Merge branch 'master' into seqtk/seq-indent-fix

.github/PULL_REQUEST_TEMPLATE.md

@@ -27,6 +27,6 @@ Closes #XXX <!-- If this PR fixes an issue, please link it here! -->
 - [ ] Add a resource `label`
 - [ ] Use BioConda and BioContainers if possible to fulfil software requirements.
 - Ensure that the test works with either Docker / Singularity. Conda CI tests can be quite flaky:
-    - [ ] `PROFILE=docker pytest --tag <MODULE> --symlink --keep-workflow-wd`
+    - [ ] `PROFILE=docker pytest --tag <MODULE> --symlink --keep-workflow-wd --git-aware`
-    - [ ] `PROFILE=singularity pytest --tag <MODULE> --symlink --keep-workflow-wd`
+    - [ ] `PROFILE=singularity pytest --tag <MODULE> --symlink --keep-workflow-wd --git-aware`
-    - [ ] `PROFILE=conda pytest --tag <MODULE> --symlink --keep-workflow-wd`
+    - [ ] `PROFILE=conda pytest --tag <MODULE> --symlink --keep-workflow-wd --git-aware`

.github/workflows/pytest-workflow.yml

@@ -86,7 +86,7 @@ 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 ${{ matrix.tags }} --symlink --kwdof
+        run: TMPDIR=~ PROFILE=${{ matrix.profile }} pytest --tag ${{ matrix.tags }} --symlink --kwdof --git-aware
 
       - name: Output log on failure
         if: failure()

modules/adapterremoval/main.nf

@@ -11,9 +11,15 @@ process ADAPTERREMOVAL {
     tuple val(meta), path(reads)
 
     output:
-    tuple val(meta), path('*.fastq.gz'), emit: reads
+    tuple val(meta), path('*.truncated.gz')         , optional: true, emit: singles_truncated
-    tuple val(meta), path('*.log')     , emit: log
+    tuple val(meta), path('*.discarded.gz')         , optional: true, emit: discarded
-    path "versions.yml"                , emit: versions
+    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
 
     when:
     task.ext.when == null || task.ext.when
@@ -28,30 +34,27 @@ process ADAPTERREMOVAL {
             --file1 $reads \\
             $args \\
             --basename $prefix \\
-            --threads $task.cpus \\
+            --threads ${task.cpus} \\
             --settings ${prefix}.log \\
-            --output1 ${prefix}.trimmed.fastq.gz \\
             --seed 42 \\
-            --gzip \\
+            --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 && !meta.collapse) {
+    } else if (!meta.single_end ) {
         """
         AdapterRemoval  \\
             --file1 ${reads[0]} \\
             --file2 ${reads[1]} \\
             $args \\
             --basename $prefix \\
-            --threads $task.cpus \\
+            --threads ${task.cpus} \\
             --settings ${prefix}.log \\
-            --output1 ${prefix}.pair1.trimmed.fastq.gz \\
-            --output2 ${prefix}.pair2.trimmed.fastq.gz \\
             --seed 42 \\
-            --gzip \\
+            --gzip
 
         cat <<-END_VERSIONS > versions.yml
         "${task.process}":
@@ -63,13 +66,12 @@ process ADAPTERREMOVAL {
         AdapterRemoval  \\
             --file1 ${reads[0]} \\
             --file2 ${reads[1]} \\
-            --collapse \\
             $args \\
             --basename $prefix \\
             --threads $task.cpus \\
             --settings ${prefix}.log \\
             --seed 42 \\
-            --gzip \\
+            --gzip
 
         cat *.collapsed.gz *.collapsed.truncated.gz > ${prefix}.merged.fastq.gz
         cat <<-END_VERSIONS > versions.yml

modules/adapterremoval/meta.yml

@@ -17,13 +17,13 @@ input:
       type: map
       description: |
         Groovy Map containing sample information
-        e.g. [ id:'test', single_end:false, collapse:false ]
+        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.
-      pattern: "*.{fq,fastq,fg.gz,fastq.gz}"
+      pattern: "*.{fq,fastq,fq.gz,fastq.gz}"
 
 output:
   - meta:
@@ -31,12 +31,45 @@ output:
       description: |
         Groovy Map containing sample information
         e.g. [ id:'test', single_end:false ]
-  - reads:
+  - singles_truncated:
       type: file
       description: |
-        List of input adapter trimmed FastQ files of size 1 or 2 for
+        Adapter trimmed FastQ files of either single-end reads, or singleton
-        single-end or collapsed data and paired-end data, respectively.
+        'orphaned' reads from merging of paired-end data (i.e., one of the pair
-      pattern: "*.{fastq.gz}"
+        was lost due to filtering thresholds).
+      pattern: "*.truncated.gz"
+  - discarded:
+      type: file
+      description: |
+        Adapter trimmed FastQ files of reads that did not pass filtering
+        thresholds.
+      pattern: "*.discarded.gz"
+  - pair1_truncated:
+      type: file
+      description: |
+        Adapter trimmed R1 FastQ files of paired-end reads that did not merge
+        with their respective R2 pair due to long templates. The respective pair
+        is stored in 'pair2_truncated'.
+      pattern: "*.pair1.truncated.gz"
+  - pair2_truncated:
+      type: file
+      description: |
+        Adapter trimmed R2 FastQ files of paired-end reads that did not merge
+        with their respective R1 pair due to long templates. The respective pair
+        is stored in 'pair1_truncated'.
+      pattern: "*.pair2.truncated.gz"
+  - collapsed:
+      type: file
+      description: |
+        Collapsed FastQ of paired-end reads that successfully merged with their
+        respective R1 pair but were not trimmed.
+      pattern: "*.collapsed.gz"
+  - collapsed_truncated:
+      type: file
+      description: |
+        Collapsed FastQ of paired-end reads that successfully merged with their
+        respective R1 pair and were trimmed of adapter due to sufficient overlap.
+      pattern: "*.collapsed.truncated.gz"
   - log:
       type: file
       description: AdapterRemoval log file
@@ -48,3 +81,4 @@ output:
 
 authors:
   - "@maxibor"
+  - "@jfy133"

modules/bcftools/annotate/main.nf

@@ -0,0 +1,42 @@
+process BCFTOOLS_ANNOTATE {
+    tag "$meta.id"
+    label 'process_low'
+
+    conda (params.enable_conda ? "bioconda::bcftools=1.15" : null)
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/bcftools:1.15--haf5b3da_0':
+        'quay.io/biocontainers/bcftools:1.15--haf5b3da_0' }"
+
+    input:
+    tuple val(meta), path(input)
+
+    output:
+    tuple val(meta), path("*_annotated.vcf.gz"), optional:true , emit: vcf
+    tuple val(meta), path("*_annotated.bcf")   , optional:true , emit: bcf
+    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 matcher = input ==~ /\S+\.*vcf\.\S*/
+    def output_suffix = matcher ? "vcf.gz" : "bcf"
+    def output_type_compressed = matcher ? "z" : "b"
+    """
+    bcftools \\
+        annotate \\
+        $args \\
+        --output ${prefix}_annotated.${output_suffix} \\
+        --output-type $output_type_compressed \\
+        --threads $task.cpus \\
+        $input
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        bcftools: \$( bcftools --version |& sed '1!d; s/^.*bcftools //' )
+    END_VERSIONS
+    """
+}

