Merge branch 'nf-core:master' into master

2024-11-10 20:23:10 +00:00 · 2022-03-18 08:14:36 +01:00 · 2022-03-18 08:14:36 +01:00 · 23613051ca
commit 23613051ca
parent b101e89e32 7436eebf33
86 changed files with 2541 additions and 106 deletions
--- a/.github/workflows/pytest-workflow.yml
+++ b/.github/workflows/pytest-workflow.yml
@ -86,17 +86,13 @@ jobs:
      # Test the module
      - name: Run pytest-workflow
        # only use one thread for pytest-workflow to avoid race condition on conda cache.
-        run: TMPDIR=~ PROFILE=${{ matrix.profile }} pytest --tag ${{ matrix.tags }} --symlink --kwdof --git-aware
+        run: TMPDIR=~ PROFILE=${{ matrix.profile }} pytest --tag ${{ matrix.tags }} --symlink --kwdof --git-aware --color=yes

      - name: Output log on failure
        if: failure()
        run: |
-          echo "======> log.out <======="
-          cat /home/runner/pytest_workflow_*/*/log.out
-          echo
-          echo
-          echo "======> log.err <======="
-          cat /home/runner/pytest_workflow_*/*/log.err
+          sudo apt install bat > /dev/null
+          batcat --decorations=always --color=always /home/runner/pytest_workflow_*/*/log.{out,err}

      - name: Upload logs on failure
        if: failure()
--- a/modules/adapterremoval/main.nf
+++ b/modules/adapterremoval/main.nf
@ -9,48 +9,34 @@ process ADAPTERREMOVAL {

    input:
    tuple val(meta), path(reads)
+    path(adapterlist)

    output:
-    tuple val(meta), path('*.truncated.gz')         , optional: true, emit: singles_truncated
-    tuple val(meta), path('*.discarded.gz')         , optional: true, emit: discarded
-    tuple val(meta), path('*.pair1.truncated.gz')   , optional: true, emit: pair1_truncated
-    tuple val(meta), path('*.pair2.truncated.gz')   , optional: true, emit: pair2_truncated
-    tuple val(meta), path('*.collapsed.gz')         , optional: true, emit: collapsed
-    tuple val(meta), path('*.collapsed.truncated')  , optional: true, emit: collapsed_truncated
-    tuple val(meta), path('*paired.gz')             , optional: true, emit: paired_interleaved
-    tuple val(meta), path('*.log')                  , emit: log
-    path "versions.yml"                             , emit: versions
+    tuple val(meta), path("${prefix}.truncated.gz")            , optional: true, emit: singles_truncated
+    tuple val(meta), path("${prefix}.discarded.gz")            , optional: true, emit: discarded
+    tuple val(meta), path("${prefix}.pair1.truncated.gz")      , optional: true, emit: pair1_truncated
+    tuple val(meta), path("${prefix}.pair2.truncated.gz")      , optional: true, emit: pair2_truncated
+    tuple val(meta), path("${prefix}.collapsed.gz")            , optional: true, emit: collapsed
+    tuple val(meta), path("${prefix}.collapsed.truncated.gz")  , optional: true, emit: collapsed_truncated
+    tuple val(meta), path("${prefix}.paired.gz")               , optional: true, emit: paired_interleaved
+    tuple val(meta), path('*.log')                             , emit: log
+    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 list = adapterlist ? "--adapter-list ${adapterlist}" : ""
+    prefix = task.ext.prefix ?: "${meta.id}"

    if (meta.single_end) {
        """
        AdapterRemoval  \\
            --file1 $reads \\
            $args \\
-            --basename $prefix \\
-            --threads ${task.cpus} \\
-            --settings ${prefix}.log \\
-            --seed 42 \\
-            --gzip
-
-        cat <<-END_VERSIONS > versions.yml
-        "${task.process}":
-            adapterremoval: \$(AdapterRemoval --version 2>&1 | sed -e "s/AdapterRemoval ver. //g")
-        END_VERSIONS
-        """
-    } else if (!meta.single_end ) {
-        """
-        AdapterRemoval  \\
-            --file1 ${reads[0]} \\
-            --file2 ${reads[1]} \\
-            $args \\
-            --basename $prefix \\
+            $adapterlist \\
+            --basename ${prefix} \\
            --threads ${task.cpus} \\
            --settings ${prefix}.log \\
            --seed 42 \\
@ -67,13 +53,13 @@ process ADAPTERREMOVAL {
            --file1 ${reads[0]} \\
            --file2 ${reads[1]} \\
            $args \\
-            --basename $prefix \\
+            $adapterlist \\
+            --basename ${prefix} \\
            --threads $task.cpus \\
            --settings ${prefix}.log \\
            --seed 42 \\
            --gzip

-        cat *.collapsed.gz *.collapsed.truncated.gz > ${prefix}.merged.fastq.gz
        cat <<-END_VERSIONS > versions.yml
        "${task.process}":
            adapterremoval: \$(AdapterRemoval --version 2>&1 | sed -e "s/AdapterRemoval ver. //g")
--- a/modules/adapterremoval/meta.yml
+++ b/modules/adapterremoval/meta.yml
@ -24,6 +24,13 @@ input:
        List of input FastQ files of size 1 and 2 for single-end and paired-end data,
        respectively.
      pattern: "*.{fq,fastq,fq.gz,fastq.gz}"
+  - adapterlist:
+      type: file
+      description:
+        Optional text file containing list of adapters to look for for removal
+        with one adapter per line. Otherwise will look for default adapters (see
+        AdapterRemoval man page), or can be modified to remove user-specified
+        adapters via ext.args.

