9e07fa1c75ef32d764274579c89b08
+    - path: output/biscuit/BiscuitIndex/genome.fasta.par.bwt
+      md5sum: 62eb83cd557a47b59589713d98024fc2
+    - path: output/biscuit/BiscuitIndex/genome.fasta.par.sa
+      md5sum: 55bcd97d7059bf73dc0d221e36e8e901
+    - path: output/biscuit/test_CpGRetentionByReadPos.txt
+      md5sum: 498b6c0af196fb34c8835371b9e9b68a
+    - path: output/biscuit/test_CpHRetentionByReadPos.txt
+      md5sum: a266942c5719cecab7f60f63cbe7335d
+    - path: output/biscuit/test_dup_report.txt
+      md5sum: 65bddf4fbe9e40d7c6c976060df53e3b
+    - path: output/biscuit/test_isize_table.txt
+      md5sum: aadf6f2e271abc334b6146cf164bdda3
+    - path: output/biscuit/test_mapq_table.txt
+      md5sum: c8adaac84bb8db3b7f48e1ed4fccad00
+    - path: output/biscuit/test_strand_table.txt
+      md5sum: 27068382ba6b2dbf313169a85c9dbb3a
+    - path: output/biscuit/test_totalReadConversionRate.txt
+      md5sum: 8f0c1fceaebfa74f2757720e3bc85fed
+    - path: output/biscuit/versions.yml
+      md5sum: a730fa4888e6882cf1b8ba92645b04ee

tests/modules/biscuit/vcf2bed/main.nf

@@ -0,0 +1,16 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { BISCUIT_VCF2BED } from '../../../../modules/biscuit/vcf2bed/main.nf'
+
+workflow test_biscuit_vcf2bed {
+
+    input = [
+        [ id:'test', single_end:false ], // meta map
+        file('https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/biscuit/test.vcf.gz', checkIfExists: true)
+    ]
+
+    BISCUIT_VCF2BED ( input )
+
+}

tests/modules/biscuit/vcf2bed/nextflow.config

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

tests/modules/biscuit/vcf2bed/test.yml

@@ -0,0 +1,10 @@
+- name: biscuit vcf2bed test_biscuit_vcf2bed
+  command: nextflow run tests/modules/biscuit/vcf2bed -entry test_biscuit_vcf2bed -c tests/config/nextflow.config
+  tags:
+    - biscuit/vcf2bed
+    - biscuit
+  files:
+    - path: output/biscuit/test.bed.gz
+      md5sum: e2dd492289dc8463f364285e31b9553a
+    - path: output/biscuit/versions.yml
+      md5sum: cd784276e2fb6739d55e1b60d12202cd