modules/bcftools/annotate/meta.yml

@@ -0,0 +1,45 @@
+name: bcftools_annotate
+description: Add or remove annotations.
+keywords:
+  - bcftools
+  - annotate
+  - vcf
+  - remove
+  - add
+tools:
+  - annotate:
+      description: Add or remove annotations.
+      homepage: http://samtools.github.io/bcftools/bcftools.html
+      documentation: https://samtools.github.io/bcftools/bcftools.html#annotate
+      doi: 10.1093/bioinformatics/btp352
+      licence: ['MIT']
+
+input:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  - input:
+      type: files
+      description: Query VCF or BCF file, can be either uncompressed or compressed
+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: Compressed annotated VCF file
+      pattern: "*_annotated.vcf.gz"
+  - bcf:
+      type: file
+      description: Compressed annotated BCF file
+      pattern: "*_annotated.bcf"
+authors:
+  - "@projectoriented"

modules/bwa/mem/main.nf

@@ -2,10 +2,10 @@ process BWA_MEM {
     tag "$meta.id"
     label 'process_high'
 
-    conda (params.enable_conda ? "bioconda::bwa=0.7.17 bioconda::samtools=1.12" : null)
+    conda (params.enable_conda ? "bioconda::bwa=0.7.17 bioconda::samtools=1.15" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/mulled-v2-fe8faa35dbf6dc65a0f7f5d4ea12e31a79f73e40:66ed1b38d280722529bb8a0167b0cf02f8a0b488-0' :
+        'https://depot.galaxyproject.org/singularity/mulled-v2-fe8faa35dbf6dc65a0f7f5d4ea12e31a79f73e40:c56a3aabc8d64e52d5b9da1e8ecec2031668596d-0' :
-        'quay.io/biocontainers/mulled-v2-fe8faa35dbf6dc65a0f7f5d4ea12e31a79f73e40:66ed1b38d280722529bb8a0167b0cf02f8a0b488-0' }"
+        'quay.io/biocontainers/mulled-v2-fe8faa35dbf6dc65a0f7f5d4ea12e31a79f73e40:c56a3aabc8d64e52d5b9da1e8ecec2031668596d-0' }"
 
     input:
     tuple val(meta), path(reads)

modules/bwa/sampe/main.nf

@@ -2,10 +2,10 @@ process BWA_SAMPE {
     tag "$meta.id"
     label 'process_medium'
 
-    conda (params.enable_conda ? "bioconda::bwa=0.7.17 bioconda::samtools=1.12" : null)
+    conda (params.enable_conda ? "bioconda::bwa=0.7.17 bioconda::samtools=1.15" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/mulled-v2-fe8faa35dbf6dc65a0f7f5d4ea12e31a79f73e40:66ed1b38d280722529bb8a0167b0cf02f8a0b488-0' :
+        'https://depot.galaxyproject.org/singularity/mulled-v2-fe8faa35dbf6dc65a0f7f5d4ea12e31a79f73e40:c56a3aabc8d64e52d5b9da1e8ecec2031668596d-0' :
-        'quay.io/biocontainers/mulled-v2-fe8faa35dbf6dc65a0f7f5d4ea12e31a79f73e40:66ed1b38d280722529bb8a0167b0cf02f8a0b488-0' }"
+        'quay.io/biocontainers/mulled-v2-fe8faa35dbf6dc65a0f7f5d4ea12e31a79f73e40:c56a3aabc8d64e52d5b9da1e8ecec2031668596d-0' }"
 
     input:
     tuple val(meta), path(reads), path(sai)

modules/bwa/samse/main.nf

@@ -2,10 +2,10 @@ process BWA_SAMSE {
     tag "$meta.id"
     label 'process_medium'
 
-    conda (params.enable_conda ? "bioconda::bwa=0.7.17 bioconda::samtools=1.12" : null)
+    conda (params.enable_conda ? "bioconda::bwa=0.7.17 bioconda::samtools=1.15" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/mulled-v2-fe8faa35dbf6dc65a0f7f5d4ea12e31a79f73e40:66ed1b38d280722529bb8a0167b0cf02f8a0b488-0' :
+        'https://depot.galaxyproject.org/singularity/mulled-v2-fe8faa35dbf6dc65a0f7f5d4ea12e31a79f73e40:c56a3aabc8d64e52d5b9da1e8ecec2031668596d-0' :
-        'quay.io/biocontainers/mulled-v2-fe8faa35dbf6dc65a0f7f5d4ea12e31a79f73e40:66ed1b38d280722529bb8a0167b0cf02f8a0b488-0' }"
+        'quay.io/biocontainers/mulled-v2-fe8faa35dbf6dc65a0f7f5d4ea12e31a79f73e40:c56a3aabc8d64e52d5b9da1e8ecec2031668596d-0' }"
 
     input:
     tuple val(meta), path(reads), path(sai)

modules/bwamem2/mem/main.nf

@@ -2,10 +2,10 @@ process BWAMEM2_MEM {
     tag "$meta.id"
     label 'process_high'
 
-    conda (params.enable_conda ? "bioconda::bwa-mem2=2.2.1 bioconda::samtools=1.12" : null)
+    conda (params.enable_conda ? "bioconda::bwa-mem2=2.2.1 bioconda::samtools=1.15" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/mulled-v2-e5d375990341c5aef3c9aff74f96f66f65375ef6:cf603b12db30ec91daa04ba45a8ee0f35bbcd1e2-0' :
+        'https://depot.galaxyproject.org/singularity/mulled-v2-e5d375990341c5aef3c9aff74f96f66f65375ef6:8ee25ae85d7a2bacac3e3139db209aff3d605a18-0' :
-        'quay.io/biocontainers/mulled-v2-e5d375990341c5aef3c9aff74f96f66f65375ef6:cf603b12db30ec91daa04ba45a8ee0f35bbcd1e2-0' }"
+        'quay.io/biocontainers/mulled-v2-e5d375990341c5aef3c9aff74f96f66f65375ef6:8ee25ae85d7a2bacac3e3139db209aff3d605a18-0' }"
 
     input:
     tuple val(meta), path(reads)