 output:
  - meta:
--- a/modules/ascat/main.nf
+++ b/modules/ascat/main.nf
@ -0,0 +1,155 @@
+process ASCAT {
+    tag "$meta.id"
+    label 'process_medium'
+
+    conda (params.enable_conda ? "bioconda::ascat=3.0.0 bioconda::cancerit-allelecount-4.3.0": null)
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/mulled-v2-c278c7398beb73294d78639a864352abef2931ce:dfe5aaa885de434adb2b490b68972c5840c6d761-0':
+        'quay.io/biocontainers/mulled-v2-c278c7398beb73294d78639a864352abef2931ce:dfe5aaa885de434adb2b490b68972c5840c6d761-0' }"
+
+    input:
+    tuple val(meta), path(input_normal), path(index_normal), path(input_tumor), path(index_tumor)
+    path(allele_files)
+    path(loci_files)
+
+    output:
+    tuple val(meta), path("*png"),               emit: png
+    tuple val(meta), path("*cnvs.txt"),          emit: cnvs
+    tuple val(meta), path("*purityploidy.txt"),  emit: purityploidy
+    tuple val(meta), path("*segments.txt"),      emit: segments
+    path "versions.yml",                         emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args           = task.ext.args        ?: ''
+    def prefix         = task.ext.prefix      ?: "${meta.id}"
+    def gender         = args.gender          ?  "$args.gender" :        "NULL"
+    def genomeVersion  = args.genomeVersion   ?  "$args.genomeVersion" : "NULL"
+    def purity         = args.purity          ?  "$args.purity" :        "NULL"
+    def ploidy         = args.ploidy          ?  "$args.ploidy" :        "NULL"
+    def gc_files       = args.gc_files        ?  "$args.gc_files" :      "NULL"
+
+    def minCounts_arg                    = args.minCounts                     ?  ",minCounts = $args.minCounts" : ""
+    def chrom_names_arg                  = args.chrom_names                   ?  ",chrom_names = $args.chrom_names" : ""
+    def min_base_qual_arg                = args.min_base_qual                 ?  ",min_base_qual = $args.min_base_qual" : ""
+    def min_map_qual_arg                 = args.min_map_qual                  ?  ",min_map_qual = $args.min_map_qual" : ""
+    def ref_fasta_arg                    = args.ref_fasta                     ?  ",ref.fasta = '$args.ref_fasta'" : ""
+    def skip_allele_counting_tumour_arg  = args.skip_allele_counting_tumour   ?  ",skip_allele_counting_tumour = $args.skip_allele_counting_tumour" : ""
+    def skip_allele_counting_normal_arg  = args.skip_allele_counting_normal   ?  ",skip_allele_counting_normal = $args.skip_allele_counting_normal" : ""
+
+
+
+    """
+    #!/usr/bin/env Rscript
+    library(RColorBrewer)
+    library(ASCAT)
+    options(bitmapType='cairo')
+
+
+    #prepare from BAM files
+    ascat.prepareHTS(
+        tumourseqfile = "$input_tumor",
+        normalseqfile = "$input_normal",
+        tumourname = "Tumour",
+        normalname = "Normal",
+        allelecounter_exe = "alleleCounter",
+        alleles.prefix = "$allele_files",
+        loci.prefix = "$loci_files",
+        gender = "$gender",
+        genomeVersion = "$genomeVersion",
+        nthreads = $task.cpus
+        $minCounts_arg
+        $chrom_names_arg
+        $min_base_qual_arg
+        $min_map_qual_arg
+        $ref_fasta_arg
+        $skip_allele_counting_tumour_arg
+        $skip_allele_counting_normal_arg
+    )
+
+
+    #Load the data
+    ascat.bc = ascat.loadData(
+        Tumor_LogR_file = "Tumour_tumourLogR.txt",
+        Tumor_BAF_file = "Tumour_normalBAF.txt",
+        Germline_LogR_file = "Tumour_normalLogR.txt",
+        Germline_BAF_file = "Tumour_normalBAF.txt",
+        genomeVersion = "$genomeVersion",
+        gender = "$gender"
+    )
+
+    #optional GC wave correction
+    if(!is.null($gc_files)){
+        ascat.bc = ascat.GCcorrect(ascat.bc, $gc_files)
+    }
+
+    #Plot the raw data
+    ascat.plotRawData(ascat.bc)
+
+    #Segment the data
+    ascat.bc = ascat.aspcf(ascat.bc)
+
+    #Plot the segmented data
+    ascat.plotSegmentedData(ascat.bc)
+
+    #Run ASCAT to fit every tumor to a model, inferring ploidy, normal cell contamination, and discrete copy numbers
+    #If psi and rho are manually set:
+    if (!is.null($purity) && !is.null($ploidy)){
+        ascat.output <- ascat.runAscat(ascat.bc, gamma=1, rho_manual=$purity, psi_manual=$ploidy)
+    } else if(!is.null($purity) && is.null($ploidy)){
+        ascat.output <- ascat.runAscat(ascat.bc, gamma=1, rho_manual=$purity)
+    } else if(!is.null($ploidy) && is.null($purity)){
+        ascat.output <- ascat.runAscat(ascat.bc, gamma=1, psi_manual=$ploidy)
+    } else {
+        ascat.output <- ascat.runAscat(ascat.bc, gamma=1)
+    }
+
+    #Write out segmented regions (including regions with one copy of each allele)
+    write.table(ascat.output[["segments"]], file=paste0("$prefix", ".segments.txt"), sep="\t", quote=F, row.names=F)
+
+    #Write out CNVs in bed format
+    cnvs=ascat.output[["segments"]][2:6]
+    write.table(cnvs, file=paste0("$prefix",".cnvs.txt"), sep="\t", quote=F, row.names=F, col.names=T)
+
+    #Write out purity and ploidy info
+    summary <- tryCatch({
+            matrix(c(ascat.output[["aberrantcellfraction"]], ascat.output[["ploidy"]]), ncol=2, byrow=TRUE)}, error = function(err) {
+                # error handler picks up where error was generated
+                print(paste("Could not find optimal solution:  ",err))
+                return(matrix(c(0,0),nrow=1,ncol=2,byrow = TRUE))
+        }
+    )
+    colnames(summary) <- c("AberrantCellFraction","Ploidy")
+    write.table(summary, file=paste0("$prefix",".purityploidy.txt"), sep="\t", quote=F, row.names=F, col.names=T)
+
+    #version export. Have to hardcode process name and software name because
+    #won't run inside an R-block
+    version_file_path="versions.yml"
+    f <- file(version_file_path,"w")
+    writeLines("ASCAT:", f)
+    writeLines(" ascat: 3.0.0",f)
+    close(f)
+    """
+
+
+    stub:
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    echo stub > ${prefix}.cnvs.txt
+    echo stub > ${prefix}.purityploidy.txt
+    echo stub > ${prefix}.segments.txt
+    echo stub > Tumour.ASCATprofile.png
+    echo stub > Tumour.ASPCF.png
+    echo stub > Tumour.germline.png
+    echo stub > Tumour.rawprofile.png
+    echo stub > Tumour.sunrise.png
+    echo stub > Tumour.tumour.png
+
+    echo 'ASCAT:' > versions.yml
+    echo ' ascat: 3.0.0' >> versions.yml
+    """
+
+
+}
--- a/modules/ascat/meta.yml
+++ b/modules/ascat/meta.yml
@ -0,0 +1,92 @@
+name: ascat
+description: copy number profiles of tumour cells.
+keywords:
+  - sort
+tools:
+  - ascat:
+      description: ASCAT is a method to derive copy number profiles of tumour cells, accounting for normal cell admixture and tumour aneuploidy. ASCAT infers tumour purity (the fraction of tumour cells) and ploidy (the amount of DNA per tumour cell), expressed as multiples of haploid genomes from SNP array or massively parallel sequencing data, and calculates whole-genome allele-specific copy number profiles (the number of copies of both parental alleles for all SNP loci across the genome).
+      homepage: None
+      documentation: None
+      tool_dev_url: https://github.com/Crick-CancerGenomics/ascat
+      doi: "10.1093/bioinformatics/btaa538"
+      licence: ['GPL v3']
+
+input:
+  - args:
+      type: map
+      description: |
+        Groovy Map containing tool parameters. MUST follow the structure/keywords below and be provided via modules.config. Parameters must be set between quotes. (optional) parameters can be removed from the map, if they are not set. For default values, please check the documentation above.
+
+        ```
+        {
+          [
+            "gender": "XX",
+            "genomeVersion": "hg19"
+            "purity": (optional),
+            "ploidy": (optional),
+            "gc_files": (optional),
+            "minCounts": (optional),
+            "chrom_names": (optional),
+            "min_base_qual": (optional),
+            "min_map_qual": (optional),
+            "ref_fasta": (optional),
+            "skip_allele_counting_tumour": (optional),
+            "skip_allele_counting_normal": (optional)
+          ]
+        }
+        ```
+
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  - input_normal:
+      type: file
+      description: BAM/CRAM/SAM file
+      pattern: "*.{bam,cram,sam}"
+  - index_normal:
+      type: file
+      description: index for normal_bam
+      pattern: "*.{bai}"
+  - input_tumor:
+      type: file
+      description: BAM/CRAM/SAM file
+      pattern: "*.{bam,cram,sam}"
+  - index_tumor:
+      type: file
+      description: index for tumor_bam
+      pattern: "*.{bai}"
+  - allele_files:
+      type: file
+      description: allele files for ASCAT. Can be downloaded here https://github.com/VanLoo-lab/ascat/tree/master/ReferenceFiles/WGS
+  - loci_files:
+      type: file
+      description: loci files for ASCAT. Can be downloaded here https://github.com/VanLoo-lab/ascat/tree/master/ReferenceFiles/WGS
+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"
+  - png:
+      type: file
+      description: ASCAT plots
+      pattern: "*.{png}"
+  - purityploidy:
+      type: file
+      description: purity and ploidy data
+      pattern: "*.purityploidy.txt"
+  - segments:
+      type: file
+      description: segments data
+      pattern: "*.segments.txt"
+authors:
+  - "@aasNGC"
+  - "@lassefolkersen"
+  - "@FriederikeHanssen"
+  - "@maxulysse"
--- a/modules/biscuit/align/main.nf
+++ b/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
+    """
+}
--- a/modules/biscuit/align/meta.yml
+++ b/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"
--- a/modules/biscuit/biscuitblaster/main.nf
+++ b/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
+    """
+}
--- a/modules/biscuit/biscuitblaster/meta.yml
+++ b/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"
--- a/modules/biscuit/bsconv/main.nf
+++ b/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
+    """
+}
--- a/modules/biscuit/bsconv/meta.yml
+++ b/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"
--- a/modules/biscuit/epiread/main.nf
+++ b/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
+    """
+}
--- a/modules/biscuit/epiread/meta.yml
+++ b/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"
--- a/modules/biscuit/index/main.nf
+++ b/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
+    """
+}
--- a/modules/biscuit/index/meta.yml
+++ b/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"
--- a/modules/biscuit/mergecg/main.nf
+++ b/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
+    """
+}
--- a/modules/biscuit/mergecg/meta.yml
+++ b/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"
--- a/modules/biscuit/pileup/main.nf
+++ b/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
+    """
+}
--- a/modules/biscuit/pileup/meta.yml
+++ b/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"
--- a/modules/biscuit/qc/main.nf
+++ b/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
+    """
+}
--- a/modules/biscuit/qc/meta.yml
+++ b/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"
--- a/modules/biscuit/vcf2bed/main.nf
+++ b/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
+    """
+}
--- a/modules/biscuit/vcf2bed/meta.yml
+++ b/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"
--- a/modules/bwa/aln/meta.yml
+++ b/modules/bwa/aln/meta.yml
@ -21,10 +21,10 @@ tools:

 input:
  - meta:
-    type: map
-    description: |
-      Groovy Map containing sample information
-      e.g. [ id:'test', single_end:false ]
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
  - reads:
      type: file
      description: |
--- a/modules/cnvpytor/callcnvs/main.nf
+++ b/modules/cnvpytor/callcnvs/main.nf
@ -0,0 +1,33 @@
+process CNVPYTOR_CALLCNVS {
+    tag "$meta.id"
+    label 'process_medium'
+
+    conda (params.enable_conda ? "bioconda::cnvpytor=1.0" : null)
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/cnvpytor:A1.0--py39h6a678da_2':
+        'quay.io/biocontainers/cnvpytor:1.0--py39h6a678da_2' }"
+
+    input:
+    tuple val(meta), path(pytor)
+
+    output:
+    tuple val(meta), path("*.tsv"), emit: cnvs
+    path "versions.yml"           , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args = task.ext.args ?: '1000'
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    cnvpytor \\
+        -root $pytor \\
+        -call $args > ${prefix}.tsv
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        cnvpytor: \$(echo \$(cnvpytor --version 2>&1) | sed 's/^.*pyCNVnator //; s/Using.*\$//' ))
+    END_VERSIONS
+    """
+}
--- a/modules/cnvpytor/callcnvs/meta.yml
+++ b/modules/cnvpytor/callcnvs/meta.yml
@ -0,0 +1,40 @@
+name: cnvpytor_callcnvs
+description: command line tool for calling CNVs in whole genome sequencing data
+  - CNV calling
+tools:
+  - cnvpytor:
+      description: calling CNVs using read depth
+      homepage: https://github.com/abyzovlab/CNVpytor
+      documentation: https://github.com/abyzovlab/CNVpytor
+      tool_dev_url: https://github.com/abyzovlab/CNVpytor
+      doi: "10.1101/2021.01.27.428472v1"
+      licence: ['MIT']
+input:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test']
+  - pytor:
+      type: file
+      description: cnvpytor root file
+      pattern: "*.{pytor}"
+
+output:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test' ]
+  - cnvs:
+      type: file
+      description: file containing identified copy numer variations
+      pattern: "*.{tsv}"
+  - versions:
+      type: file
+      description: File containing software versions
+      pattern: "versions.yml"
+
+
+authors:
+  - "@sima-r"
--- a/modules/cnvpytor/histogram/main.nf
+++ b/modules/cnvpytor/histogram/main.nf
@ -0,0 +1,32 @@
+process CNVPYTOR_HISTOGRAM {
+    tag "$meta.id"
+    label 'process_medium'
+
+    conda (params.enable_conda ? "bioconda::cnvpytor=1.0" : null)
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/cnvpytor:A1.0--py39h6a678da_2':
+        'quay.io/biocontainers/cnvpytor:1.0--py39h6a678da_2' }"
+
+    input:
+    tuple val(meta), path(pytor)
+
+    output:
+    tuple val(meta), path("${pytor.baseName}.pytor")	, emit: pytor
+    path "versions.yml"                                 , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args = task.ext.args ?: '1000'
+    """
+    cnvpytor \\
+        -root $pytor \\
+        -his $args
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        cnvpytor: \$(echo \$(cnvpytor --version 2>&1) | sed 's/^.*pyCNVnator //; s/Using.*\$//' ))
+    END_VERSIONS
+    """
+}
--- a/modules/cnvpytor/histogram/meta.yml
+++ b/modules/cnvpytor/histogram/meta.yml
@ -0,0 +1,42 @@
+name: cnvpytor_histogram
+description: calculates read depth histograms
+keywords:
+  - cnv calling
+  - histogram
+tools:
+  - cnvpytor:
+      description: calling CNVs using read depth
+      homepage: https://github.com/abyzovlab/CNVpytor
+      documentation: https://github.com/abyzovlab/CNVpytor
+      tool_dev_url: https://github.com/abyzovlab/CNVpytor
+      doi: "10.1101/2021.01.27.428472v1"
+      licence: ['MIT']
+
+input:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test' ]
+  - pytor:
+      type: file
+      description: pytor file containing read depth data
+      pattern: "*.{pytor}"
+
+output:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test' ]
+  - pytor:
+      type: file
+      description: pytor file containing read depth histograms binned based on given bin size(s)
+      pattern: "*.{pytor}"
+  - versions:
+      type: file
+      description: File containing software versions
+      pattern: "versions.yml"
+
+authors:
+  - "@sima-r"
--- a/modules/cnvpytor/importreaddepth/main.nf
+++ b/modules/cnvpytor/importreaddepth/main.nf
@ -0,0 +1,38 @@
+process CNVPYTOR_IMPORTREADDEPTH {
+    tag "$meta.id"
+    label 'process_medium'
+
+    conda (params.enable_conda ? "bioconda::cnvpytor=1.0" : null)
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/cnvpytor:A1.0--py39h6a678da_2':
+        'quay.io/biocontainers/cnvpytor:1.0--py39h6a678da_2' }"
+
+    input:
+    tuple val(meta), path(input_file), path(index)
+    path fasta
+    path fai
+
+    output:
+    tuple val(meta), path("*.pytor")	, emit: pytor
+    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 reference = fasta ? "-T ${fasta}" : ''
+    """
+    cnvpytor \\
+        -root ${prefix}.pytor \\
+        -rd $input_file \\
+        $args \\
+        $reference
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        cnvpytor: \$(echo \$(cnvpytor --version 2>&1) | sed 's/^.*pyCNVnator //; s/Using.*\$//' ))
+    END_VERSIONS
+    """
+}
--- a/modules/cnvpytor/importreaddepth/meta.yml
+++ b/modules/cnvpytor/importreaddepth/meta.yml
@ -0,0 +1,55 @@
+name: cnvpytor_importreaddepth
+description: command line tool for CNV/CNA analysis. This step imports the read depth data into a root pytor file.
+keywords:
+  - read depth
+  - cnv calling
+tools:
+  - cnvpytor -rd:
+      description: calling CNVs using read depth
+      homepage: https://github.com/abyzovlab/CNVpytor
+      documentation: https://github.com/abyzovlab/CNVpytor
+      tool_dev_url: https://github.com/abyzovlab/CNVpytor
+      doi: "10.1101/2021.01.27.428472v1"
+      licence: ['MIT']
+
+input:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test' ]
+  - input_file:
+      type: file
+      description: BAM/CRAM/SAM file
+      pattern: "*.{bam,cram}"
+  - index:
+      type: file
+      description: bam file index
+      pattern: "*.{bai,crai}"
+  - fasta:
+      type: file
+      description: specifies reference genome file (only for cram file without reference genome)
+      pattern: "*.{fasta,fasta.gz,fa,fa.gz}"
+  - fai:
+    type: file
+    description: Index of reference fasta file
+    pattern: "*.fai"
+
+
+output:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test' ]
+  - pytor:
+      type: file
+      description: read depth root file in which read depth data binned to 100 base pair bins will be stored.
+      pattern: "*.{pytor}"
+  - versions:
+      type: file
+      description: File containing software versions
+      pattern: "versions.yml"
+
+authors:
+  - "@sima-r"
--- a/modules/cnvpytor/partition/main.nf
+++ b/modules/cnvpytor/partition/main.nf
@ -0,0 +1,32 @@
+process CNVPYTOR_PARTITION {
+    tag "$meta.id"
+    label 'process_medium'
+
+    conda (params.enable_conda ? "bioconda::cnvpytor=1.0" : null)
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/cnvpytor:A1.0--py39h6a678da_2':
+        'quay.io/biocontainers/cnvpytor:1.0--py39h6a678da_2' }"
+
+    input:
+    tuple val(meta), path(pytor)
+
+    output:
+    tuple val(meta), path("${pytor.baseName}.pytor"), emit: pytor
+    path "versions.yml"                             , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args = task.ext.args ?: '1000'
+    """
+    cnvpytor \\
+        -root $pytor \\
+        -partition $args
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        cnvpytor: \$(echo \$(cnvpytor --version 2>&1) | sed 's/^.*pyCNVnator //; s/Using.*\$//' ))
+    END_VERSIONS
+    """
+}
--- a/modules/cnvpytor/partition/meta.yml
+++ b/modules/cnvpytor/partition/meta.yml
@ -0,0 +1,42 @@
+name: cnvpytor_partition
+description: partitioning read depth histograms
+keywords:
+  - cnv calling
+  - partition histograms
+tools:
+  - cnvpytor:
+      description: calling CNVs using read depth
+      homepage: https://github.com/abyzovlab/CNVpytor
+      documentation: https://github.com/abyzovlab/CNVpytor
+      tool_dev_url: https://github.com/abyzovlab/CNVpytor
+      doi: "10.1101/2021.01.27.428472v1"
+      licence: ['MIT']
+
+input:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test' ]
+  - pytor:
+      type: file
+      description: pytor file containing read depth data
+      pattern: "*.{pytor}"
+
+output:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test' ]
+  - partitions:
+      type: file
+      description: pytor file containing partitions of read depth histograms using mean-shift method
+      pattern: "*.{pytor}"
+  - versions:
+      type: file
+      description: File containing software versions
+      pattern: "versions.yml"
+
+authors:
+  - "@sima-r"
--- a/modules/controlfreec/meta.yml
+++ b/modules/controlfreec/meta.yml
@ -17,57 +17,57 @@ tools:

 input:
  - args:
-    type: map
-    description: |
-      Groovy Map containing tool parameters. MUST follow the structure/keywords below and be provided via modules.config.
-      <optional> parameters can be removed from the map, if they are not set. All value must be surrounded by quotes, meta map parameters can be set with, i.e. sex = meta.sex:
-      For default values, please check the documentation above.
+      type: map
+      description: |
+        Groovy Map containing tool parameters. MUST follow the structure/keywords below and be provided via modules.config.
+        Parameters marked as (optional) can be removed from the map, if they are not set. All values must be surrounded by quotes, meta map parameters can be set with, i.e. `sex = meta.sex`:
+        For default values, please check the documentation above.

-      ```
-      {
-        [
-          "general" :[
-              "bedgraphoutput": <optional>,
-              "breakpointthreshold": <optional>,
-              "breakpointtype": <optional>,
-              "coefficientofvariation": <optional>,
-              "contamination": <optional>,
-              "contaminationadjustment": <optional>,
-              "degree": <optional>,
-              "forcegccontentnormalization": <optional>,
-              "gccontentprofile": <optional>,
-              "intercept": <optional>,
-              "mincnalength": <optional>,
-              "minmappabilityperwindow": <optional>,
-              "minexpectedgc": <optional>,
-              "maxexpectedgc": <optional>,
-              "minimalsubclonepresence": <optional>,
-              "noisydata": <optional>,
-              "ploidy": <optional>,
-              "printNA": <optional>,
-              "readcountthreshold": <optional >,
-              "sex": <optional>,
-              "step": <optional value>,
-              "telocentromeric": <optional>,
-              "uniquematch": <optional>,
-              "window": <optional>
-          ],
-          "control":[
-              "inputformat": <required>,
-              "mateorientation": <optional>,
-          ],
-          "sample":[
-              "inputformat": <required>,
-              "mateorientation": <optional>,
-          ],
-          "BAF":[
-              "minimalcoverageperposition": <optional>,
-              "minimalqualityperposition": <optional>,
-              "shiftinquality": <optional>
+        ```
+        {
+          [
+            "general" :[
+                "bedgraphoutput": (optional),
+                "breakpointthreshold": (optional),
+                "breakpointtype": (optional),
+                "coefficientofvariation": (optional),
+                "contamination": (optional),
+                "contaminationadjustment": (optional),
+                "degree": (optional),
+                "forcegccontentnormalization": (optional),
+                "gccontentprofile": (optional),
+                "intercept": (optional),
+                "mincnalength": (optional),
+                "minmappabilityperwindow": (optional),
+                "minexpectedgc": (optional),
+                "maxexpectedgc": (optional),
+                "minimalsubclonepresence": (optional),
+                "noisydata": (optional),
+                "ploidy": (optional),
+                "printNA": (optional),
+                "readcountthreshold": (optional),
+                "sex": (optional),
+                "step": (optional),
+                "telocentromeric": (optional),
+                "uniquematch": (optional),
+                "window": (optional)
+            ],
+            "control":[
+                "inputformat": (required),
+                "mateorientation": (optional),
+            ],
+            "sample":[
+                "inputformat": (required),
+                "mateorientation": (optional),
+            ],
+            "BAF":[
+                "minimalcoverageperposition": (optional),
+                "minimalqualityperposition": (optional),
+                "shiftinquality": (optional)
+            ]
          ]
-        ]
-      }
-      ```
+        }
+        ```

  - meta:
      type: map
--- a/modules/deeparg/downloaddata/main.nf
+++ b/modules/deeparg/downloaddata/main.nf
@ -7,6 +7,12 @@ process DEEPARG_DOWNLOADDATA {
    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
        'https://depot.galaxyproject.org/singularity/deeparg:1.0.2--pyhdfd78af_1' :
        'quay.io/biocontainers/deeparg:1.0.2--pyhdfd78af_1' }"
+    /*
+    We have to force singularity to run with --fakeroot to allow reading of a problematic file with borked read-write permissions in an upstream dependency (theanos).
+    This flag may not be available on all systems and may be considered a security problem. so please document and /or warn for this in your pipeline!
+    */
+    containerOptions { "${workflow.containerEngine}" == 'singularity' ? '--fakeroot' : '' }
+

    input:

--- a/modules/deeparg/predict/main.nf
+++ b/modules/deeparg/predict/main.nf
@ -8,6 +8,11 @@ process DEEPARG_PREDICT {
    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
        'https://depot.galaxyproject.org/singularity//deeparg:1.0.2--pyhdfd78af_1' :
        'quay.io/biocontainers/deeparg:1.0.2--pyhdfd78af_1' }"
+    /*
+    We have to force singularity to run with --fakeroot to allow reading of a problematic file with borked read-write permissions in an upstream dependency (theanos).
+    This flag may not be available on all systems and may be considered a security problem. so please document and /or warn for this in your pipeline!
+    */
+    containerOptions { "${workflow.containerEngine}" == 'singularity' ? '--fakeroot' : '' }

    input:
    tuple val(meta), path(fasta), val(model)
--- a/modules/optitype/main.nf
+++ b/modules/optitype/main.nf
@ -8,7 +8,7 @@ process OPTITYPE {
        'quay.io/biocontainers/optitype:1.3.5--0' }"

    input:
-    tuple val(meta), path(bam)
+    tuple val(meta), path(bam), path(bai)

    output:
    tuple val(meta), path("${prefix}"), emit: output
--- a/modules/optitype/meta.yml
+++ b/modules/optitype/meta.yml
@ -22,6 +22,10 @@ input:
      type: file
      description: BAM file
      pattern: "*.{bam}"
+  - bai:
+      type: file
+      description: BAM index file
+      pattern: "*.{bai}"

 output:
  - meta:
--- a/tests/config/nextflow.config
+++ b/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'
 }
--- a/tests/config/pytest_modules.yml
+++ b/tests/config/pytest_modules.yml
@ -46,6 +46,10 @@ artic/minion:
  - modules/artic/minion/**
  - tests/modules/artic/minion/**

+ascat:
+  - modules/ascat/**
+  - tests/modules/ascat/**
+
 assemblyscan:
  - modules/assemblyscan/**
  - tests/modules/assemblyscan/**
@ -198,6 +202,49 @@ 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/**
--- a/tests/config/test_data.config
+++ b/tests/config/test_data.config
@ -192,7 +192,8 @@ params {
                test_paired_end_umi_unsorted_bam                        = "${test_data_dir}/genomics/homo_sapiens/illumina/bam/umi/test.paired_end.umi_unsorted.bam"
                test_paired_end_umi_unsorted_tagged_bam                 = "${test_data_dir}/genomics/homo_sapiens/illumina/bam/umi/test.paired_end.unsorted_tagged.bam"
                test_paired_end_hla                                     = "${test_data_dir}/genomics/homo_sapiens/illumina/bam/example_hla_pe.bam"
-
+                test_paired_end_hla_sorted_bam                          = "${test_data_dir}/genomics/homo_sapiens/illumina/bam/example_hla_pe.sorted.bam"
+                test_paired_end_hla_sorted_bam_bai                      = "${test_data_dir}/genomics/homo_sapiens/illumina/bam/example_hla_pe.sorted.bam.bai"
                test2_paired_end_sorted_bam                    = "${test_data_dir}/genomics/homo_sapiens/illumina/bam/test2.paired_end.sorted.bam"
                test2_paired_end_sorted_bam_bai                = "${test_data_dir}/genomics/homo_sapiens/illumina/bam/test2.paired_end.sorted.bam.bai"
                test2_paired_end_name_sorted_bam               = "${test_data_dir}/genomics/homo_sapiens/illumina/bam/test2.paired_end.name.sorted.bam"
@ -295,6 +296,8 @@ params {

                test_rnaseq_vcf                               =  "${test_data_dir}/genomics/homo_sapiens/illumina/vcf/test.rnaseq.vcf"
                test_sv_vcf                                   =  "${test_data_dir}/genomics/homo_sapiens/illumina/vcf/sv_query.vcf.gz"
+
+                test_pytor                                    = "${test_data_dir}/genomics/homo_sapiens/illumina/pytor/test.pytor"
            }
            'pacbio' {
                primers                                       = "${test_data_dir}/genomics/homo_sapiens/pacbio/fasta/primers.fasta"
--- a/tests/modules/adapterremoval/main.nf
+++ b/tests/modules/adapterremoval/main.nf
@ -2,14 +2,16 @@

 nextflow.enable.dsl = 2

-include { ADAPTERREMOVAL } from '../../../modules/adapterremoval/main.nf'
+include { ADAPTERREMOVAL                            } from '../../../modules/adapterremoval/main.nf'
+include { ADAPTERREMOVAL as ADAPTERREMOVAL_COLLAPSE } from '../../../modules/adapterremoval/main.nf'
+

 workflow test_adapterremoval_single_end {
    input = [ [ id:'test', single_end:true, collapse:false ], // meta map
              file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true)
            ]