modules/controlfreec/main.nf

@@ -0,0 +1,158 @@
+process CONTROLFREEC {
+    tag "$meta.id"
+    label 'process_low'
+
+    conda (params.enable_conda ? "bioconda::control-freec=11.6" : null)
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/control-freec:11.6--h1b792b2_1':
+        'quay.io/biocontainers/control-freec:11.6--h1b792b2_1' }"
+
+    input:
+    tuple val(meta), path(mpileup_normal), path(mpileup_tumor), path(cpn_normal), path(cpn_tumor), path(minipileup_normal), path(minipileup_tumor)
+    path fasta
+    path fai
+    path snp_position
+    path known_snps
+    path known_snps_tbi
+    path chr_directory
+    path mappability
+    path target_bed
+    path gccontent_profile
+
+    output:
+    tuple val(meta), path("*_ratio.BedGraph")   , emit: bedgraph, optional: true
+    tuple val(meta), path("*_control.cpn")      , emit: control_cpn
+    tuple val(meta), path("*_sample.cpn")       , emit: sample_cpn
+    tuple val(meta), path("GC_profile.*.cpn")   , emit: gcprofile_cpn, optional:true
+    tuple val(meta), path("*_BAF.txt")          , emit: BAF
+    tuple val(meta), path("*_CNVs")             , emit: CNV
+    tuple val(meta), path("*_info.txt")         , emit: info
+    tuple val(meta), path("*_ratio.txt")        , emit: ratio
+    tuple val(meta), path("config.txt")         , emit: config
+    path "versions.yml"                         , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    //"General" configurations
+    def bedgraphoutput              = task.ext.args?["general"]?["bedgraphoutput"]              ? "BedGraphOutput = ${task.ext.args["general"]["bedgraphoutput"]}"                              : ""
+    def chr_files                   = chr_directory                                             ? "chrFiles =\${PWD}/${chr_directory}"                                                          : ""
+    def chr_length                  = fai                                                       ? "chrLenFile = \${PWD}/${fai}"                                                                 : ""
+    def breakpointthreshold         = task.ext.args?["general"]?["breakpointthreshold"]         ? "breakPointThreshold = ${task.ext.args["general"]["breakpointthreshold"]}"                    : ""
+    def breakpointtype              = task.ext.args?["general"]?["breakpointtype"]              ? "breakPointType = ${task.ext.args["general"]["breakpointtype"]}"                              : ""
+    def coefficientofvariation      = task.ext.args?["general"]?["coefficient"]                 ? "coefficientOfVariation = ${task.ext.args["general"]["coefficientofvariation"]}"              : ""
+    def contamination               = task.ext.args?["general"]?["contamination"]               ? "contamination = ${task.ext.args["general"]["contamination"]}"                                : ""
+    def contaminationadjustment     = task.ext.args?["general"]?["contaminationadjustment"]     ? "contaminationAdjustment = ${task.ext.args["general"]["contaminationadjustment"]}"            : ""
+    def degree                      = task.ext.args?["general"]?["degree"]                      ? "degree = ${task.ext.args["general"]["degree"]}"                                              : ""
+    def forcegccontentnormalization = task.ext.args?["general"]?["forcegccontentnormalization"] ? "forceGCcontentNormalization = ${task.ext.args["general"]["forcegccontentnormalization"]}"    : ""
+    def gccontentprofile            = gccontent_profile                                         ? "GCcontentProfile = ${gccontent_profile}"                                                     : ""
+    def mappability                 = mappability                                               ? "gemMappabilityFile = \${PWD}/${mappability}"                                                 : ""
+    def intercept                   = task.ext.args?["general"]?["intercept"]                   ? "intercept = ${task.ext.args["general"]["intercept"]}"                                         : ""
+    def mincnalength                = task.ext.args?["general"]?["mincnalength"]                ? "minCNAlength = ${task.ext.args["general"]["mincnalength"]}"                                  : ""
+    def minmappabilityperwindow     = task.ext.args?["general"]?["minmappabilityperwindow"]     ? "minMappabilityPerWindow = ${task.ext.args["general"]["minmappabilityperwindow"]}"            : ""
+    def minexpectedgc               = task.ext.args?["general"]?["minexpectedgc"]               ? "minExpectedGC = ${task.ext.args["general"]["minexpectedgc"]}"                                : ""
+    def maxexpectedgc               = task.ext.args?["general"]?["maxexpectedgc"]               ? "maxExpectedGC = ${task.ext.args["general"]["maxexpectedgc"]}"                                : ""
+    def minimalsubclonepresence     = task.ext.args?["general"]?["minimalsubclonepresence"]     ? "minimalSubclonePresence = ${task.ext.args["general"]["minimalsubclonepresence"]}"            : ""
+    def noisydata                   = task.ext.args?["general"]?["noisydata"]                   ? "noisyData = ${task.ext.args["general"]["noisydata"]}"                                        : ""
+    def output                      = task.ext.prefix                                           ? "outputDir = \${PWD}/${task.ext.prefix}"  : ""
+    def ploidy                      = task.ext.args?["general"]?["ploidy"]                      ? "ploidy = ${task.ext.args["general"]["ploidy"]}"                                              : ""
+    def printNA                     = task.ext.args?["general"]?["printNA"]                     ? "printNA = ${task.ext.args["general"]["printNA"]}"                                            : ""
+    def readcountthreshold          = task.ext.args?["general"]?["readcountthreshold"]          ? "readCountThreshold = ${task.ext.args["general"]["readcountthreshold"]}"                      : ""
+    def sex                         = task.ext.args?["general"]?["sex"]                         ? "sex = ${task.ext.args["general"]["sex"]}"                                                    : ""
+    def step                        = task.ext.args?["general"]?["step"]                        ? "step = ${task.ext.args["general"]["step"]}"                                                  : ""