-    ADAPTERREMOVAL ( input )
+    ADAPTERREMOVAL ( input, [] )
 }

 workflow test_adapterremoval_paired_end {
@ -18,15 +20,15 @@ workflow test_adapterremoval_paired_end {
                file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true) ]
            ]

-    ADAPTERREMOVAL ( input )
+    ADAPTERREMOVAL ( input, [] )
 }

 workflow test_adapterremoval_paired_end_collapse {
-    input = [ [ id:'test', single_end:false, collapse:true ], // meta map
+    input = [ [ id:'test', single_end:false ], // meta map
              [ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
                file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true) ]
            ]

-    ADAPTERREMOVAL ( input )
+    ADAPTERREMOVAL_COLLAPSE ( input, [] )
 }

--- a/tests/modules/adapterremoval/nextflow.config
+++ b/tests/modules/adapterremoval/nextflow.config
@ -2,4 +2,8 @@ process {

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

+    withName: ADAPTERREMOVAL_COLLAPSE {
+        ext.args = "--collapse"
+    }
+
 }
--- a/tests/modules/adapterremoval/test.yml
+++ b/tests/modules/adapterremoval/test.yml
@ -23,7 +23,6 @@
      md5sum: 294a6277f0139bd597e57c6fa31f39c7
    - path: output/adapterremoval/test.pair2.truncated.gz
      md5sum: de7b38e2c881bced8671acb1ab452d78
-    - path: output/adapterremoval/test.singleton.truncated.gz
    - path: output/adapterremoval/versions.yml
      md5sum: fa621c887897da5a379c719399c17db7