+    def telocentromeric             = task.ext.args?["general"]?["telocentromeric"]             ? "telocentromeric = ${task.ext.args["general"]["telocentromeric"]} "                           : ""
+    def uniquematch                 = task.ext.args?["general"]?["uniquematch"]                 ? "uniqueMatch = ${task.ext.args["general"]["uniquematch"]}"                                    : ""
+    def window                      = task.ext.args?["general"]?["window"]                      ? "window = ${task.ext.args["general"]["window"]}"                                              : ""
+
+    //"Control" configurations
+    def matefile_normal             = mpileup_normal                                            ? "mateFile = \${PWD}/${mpileup_normal}"                                                        : ""
+    def matecopynumberfile_normal   = cpn_normal                                                ? "mateCopyNumberFile = \${PWD}/${cpn_normal}"                                                  : ""
+    def minipileup_normal           = minipileup_normal                                         ? "miniPileup = \${PWD}/${minipileup_normal}"                                                   : ""
+    def inputformat_normal          = task.ext.args?["control"]?["inputformat"]                 ? "inputFormat = ${task.ext.args["control"]["inputformat"]}"                                    : ""
+    def mateorientation_normal      = task.ext.args?["control"]?["mateorientation"]             ? "mateOrientation = ${task.ext.args["control"]["mateorientation"]}"                            : ""
+
+    //"Sample" configuration
+    def matefile_tumor             = mpileup_tumor                                              ? "mateFile = \${PWD}/${mpileup_tumor}"                                                         : ""
+    def matecopynumberfile_tumor   = cpn_tumor                                                  ? "mateCopyNumberFile = \${PWD}/${cpn_tumor}"                                                   : ""
+    def minipileup_tumor           = minipileup_tumor                                           ? "miniPileup = \${PWD}/${minipileup_tumor}"                                                    : ""
+    def inputformat_tumor          = task.ext.args?["sample"]?["inputformat"]                   ? "inputFormat = ${task.ext.args["sample"]["inputformat"]}"                                     : ""
+    def mateorientation_tumor      = task.ext.args?["sample"]?["mateorientation"]               ? "mateOrientation = ${task.ext.args["sample"]["mateorientation"]}"                             : ""
+
+    //"BAF" configuration
+    def makepileup                 = snp_position                                               ? "makePileup = \${PWD}/${snp_position}"                                                        : ""
+    def fastafile                  = fasta                                                      ? "fastaFile = \${PWD}/${fasta}"                                                                : ""
+    def minimalcoverageperposition = task.ext.args?["BAF"]?["minimalcoverageperposition"]       ? "minimalCoveragePerPosition = ${task.ext.args["BAF"]["minimalcoverageperposition"]}"          : ""
+    def minimalqualityperposition  = task.ext.args?["BAF"]?["minimalqualityperposition"]        ? "minimalQualityPerPosition = ${task.ext.args["BAF"]["minimalqualityperposition"]}"            : ""
+    def shiftinquality             = task.ext.args?["BAF"]?["shiftinquality"]                   ? "shiftInQuality = ${task.ext.args["BAF"]["shiftinquality"]}"                                  : ""
+    def snpfile                    = known_snps                                                 ? "SNPfile = \$PWD/${known_snps}"                                                               : ""
+
+    //"Target" configuration
+    def target_bed                 = target_bed                                                 ? "captureRegions = ${target_bed}"                                                              : ""
+    """
+    touch config.txt
+
+    echo "[general]" >> config.txt
+    echo ${bedgraphoutput} >> config.txt
+    echo ${breakpointthreshold} >> config.txt
+    echo ${breakpointtype} >> config.txt
+    echo ${chr_files} >> config.txt
+    echo ${chr_length} >> config.txt
+    echo ${coefficientofvariation} >> config.txt
+    echo ${contamination} >> config.txt
+    echo ${contaminationadjustment} >> config.txt
+    echo ${degree} >> config.txt
+    echo ${forcegccontentnormalization} >> config.txt
+    echo ${gccontentprofile} >> config.txt
+    echo ${mappability} >> config.txt
+    echo ${intercept} >> config.txt
+    echo ${mincnalength} >> config.txt
+    echo ${minmappabilityperwindow} >> config.txt
+    echo ${minexpectedgc} >> config.txt
+    echo ${maxexpectedgc} >> config.txt
+    echo ${minimalsubclonepresence} >> config.txt
+    echo "maxThreads = ${task.cpus}" >> config.txt
+    echo ${noisydata} >> config.txt
+    echo ${output} >> config.txt
+    echo ${ploidy} >> config.txt
+    echo ${printNA} >> config.txt
+    echo ${readcountthreshold} >> config.txt
+    echo ${sex} >> config.txt
+    echo ${step} >> config.txt
+    echo ${telocentromeric} >> config.txt
+    echo ${uniquematch} >> config.txt
+    echo ${window} >> config.txt
+
+    echo "[control]" >> config.txt
+    echo ${matefile_normal} >> config.txt
+    echo ${matecopynumberfile_normal} >> config.txt
+    echo ${minipileup_normal} >> config.txt
+    echo ${inputformat_normal} >> config.txt
+    echo ${mateorientation_normal} >> config.txt
+
+    echo "[sample]" >> config.txt
+    echo ${matefile_tumor} >> config.txt
+    echo ${matecopynumberfile_tumor} >> config.txt
+    echo ${minipileup_tumor} >> config.txt
+    echo ${inputformat_tumor} >> config.txt
+    echo ${mateorientation_tumor} >> config.txt
+
+    echo "[BAF]" >> config.txt
+    echo ${makepileup} >> config.txt
+    echo ${fastafile} >> config.txt
+    echo ${minimalcoverageperposition} >> config.txt
+    echo ${minimalqualityperposition} >> config.txt
+    echo ${shiftinquality} >> config.txt
+    echo ${snpfile} >> config.txt
+
+    echo "[target]" >> config.txt
+    echo ${target_bed} >> config.txt
+
+    freec -conf config.txt
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        controlfreec: \$(echo \$(freec -version 2>&1) | sed 's/^.*Control-FREEC  //; s/:.*\$//' | sed -e "s/Control-FREEC v//g" )
+    END_VERSIONS
+    """
+}