@ -32,13 +31,15 @@
  tags:
    - adapterremoval
  files:
+    - path: output/adapterremoval/test.collapsed.gz
+      md5sum: ff956de3532599a56c3efe5369f0953f
+    - path: output/adapterremoval/test.collapsed.truncated.gz
    - path: output/adapterremoval/test.discarded.gz
    - path: output/adapterremoval/test.log
-      md5sum: b8a451d3981b327f3fdb44f40ba2d6d1
+      md5sum: 7f0b2328152226e46101a535cce718b3
    - path: output/adapterremoval/test.pair1.truncated.gz
-      md5sum: 294a6277f0139bd597e57c6fa31f39c7
+      md5sum: 683be19bc1c83008944b6b719bfa34e1
    - path: output/adapterremoval/test.pair2.truncated.gz
-      md5sum: de7b38e2c881bced8671acb1ab452d78
-    - path: output/adapterremoval/test.singleton.truncated.gz
+      md5sum: e6548fe061f3ef86368b26da930174d0
    - path: output/adapterremoval/versions.yml
-      md5sum: fd428f92a8446e0b34c5ae1c447215b8
+      md5sum: 78f589bb313c8da0147ca8ce77d7f3bf
--- a/tests/modules/ascat/main.nf
+++ b/tests/modules/ascat/main.nf
@ -0,0 +1,64 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { ASCAT as ASCAT_SIMPLE} from '../../../modules/ascat/main.nf'
+include { ASCAT as ASCAT_PLOIDY_AND_PURITY} from '../../../modules/ascat/main.nf'
+include { ASCAT as ASCAT_CRAM} from '../../../modules/ascat/main.nf'
+
+
+
+
+workflow test_ascat {
+    input = [
+        [ id:'test', single_end:false ], // 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)
+    ]
+
+    ASCAT_SIMPLE ( input , [], [])
+}
+
+
+
+
+
+// extended tests running with 1000 genomes data. Data is downloaded as follows:
+// wget ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/phase1/data/HG00154/alignment/HG00154.mapped.ILLUMINA.bwa.GBR.low_coverage.20101123.bam
+// wget ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/phase1/data/HG00154/alignment/HG00154.mapped.ILLUMINA.bwa.GBR.low_coverage.20101123.bam.bai
+// wget http://ftp.1000genomes.ebi.ac.uk/vol1/ftp/phase1/data/HG00155/alignment/HG00155.mapped.ILLUMINA.bwa.GBR.low_coverage.20101123.bam
+// wget http://ftp.1000genomes.ebi.ac.uk/vol1/ftp/phase1/data/HG00155/alignment/HG00155.mapped.ILLUMINA.bwa.GBR.low_coverage.20101123.bam.bai
+//workflow test_ascat_with_ploidy_and_purity {  
+//   input = [
+//        [ id:'test', single_end:false ], // meta map
+//        file("/home/ec2-user/input_files/bams/HG00154.mapped.ILLUMINA.bwa.GBR.low_coverage.20101123.bam", checkIfExists: true),
+//        file("/home/ec2-user/input_files/bams/HG00154.mapped.ILLUMINA.bwa.GBR.low_coverage.20101123.bam.bai", checkIfExists: true),
+//        file("/home/ec2-user/input_files/bams/test2.bam", checkIfExists: true),
+//        file("/home/ec2-user/input_files/bams/test2.bam.bai", checkIfExists: true)
+//    ]
+//
+//    ASCAT_PLOIDY_AND_PURITY ( input , "/home/ec2-user/input_files/allele_files/G1000_alleles_hg19_chr", "/home/ec2-user/input_files/loci_files/G1000_alleles_hg19_chr")
+//}
+
+
+// extended tests running with 1000 genomes data. Data is downloaded as follows:
+// wget ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/phase3/data/HG00145/alignment/HG00145.mapped.ILLUMINA.bwa.GBR.low_coverage.20120522.bam.cram.crai
+// wget ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/phase3/data/HG00145/alignment/HG00145.mapped.ILLUMINA.bwa.GBR.low_coverage.20120522.bam.cram
+// wget ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/phase3/data/HG00146/alignment/HG00146.mapped.ILLUMINA.bwa.GBR.low_coverage.20120522.bam.cram.crai
+// wget ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/phase3/data/HG00146/alignment/HG00146.mapped.ILLUMINA.bwa.GBR.low_coverage.20120522.bam.cram
+//workflow test_ascat_with_crams {
+//    input = [
+//        [ id:'test', single_end:false ], // meta map
+//        file("/home/ec2-user/input_files/crams/HG00145.mapped.ILLUMINA.bwa.GBR.low_coverage.20120522.bam.cram", checkIfExists: true),
+//        file("/home/ec2-user/input_files/crams/HG00145.mapped.ILLUMINA.bwa.GBR.low_coverage.20120522.bam.cram.crai", checkIfExists: true),
+//        file("/home/ec2-user/input_files/crams/duplicate_test.cram", checkIfExists: true),
+//        file("/home/ec2-user/input_files/crams/duplicate_test.cram.crai", checkIfExists: true)
+//    ]
+//
+//    ASCAT_CRAM ( input , "/home/ec2-user/input_files/allele_files/G1000_alleles_hg19_chr", "/home/ec2-user/input_files/loci_files/G1000_alleles_hg19_chr")
+//}
+
+
+
--- a/tests/modules/ascat/nextflow.config
+++ b/tests/modules/ascat/nextflow.config
@ -0,0 +1,39 @@
+process {
+
+    publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+ 
+
+    withName: ASCAT_SIMPLE {
+        ext.args = [
+          gender    :  'XY',
+          genomeVersion : 'hg19',
+          minCounts :  '1',
+          min_base_qual : '1',
+          min_map_qual  : '1',
+          chrom_names  : 'c("21","22")'
+                  ]
+    }
+
+
+
+    withName: ASCAT_PLOIDY_AND_PURITY {
+        ext.args = [
+          gender : 'XX', 
+          genomeVersion : 'hg19',
+          ploidy  : '1.7', 
+          purity : '0.24',
+          chrom_names  : 'c("21","22")'
+                  ]
+    }
+
+    withName: ASCAT_CRAM {
+        ext.args = [
+          gender    : 'XX', 
+          genomeVersion : 'hg19',
+          ref_fasta : '/home/ec2-user/input_files/fasta/human_g1k_v37.fasta',
+          chrom_names  : 'c("21","22")'
+                  ]
+    }
+
+}
+
--- a/tests/modules/ascat/test.yml
+++ b/tests/modules/ascat/test.yml
@ -0,0 +1,25 @@
+- name: ascat test_ascat
+  command: nextflow run tests/modules/ascat -entry test_ascat -c tests/config/nextflow.config -stub-run
+  tags:
+    - ascat
+  files:
+    - path: output/ascat/Tumour.ASCATprofile.png
+      md5sum: f50b84b1db4b83ba62ec1deacc69c260
+    - path: output/ascat/Tumour.ASPCF.png
+      md5sum: f50b84b1db4b83ba62ec1deacc69c260
+    - path: output/ascat/Tumour.germline.png
+      md5sum: f50b84b1db4b83ba62ec1deacc69c260
+    - path: output/ascat/Tumour.rawprofile.png
+      md5sum: f50b84b1db4b83ba62ec1deacc69c260
+    - path: output/ascat/Tumour.sunrise.png
+      md5sum: f50b84b1db4b83ba62ec1deacc69c260
+    - path: output/ascat/Tumour.tumour.png
+      md5sum: f50b84b1db4b83ba62ec1deacc69c260
+    - path: output/ascat/test.cnvs.txt
+      md5sum: f50b84b1db4b83ba62ec1deacc69c260
+    - path: output/ascat/test.purityploidy.txt
+      md5sum: f50b84b1db4b83ba62ec1deacc69c260
+    - path: output/ascat/test.segments.txt
+      md5sum: f50b84b1db4b83ba62ec1deacc69c260
+    - path: output/ascat/versions.yml
+      md5sum: 1af20694ec11004c4f8bc0c609b06386
--- a/tests/modules/biscuit/align/main.nf
+++ b/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 )
+}
--- a/tests/modules/biscuit/align/nextflow.config
+++ b/tests/modules/biscuit/align/nextflow.config
@ -0,0 +1,5 @@
+process {
+
+    publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+}
--- a/tests/modules/biscuit/align/test.yml
+++ b/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
--- a/tests/modules/biscuit/biscuitblaster/main.nf
+++ b/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 )
+}
--- a/tests/modules/biscuit/biscuitblaster/nextflow.config
+++ b/tests/modules/biscuit/biscuitblaster/nextflow.config
@ -0,0 +1,5 @@
+process {
+
+    publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+}
--- a/tests/modules/biscuit/biscuitblaster/test.yml
+++ b/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
--- a/tests/modules/biscuit/bsconv/main.nf
+++ b/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 )
+}
--- a/tests/modules/biscuit/bsconv/nextflow.config
+++ b/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'
+    }
+
+}
+
--- a/tests/modules/biscuit/bsconv/test.yml
+++ b/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
--- a/tests/modules/biscuit/epiread/main.nf
+++ b/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 )
+}
--- a/tests/modules/biscuit/epiread/nextflow.config
+++ b/tests/modules/biscuit/epiread/nextflow.config
@ -0,0 +1,5 @@
+process {
+
+    publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+}
--- a/tests/modules/biscuit/epiread/test.yml
+++ b/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
--- a/tests/modules/biscuit/index/main.nf