modules/controlfreec/meta.yml

@@ -0,0 +1,183 @@
+name: controlfreec
+description: Copy number and genotype annotation from whole genome and whole exome sequencing data
+keywords:
+  - cna
+  - cnv
+  - somatic
+  - single
+  - tumor-only
+tools:
+  - controlfreec:
+      description: Copy number and genotype annotation from whole genome and whole exome sequencing data.
+      homepage: http://boevalab.inf.ethz.ch/FREEC
+      documentation: http://boevalab.inf.ethz.ch/FREEC/tutorial.html
+      tool_dev_url: https://github.com/BoevaLab/FREEC/
+      doi: "10.1093/bioinformatics/btq635"
+      licence: ['GPL >=2']
+
+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.
+
+      ```
+      {
+        [
+          "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>
+          ]
+        ]
+      }
+      ```
+
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  - mateFile_normal:
+      type: file
+      description: File with mapped reads
+      pattern: "*.{sam,bam,pileup(.gz),bowtie(.gz),eland(.gz),arachne(.gz),psl(.gz),bed(.gz)}"
+  - mateFile_tumor:
+      type: file
+      description: File with mapped reads
+      pattern: "*.{sam,bam,pileup(.gz),bowtie(.gz),eland(.gz),arachne(.gz),psl(.gz),bed(.gz)}"
+  - cpn_normal:
+      type: file
+      description: Raw copy number profiles (optional)
+      pattern: "*.cpn"
+  - cpn_tumor:
+      type: file
+      description: Raw copy number profiles (optional)
+      pattern: "*.cpn"
+  - minipileup_normal:
+      type: file
+      description: miniPileup file from previous run (optional)
+      pattern: "*.pileup"
+  - minipileup_tumor:
+      type: file
+      description: miniPileup file from previous run (optional)
+      pattern: "*.pileup"
+  - fasta:
+      type: file
+      description: Reference file (optional; required if args 'makePileup' is set)
+      pattern: "*.{fasta,fna,fa}"
+  - fai:
+      type: file
+      description: Fasta index
+      pattern: "*.fai"
+  - snp_position:
+      type: file
+      description:
+      pattern: "*.{}"
+  - known_snps:
+      type: file
+      description: File with known SNPs
+      pattern: "*.{vcf,vcf.gz}"
+  - known_snps_tbi:
+      type: file
+      description: Index of known_snps
+      pattern: "*.tbi"
+  - chr_directory:
+      type: file
+      description: Path to directory with chromosome fasta files (optional, required if gccontentprofile is not provided)
+      pattern: "*/"
+  - mappability:
+      type: file
+      description: Contains information of mappable positions (optional)
+      pattern: "*.gem"
+  - target_bed:
+      type: file
+      description: Sorted bed file containing capture regions (optional)
+      pattern: "*.bed"
+
+
+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"
+  - bedgraph:
+      type: file
+      description: Bedgraph format for the UCSC genome browser
+      pattern: ".bedgraph"
+  - control_cpn:
+      type: file
+      description: files with raw copy number profiles
+      pattern: "*_control.cpn"
+  - sample_cpn:
+      type: file
+      description: files with raw copy number profiles
+      pattern: "*_sample.cpn"
+  - gcprofile_cpn:
+      type: file
+      description: file with GC-content profile.
+      pattern: "GC_profile.*.cpn"
+  - BAF:
+      type: file
+      description: file B-allele frequencies for each possibly heterozygous SNP position
+      pattern: "*_BAF.txt"
+  - CNV:
+      type: file
+      description: file with coordinates of predicted copy number alterations.
+      pattern: "*_CNVs"
+  - info:
+      type: file
+      description: parsable file with information about FREEC run
+      pattern: "*_info.txt"
+  - ratio:
+      type: file
+      description: file with ratios and predicted copy number alterations for each window
+      pattern: "*_ratio.txt"
+  - config:
+      type: file
+      description: Config file used to run Control-FREEC
+      pattern: "config.txt"
+
+authors:
+  - "@FriederikeHanssen"

modules/custom/getchromsizes/main.nf

@@ -2,10 +2,10 @@ process CUSTOM_GETCHROMSIZES {
     tag "$fasta"
     label 'process_low'
 
-    conda (params.enable_conda ? "bioconda::samtools=1.14" : null)
+    conda (params.enable_conda ? "bioconda::samtools=1.15" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/samtools:1.14--hb421002_0' :
+        'https://depot.galaxyproject.org/singularity/samtools:1.15--h1170115_1' :
-        'quay.io/biocontainers/samtools:1.14--hb421002_0' }"
+        'quay.io/biocontainers/samtools:1.15--h1170115_1' }"
 
     input:
     path fasta

modules/deepvariant/main.nf

@@ -17,8 +17,8 @@ process DEEPVARIANT {
     path(fai)
 
     output:
-    tuple val(meta), path("*.vcf.gz") ,  emit: vcf
+    tuple val(meta), path("${prefix}.vcf.gz") ,  emit: vcf
-    tuple val(meta), path("*g.vcf.gz"),  emit: gvcf
+    tuple val(meta), path("${prefix}.g.vcf.gz"),  emit: gvcf
     path "versions.yml"               ,  emit: versions
 
     when:
@@ -26,7 +26,7 @@ process DEEPVARIANT {
 
     script:
     def args = task.ext.args ?: ''
-    def prefix = task.ext.prefix ?: "${meta.id}"
+    prefix = task.ext.prefix ?: "${meta.id}"
     def regions = intervals ? "--regions ${intervals}" : ""
 
     """

modules/faqcs/main.nf

@@ -13,6 +13,7 @@ process FAQCS {
     output:
     tuple val(meta), path('*.trimmed.fastq.gz')           , emit: reads
     tuple val(meta), path('*.stats.txt')                  , emit: stats
+    tuple val(meta), path('*.txt')                        , optional:true, emit: txt
     tuple val(meta), path('*_qc_report.pdf')              , optional:true, emit: statspdf
     tuple val(meta), path('*.log')                        , emit: log
     tuple val(meta), path('*.discard.fastq.gz')           , optional:true, emit: reads_fail

modules/faqcs/meta.yml

@@ -54,6 +54,10 @@ output:
       type: file
       description: trimming/qc text stats file
       pattern: "*.stats.txt"
+  - txt:
+      type: file
+      description: trimming/qc text txt files from --debug option
+      pattern: "*.txt"
   - statspdf:
       type: file
       description: trimming/qc pdf report file

modules/hamronization/deeparg/main.nf

@@ -0,0 +1,44 @@
+process HAMRONIZATION_DEEPARG {
+    tag "$meta.id"
+    label 'process_low'
+
+    conda (params.enable_conda ? "bioconda::hamronization=1.0.3" : null)
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/hamronization:1.0.3--py_0':
+        'quay.io/biocontainers/hamronization:1.0.3--py_0' }"
+
+    input:
+    tuple val(meta), path(report)
+    val(format)
+    val(software_version)
+    val(reference_db_version)
+
+    output:
+    tuple val(meta), path("*.json"), optional: true, emit: json
+    tuple val(meta), path("*.tsv") , optional: true, emit: tsv
+    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}"
+    """
+    hamronize \\
+        deeparg \\
+        ${report} \\
+        $args \\
+        --format ${format} \\
+        --analysis_software_version ${software_version} \\
+        --reference_database_version ${reference_db_version} \\
+        --input_file_name ${prefix} \\
+        > ${prefix}.${format}
+
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        hamronization: \$(echo \$(hamronize --version 2>&1) | cut -f 2 -d ' ' )
+    END_VERSIONS
+    """
+}

modules/hamronization/deeparg/meta.yml

@@ -0,0 +1,60 @@
+name: hamronization_deeparg
+description: Tool to convert and summarize DeepARG outputs using the hAMRonization specification
+keywords:
+  - amr
+  - antimicrobial resistance
+  - reporting
+  - deeparg
+tools:
+  - hamronization:
+      description: Tool to convert and summarize AMR gene detection outputs using the hAMRonization specification
+      homepage: https://github.com/pha4ge/hAMRonization/blob/master/README.md
+      documentation: https://github.com/pha4ge/hAMRonization/blob/master/README.md
+      tool_dev_url: https://github.com/pha4ge/hAMRonization
+      doi: ""
+      licence: ['GNU Lesser General Public v3 (LGPL v3)']
+
+input:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  - report:
+      type: file
+      description: Output .mapping.ARG file from DeepARG
+      pattern: "*.mapping.ARG"
+  - format:
+      type: value
+      description: Type of report file to be produced
+      pattern: "tsv|json"
+  - software_version:
+      type: value
+      description: Version of DeepARG used
+      pattern: "[0-9].[0-9].[0-9]"
+  - reference_db_version:
+      type: value
+      description: Database version of DeepARG used
+      pattern: "[0-9]"
+
+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"
+  - json:
+      type: file
+      description: hAMRonised report in JSON format
+      pattern: "*.json"
+  - tsv:
+      type: file
+      description: hAMRonised report in TSV format
+      pattern: "*.json"
+
+authors:
+  - "@jfy133"

modules/hamronization/summarize/main.nf

@@ -0,0 +1,38 @@
+process HAMRONIZATION_SUMMARIZE {
+    label 'process_low'
+
+    conda (params.enable_conda ? "bioconda::hamronization=1.0.3" : null)
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/hamronization:1.0.3--py_0':
+        'quay.io/biocontainers/hamronization:1.0.3--py_0' }"
+
+    input:
+    path(reports)
+    val(format)
+
+    output:
+    path("hamronization_combined_report.json"), optional: true, emit: json
+    path("hamronization_combined_report.tsv") , optional: true, emit: tsv
+    path("hamronization_combined_report.html"), optional: true, emit: html
+    path "versions.yml"                       , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args = task.ext.args ?: ''
+    def outformat = format == 'interactive' ? 'html' : format
+    """
+    hamronize \\
+        summarize \\
+        ${reports.join(' ')} \\
+        -t ${format} \\
+        $args \\
+        -o hamronization_combined_report.${outformat}
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        hamronization: \$(echo \$(hamronize --version 2>&1) | cut -f 2 -d ' ' )
+    END_VERSIONS
+    """
+}

modules/hamronization/summarize/meta.yml

@@ -0,0 +1,45 @@
+name: hamronization_summarize
+description: Tool to summarize and combine all hAMRonization reports into a single file
+keywords:
+  - amr
+  - antimicrobial resistance
+  - reporting
+tools:
+  - hamronization:
+      description: Tool to convert and summarize AMR gene detection outputs using the hAMRonization specification
+      homepage: https://github.com/pha4ge/hAMRonization/blob/master/README.md
+      documentation: https://github.com/pha4ge/hAMRonization/blob/master/README.md
+      tool_dev_url: https://github.com/pha4ge/hAMRonization
+      doi: ""
+      licence: ['GNU Lesser General Public v3 (LGPL v3)']
+
+input:
+  - reports:
+      type: file
+      description: List of multiple hAMRonization reports in either JSON or TSV format
+      pattern: "*.{json,tsv}"
+  - format:
+      type: value
+      description: Type of final combined report file to be produced
+      pattern: "tsv|json|interactive"
+
+output:
+  - versions:
+      type: file
+      description: File containing software versions
+      pattern: "versions.yml"
+  - json:
+      type: file
+      description: hAMRonised summary in JSON format
+      pattern: "*.json"
+  - tsv:
+      type: file
+      description: hAMRonised summary in TSV format
+      pattern: "*.json"
+  - html:
+      type: file
+      description: hAMRonised summary in HTML format
+      pattern: "*.html"
+
+authors:
+  - "@jfy133"

modules/hpsuissero/main.nf

@@ -0,0 +1,44 @@
+def VERSION = '1.0.1' // Version information not provided by tool on CLI
+
+process HPSUISSERO {
+    tag "$meta.id"
+    label 'process_low'
+
+    conda (params.enable_conda ? "bioconda::hpsuissero=1.0.1" : null)
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/hpsuissero%3A1.0.1--hdfd78af_0':
+        'quay.io/biocontainers/hpsuissero:1.0.1--hdfd78af_0' }"
+
+    input:
+    tuple val(meta), path(fasta)
+
+    output:
+    tuple val(meta), path("*.tsv"), emit: tsv
+    path "versions.yml"           , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    def is_compressed = fasta.getName().endsWith(".gz") ? true : false
+    def fasta_name = fasta.getName().replace(".gz", "")
+    """
+    if [ "$is_compressed" == "true" ]; then
+        gzip -c -d $fasta > $fasta_name
+    fi
+
+    HpsuisSero.sh \\
+        -i $fasta_name \\
+        -o ./ \\
+        -s $prefix \\
+        -x fasta \\
+        -t $task.cpus
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        hpsuissero: $VERSION
+    END_VERSIONS
+    """
+}

modules/hpsuissero/meta.yml

@@ -0,0 +1,43 @@
+name: hpsuissero
+description: Serotype prediction of Haemophilus parasuis assemblies
+keywords:
+  - bacteria
+  - fasta
+  - haemophilus
+tools:
+  - hpsuissero:
+      description: Rapid Haemophilus parasuis serotyping pipeline for Nanpore data
+      homepage: https://github.com/jimmyliu1326/HpsuisSero
+      documentation: https://github.com/jimmyliu1326/HpsuisSero
+      tool_dev_url: https://github.com/jimmyliu1326/HpsuisSero
+      doi: ""
+      licence: ['MIT']
+
+input:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  - fasta:
+      type: file
+      description: Assembly in FASTA format
+      pattern: "*.{fasta,fasta.gz,fa,fa.gz,fna,fna.gz,faa,faa.gz}"
+
+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"
+  - tsv:
+      type: file
+      description: Tab-delimited serotype prediction
+      pattern: "*.{tsv}"
+
+authors:
+  - "@rpetit3"

modules/leehom/meta.yml

@@ -61,11 +61,11 @@ output:
       pattern: "*.r1.fail.fq.gz"
   - unmerged_r2_fq_pass:
       type: file
-      description: Passed unmerged R1 FASTQs
+      description: Passed unmerged R2 FASTQs
       pattern: "*.r2.fq.gz"
   - unmerged_r2_fq_pass:
       type: file
-      description: Failed unmerged R1 FASTQs
+      description: Failed unmerged R2 FASTQs
       pattern: "*.r2.fail.fq.gz"
   - log:
       type: file

modules/mafft/main.nf

@@ -0,0 +1,35 @@
+process MAFFT {
+    tag "$meta.id"
+    label 'process_high'
+
+    conda (params.enable_conda ? "bioconda::mafft=7.490" : null)
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/mafft:7.490--h779adbc_0':
+        'quay.io/biocontainers/mafft:7.490--h779adbc_0' }"
+
+    input:
+    tuple val(meta), path(fasta)
+
+    output:
+    tuple val(meta), path("*.fas"), emit: fas
+    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}"
+    """
+    mafft \\
+        --thread ${task.cpus} \\
+        ${args} \\
+        ${fasta} \\
+        > ${prefix}.fas
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        mafft: \$(mafft --version 2>&1 | sed 's/^v//' | sed 's/ (.*)//')
+    END_VERSIONS
+    """
+}