+++ b/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 )
+}
--- a/tests/modules/biscuit/index/nextflow.config
+++ b/tests/modules/biscuit/index/nextflow.config
@ -0,0 +1,5 @@
+process {
+
+    publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+}
--- a/tests/modules/biscuit/index/test.yml
+++ b/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
--- a/tests/modules/biscuit/mergecg/main.nf
+++ b/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 )
+}
--- a/tests/modules/biscuit/mergecg/nextflow.config
+++ b/tests/modules/biscuit/mergecg/nextflow.config
@ -0,0 +1,5 @@
+process {
+
+    publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+}
--- a/tests/modules/biscuit/mergecg/test.yml
+++ b/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
--- a/tests/modules/biscuit/pileup/main.nf
+++ b/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 )
+
+}
--- a/tests/modules/biscuit/pileup/nextflow.config
+++ b/tests/modules/biscuit/pileup/nextflow.config
@ -0,0 +1,5 @@
+process {
+
+    publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+}
--- a/tests/modules/biscuit/pileup/test.yml
+++ b/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
--- a/tests/modules/biscuit/qc/main.nf
+++ b/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 )
+}
--- a/tests/modules/biscuit/qc/nextflow.config
+++ b/tests/modules/biscuit/qc/nextflow.config
@ -0,0 +1,5 @@
+process {
+
+    publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+}
--- a/tests/modules/biscuit/qc/test.yml
+++ b/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
--- a/tests/modules/biscuit/vcf2bed/main.nf
+++ b/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 )
+
+}
--- a/tests/modules/biscuit/vcf2bed/nextflow.config
+++ b/tests/modules/biscuit/vcf2bed/nextflow.config
@ -0,0 +1,5 @@
+process {
+
+    publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+}
--- a/tests/modules/biscuit/vcf2bed/test.yml
+++ b/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
--- a/tests/modules/cnvpytor/callcnvs/main.nf
+++ b/tests/modules/cnvpytor/callcnvs/main.nf
@ -0,0 +1,15 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { CNVPYTOR_CALLCNVS } from '../../../../modules/cnvpytor/callcnvs/main.nf'
+
+workflow test_cnvpytor_callcnvs {
+
+    input = [
+        [ id:'test'], // meta map
+        file(params.test_data['homo_sapiens']['illumina']['test_pytor'], checkIfExists: true)
+    ]
+
+    CNVPYTOR_CALLCNVS ( input )
+}
--- a/tests/modules/cnvpytor/callcnvs/nextflow.config
+++ b/tests/modules/cnvpytor/callcnvs/nextflow.config
@ -0,0 +1,7 @@
+process {
+
+    publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+    withName: CNVPYTOR_CALLCNVS {
+        ext.args = '10000'
+    }
+}
--- a/tests/modules/cnvpytor/callcnvs/test.yml
+++ b/tests/modules/cnvpytor/callcnvs/test.yml
@ -0,0 +1,10 @@
+- name: cnvpytor callcnvs test_cnvpytor_callcnvs
+  command: nextflow run tests/modules/cnvpytor/callcnvs -entry test_cnvpytor_callcnvs -c tests/config/nextflow.config
+  tags:
+    - cnvpytor
+    - cnvpytor/callcnvs
+  files:
+    - path: output/cnvpytor/calls.10000.tsv
+      md5sum: d41d8cd98f00b204e9800998ecf8427e
+    - path: output/cnvpytor/versions.yml
+      md5sum: 5fe6ca3ef5c40f9dbf487f28db237821
--- a/tests/modules/cnvpytor/histogram/main.nf
+++ b/tests/modules/cnvpytor/histogram/main.nf
@ -0,0 +1,15 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { CNVPYTOR_HISTOGRAM } from '../../../../modules/cnvpytor/histogram/main.nf'
+
+workflow test_cnvpytor_histogram {
+
+    input = [
+        [ id:'test'], // meta map
+        file(params.test_data['homo_sapiens']['illumina']['test_pytor'], checkIfExists: true),
+    ]
+
+    CNVPYTOR_HISTOGRAM ( input )
+}
--- a/tests/modules/cnvpytor/histogram/nextflow.config
+++ b/tests/modules/cnvpytor/histogram/nextflow.config
@ -0,0 +1,7 @@
+process {
+
+    publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+    withName: CNVPYTOR_HISTOGRAM {
+        ext.args = '10000 100000'
+    }
+}
--- a/tests/modules/cnvpytor/histogram/test.yml
+++ b/tests/modules/cnvpytor/histogram/test.yml
@ -0,0 +1,10 @@
+- name: cnvpytor histogram test_cnvpytor_histogram
+  command: nextflow run tests/modules/cnvpytor/histogram -entry test_cnvpytor_histogram -c tests/config/nextflow.config
+  tags:
+    - cnvpytor
+    - cnvpytor/histogram
+  files:
+    - path: output/cnvpytor/test.pytor
+      md5sum: aa03a8fa15b39f77816705a48e10312a
+    - path: output/cnvpytor/versions.yml
+      md5sum: 9a4b176afd5f1a3edeb37eeb301cf464
--- a/tests/modules/cnvpytor/importreaddepth/main.nf
+++ b/tests/modules/cnvpytor/importreaddepth/main.nf
@ -0,0 +1,32 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { CNVPYTOR_IMPORTREADDEPTH } from '../../../../modules/cnvpytor/importreaddepth/main.nf'
+
+
+workflow test_cnvpytor_importreaddepth {
+
+    input = [
+        [ id: 'test' ], // meta map
+        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)
+    ]
+
+    CNVPYTOR_IMPORTREADDEPTH (input, [], [])
+}
+
+workflow test_cnvpytor_importreaddepth_cram {
+
+    input = [
+        [ id: 'test' ], // meta map
+        file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram'], checkIfExists: true),
+        file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram_crai'], checkIfExists: true)
+    ]
+
+    fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
+
+    fai = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)
+
+    CNVPYTOR_IMPORTREADDEPTH (input, fasta, fai)
+}
--- a/tests/modules/cnvpytor/importreaddepth/nextflow.config
+++ b/tests/modules/cnvpytor/importreaddepth/nextflow.config
@ -0,0 +1,12 @@
+process {
+
+    publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+    withName: CNVPYTOR_IMPORTREADDEPTH {
+        ext.args = {params.cnvpytor_chr ? "-chrom ${params.cnvpytor_chr}" : '' }
+            }
+}
+
+params {
+    cnvpytor_chr = '' // specifies chromosome name(s) the same way as they are described in the sam/bam/cram header e.g. '1 2' or 'chr1 chr2'.
+    }
--- a/tests/modules/cnvpytor/partition/main.nf
+++ b/tests/modules/cnvpytor/partition/main.nf
@ -0,0 +1,15 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { CNVPYTOR_PARTITION } from '../../../../modules/cnvpytor/partition/main.nf'
+
+workflow test_cnvpytor_partition {
+
+    input = [
+        [ id:'test'], // meta map
+        file(params.test_data['homo_sapiens']['illumina']['test_pytor'], checkIfExists: true)
+    ]
+
+    CNVPYTOR_PARTITION ( input )
+}
--- a/tests/modules/cnvpytor/partition/nextflow.config
+++ b/tests/modules/cnvpytor/partition/nextflow.config
@ -0,0 +1,7 @@
+process {
+
+    publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+    withName: CNVPYTOR_PARTITION {
+        ext.args = '10000 100000'
+    }
+}
--- a/tests/modules/cnvpytor/partition/test.yml
+++ b/tests/modules/cnvpytor/partition/test.yml
@ -0,0 +1,10 @@
+- name: cnvpytor partition test_cnvpytor_partition
+  command: nextflow run tests/modules/cnvpytor/partition -entry test_cnvpytor_partition -c tests/config/nextflow.config
+  tags:
+    - cnvpytor
+    - cnvpytor/partition
+  files:
+    - path: output/cnvpytor/test.pytor
+      md5sum: aa03a8fa15b39f77816705a48e10312a
+    - path: output/cnvpytor/versions.yml
+      md5sum: 8a04506554c58cd170cc050fd9904c6f
--- a/tests/modules/optitype/main.nf
+++ b/tests/modules/optitype/main.nf
@ -6,7 +6,8 @@ include { OPTITYPE } from '../../../modules/optitype/main.nf'

 workflow test_optitype {
    input = [ [ id:'test', seq_type:'dna' ], // meta map
-              file(params.test_data['homo_sapiens']['illumina']['test_paired_end_hla'], checkIfExists: true)
+              file(params.test_data['homo_sapiens']['illumina']['test_paired_end_hla_sorted_bam'], checkIfExists: true),
+              file(params.test_data['homo_sapiens']['illumina']['test_paired_end_hla_sorted_bam_bai'], checkIfExists: true)
            ]

    OPTITYPE ( input )
--- a/tests/modules/optitype/test.yml
+++ b/tests/modules/optitype/test.yml
@ -6,4 +6,4 @@
    - path: output/optitype/test/test_coverage_plot.pdf
    - path: output/optitype/test/test_result.tsv
      contains:
-        - "1446"
+        - "1439"