modules/mafft/meta.yml

@@ -0,0 +1,42 @@
+name: mafft
+description: Multiple sequence alignment using MAFFT
+keywords:
+  - msa
+  - multiple sequence alignment
+tools:
+  - mafft:
+      description: Multiple alignment program for amino acid or nucleotide sequences based on fast Fourier transform
+      homepage: https://mafft.cbrc.jp/alignment/software/
+      documentation: https://mafft.cbrc.jp/alignment/software/manual/manual.html
+      tool_dev_url: https://mafft.cbrc.jp/alignment/software/source.html
+      doi: "10.1093/nar/gkf436"
+      licence: ['BSD']
+
+input:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  - fasta:
+      type: file
+      description: FASTA file containing the sequences to align
+      pattern: "*.{fa,fasta}"
+
+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"
+  - fas:
+      type: file
+      description: Aligned sequences in FASTA format
+      pattern: "*.{fas}"
+
+authors:
+  - "@MillironX"

modules/malt/run/main.nf

@@ -1,4 +1,5 @@
 process MALT_RUN {
+    tag "$meta.id"
     label 'process_high'
 
     conda (params.enable_conda ? "bioconda::malt=0.53" : null)
@@ -7,21 +8,22 @@ process MALT_RUN {
         'quay.io/biocontainers/malt:0.53--hdfd78af_0' }"
 
     input:
-    path fastqs
+    tuple val(meta), path(fastqs)
     val mode
     path index
 
     output:
-    path "*.rma6"                          , emit: rma6
+    tuple val(meta), path("*.rma6")                          , emit: rma6
-    path "*.{tab,text,sam}",  optional:true, emit: alignments
+    tuple val(meta), path("*.{tab,text,sam}"),  optional:true, emit: alignments
-    path "*.log"                           , emit: log
+    tuple val(meta), path("*.log")                           , emit: log
-    path "versions.yml"                    , emit: versions
+    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 avail_mem = 6
     if (!task.memory) {
         log.info '[MALT_RUN] Available memory not known - defaulting to 6GB. Specify process memory requirements to change this.'
@@ -38,7 +40,7 @@ process MALT_RUN {
         $args \\
         --inFile ${fastqs.join(' ')} \\
         -m $mode \\
-        --index $index/ |&tee malt-run.log
+        --index $index/ |&tee ${prefix}-malt-run.log
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":

modules/malt/run/meta.yml

@@ -19,6 +19,11 @@ tools:
       licence: ["GPL v3"]
 
 input:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
   - fastqs:
       type: file
       description: Input FASTQ files
@@ -47,7 +52,7 @@ output:
   - log:
       type: file
       description: Log of verbose MALT stdout
-      pattern: "malt-run.log"
+      pattern: "*-malt-run.log"
 
 authors:
   - "@jfy133"

modules/maxbin2/main.nf

@@ -29,8 +29,9 @@ process MAXBIN2 {
     def prefix = task.ext.prefix ?: "${meta.id}"
     def associate_files = reads ? "-reads $reads" : "-abund $abund"
     """
+    mkdir input/ && mv $contigs input/
     run_MaxBin.pl \\
-        -contig $contigs \\
+        -contig input/$contigs \\
         $associate_files \\
         -thread $task.cpus \\
         $args \\

modules/picard/cleansam/main.nf

@@ -1,6 +1,6 @@
 process PICARD_CLEANSAM {
     tag "$meta.id"
-    label 'process_low'
+    label 'process_medium'
 
     conda (params.enable_conda ? "bioconda::picard=2.26.9" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
@@ -8,10 +8,10 @@ process PICARD_CLEANSAM {
         'quay.io/biocontainers/picard:2.26.9--hdfd78af_0' }"
 
     input:
-    tuple val(meta), path(sam)
+    tuple val(meta), path(bam)
 
     output:
-    tuple val(meta), path("*.sam"), emit: sam
+    tuple val(meta), path("*.bam"), emit: bam
     path "versions.yml"           , emit: versions
 
     when:
@@ -20,7 +20,6 @@ process PICARD_CLEANSAM {
     script:
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
-    def STRINGENCY = task.ext.stringency ?: "STRICT"
     def avail_mem = 3
     if (!task.memory) {
         log.info '[Picard CleanSam] Available memory not known - defaulting to 3GB. Specify process memory requirements to change this.'
@@ -32,9 +31,8 @@ process PICARD_CLEANSAM {
         -Xmx${avail_mem}g \\
         CleanSam  \\
         ${args} \\
-        -I ${sam} \\
+        -I ${bam} \\
-        -O ${prefix}.sam \\
+        -O ${prefix}.bam
-        --VALIDATION_STRINGENCY ${STRINGENCY}
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":

modules/picard/cleansam/meta.yml

@@ -1,8 +1,7 @@
 name: picard_cleansam
-description: Cleans the provided SAM/BAM, soft-clipping beyond-end-of-reference alignments and setting MAPQ to 0 for unmapped reads
+description: Cleans the provided BAM, soft-clipping beyond-end-of-reference alignments and setting MAPQ to 0 for unmapped reads
 keywords:
   - clean
-  - sam
   - bam
 tools:
   - picard:
@@ -22,8 +21,8 @@ input:
         e.g. [ id:'test', single_end:false ]
   - sam:
       type: file
-      description: SAM file
+      description: BAM file
-      pattern: "*.{sam}"
+      pattern: "*.{bam}"
 
 output:
   - meta:
@@ -37,8 +36,8 @@ output:
       pattern: "versions.yml"
   - sam:
       type: file
-      description: Cleaned SAM file
+      description: Cleaned BAM file
-      pattern: "*.{sam}"
+      pattern: "*.{bam}"
 
 authors:
   - "@sateeshperi"

modules/picard/sortvcf/main.nf

@@ -0,0 +1,49 @@
+process PICARD_SORTVCF {
+    tag "$meta.id"
+    label 'process_medium'
+
+    conda (params.enable_conda ? "bioconda::picard=2.26.10" : null)
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/picard:2.26.10--hdfd78af_0' :
+        'quay.io/biocontainers/picard:2.26.10--hdfd78af_0' }"
+
+    input:
+    tuple val(meta), path(vcf)
+    path reference
+    path sequence_dict
+
+    output:
+    tuple val(meta), path("*_sorted.vcf.gz"), emit: vcf
+    path "versions.yml"                     , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    def seq_dict = sequence_dict ? "-SEQUENCE_DICTIONARY $sequence_dict" : ""
+    def reference = reference ? "-REFERENCE_SEQUENCE $reference" : ""
+    def avail_mem = 3
+    if (!task.memory) {
+        log.info '[Picard SortVcf] Available memory not known - defaulting to 3GB. Specify process memory requirements to change this.'
+    } else {
+        avail_mem = task.memory.giga
+    }
+
+    """
+    picard \\
+        SortVcf \\
+        -Xmx${avail_mem}g \\
+        --INPUT $vcf \\
+        $args \\
+        $seq_dict \\
+        $reference \\
+        --OUTPUT ${prefix}_sorted.vcf.gz
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        picard: \$(picard SortVcf --version 2>&1 | grep -o 'Version:.*' | cut -f2- -d:)
+    END_VERSIONS
+    """
+}

modules/picard/sortvcf/meta.yml

@@ -0,0 +1,40 @@
+name: picard_sortvcf
+description: Sorts vcf files
+keywords:
+  - sort
+  - vcf
+tools:
+  - picard:
+      description: Java tools for working with NGS data in the BAM/CRAM/SAM and VCF format
+      homepage: https://broadinstitute.github.io/picard/
+      documentation: https://broadinstitute.github.io/picard/command-line-overview.html#SortVcf
+      licence: ['MIT']
+
+input:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  - vcf:
+      type: file
+      description: VCF file
+      pattern: "*.{vcf,vcf.gz}"
+
+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: Sorted VCF file
+      pattern: "*.{vcf}"
+
+authors:
+  - "@ramprasadn"

modules/plink2/extract/main.nf

@@ -23,11 +23,13 @@ process PLINK2_EXTRACT {
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
     if( "$pgen" == "${prefix}.pgen" ) error "Input and output names are the same, use \"task.ext.prefix\" in modules.config to disambiguate!"
+    def mem_mb = task.memory.toMega()
     """
     plink2 \\
+        --threads $task.cpus \\
+        --memory $mem_mb \\
         --pfile ${pgen.baseName} \\
         $args \\
-        --threads $task.cpus \\
         --extract $variants \\
         --make-pgen vzs \\
         --out ${prefix}

modules/plink2/score/main.nf

@@ -0,0 +1,39 @@
+process PLINK2_SCORE {
+    tag "$meta.id"
+    label 'process_low'
+
+    conda (params.enable_conda ? "bioconda::plink2=2.00a2.3" : null)
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/plink2:2.00a2.3--h712d239_1' :
+        'quay.io/biocontainers/plink2:2.00a2.3--h712d239_1' }"
+
+    input:
+    tuple val(meta), path(pgen), path(psam), path(pvar)
+    path(scorefile)
+
+    output:
+    tuple val(meta), path("*.sscore"), emit: score
+    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 mem_mb = task.memory.toMega() // plink is greedy
+    """
+    plink2 \\
+        --threads $task.cpus \\
+        --memory $mem_mb \\
+        --pfile ${pgen.baseName} vzs \\
+        --score ${scorefile} \\
+        $args \\
+        --out ${prefix}
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        plink2: \$(plink2 --version 2>&1 | sed 's/^PLINK v//; s/ 64.*\$//' )
+    END_VERSIONS
+    """
+}

modules/plink2/score/meta.yml

@@ -0,0 +1,56 @@
+name: plink2_score
+description: Apply a scoring system to each sample in a plink 2 fileset
+keywords:
+  - plink2
+  - score
+tools:
+  - plink2:
+      description: |
+          Whole genome association analysis toolset, designed to perform a range
+          of basic, large-scale analyses in a computationally efficient manner
+      homepage: http://www.cog-genomics.org/plink/2.0/
+      documentation: http://www.cog-genomics.org/plink/2.0/general_usage
+      tool_dev_url: None
+      doi: "10.1186/s13742-015-0047-8"
+      licence: ['GPL v3']
+
+input:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  - pgen:
+      type: file
+      description: PLINK 2 binary genotype table
+      pattern: "*.{pgen}"
+  - psam:
+      type: file
+      description: PLINK 2 sample information file
+      pattern: "*.{psam}"
+  - pvar:
+      type: file
+      description: PLINK 2 variant information file
+      pattern: "*.{pvar}"
+  - scorefile:
+      type: file
+      description: A text file containing variant identifiers and weights
+      pattern: "*.{scores,txt,scorefile}"
+
+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"
+  - score:
+      type: file
+      description: A text file containing sample scores, in plink 2 .sscore format
+      pattern: "*.{sscore}"
+
+authors:
+  - "@nebfield"

modules/plink2/vcf/main.nf

@@ -11,10 +11,10 @@ process PLINK2_VCF {
     tuple val(meta), path(vcf)
 
     output:
-    tuple val(meta), path("*.pgen"), emit: pgen
+    tuple val(meta), path("*.pgen")    , emit: pgen
-    tuple val(meta), path("*.psam"), emit: psam
+    tuple val(meta), path("*.psam")    , emit: psam
-    tuple val(meta), path("*.pvar"), emit: pvar
+    tuple val(meta), path("*.pvar.zst"), emit: pvar
-    path "versions.yml"            , emit: versions
+    path "versions.yml"                , emit: versions
 
     when:
     task.ext.when == null || task.ext.when
@@ -22,10 +22,14 @@ process PLINK2_VCF {
     script:
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
+    def mem_mb = task.memory.toMega()
     """
     plink2 \\
+        --threads $task.cpus \\
+        --memory $mem_mb \\
         $args \\
         --vcf $vcf \\
+        --make-pgen vzs \\
         --out ${prefix}
 
     cat <<-END_VERSIONS > versions.yml

modules/plink2/vcf/meta.yml

@@ -46,7 +46,7 @@ output:
   - pvar:
       type: file
       description: PLINK 2 variant information file
-      pattern: "*.{psam}"
+      pattern: "*.{pvar.zst}"
 
 authors:
   - "@nebfield"

modules/qualimap/bamqccram/main.nf

@@ -2,10 +2,10 @@ process QUALIMAP_BAMQCCRAM {
     tag "$meta.id"
     label 'process_medium'
 
-    conda (params.enable_conda ? "bioconda::qualimap=2.2.2d bioconda::samtools=1.12" : null)
+    conda (params.enable_conda ? "bioconda::qualimap=2.2.2d bioconda::samtools=1.15" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/mulled-v2-d3934ca6bb4e61334891ffa2e9a4c87a530e3188:4bf11d12f2c3eccf1eb585097c0b6fd31c18c418-0' :
+        'https://depot.galaxyproject.org/singularity/mulled-v2-d3934ca6bb4e61334891ffa2e9a4c87a530e3188:9838874d42d4477d5042782ee019cec9854da7d5-0' :
-        'quay.io/biocontainers/mulled-v2-d3934ca6bb4e61334891ffa2e9a4c87a530e3188:4bf11d12f2c3eccf1eb585097c0b6fd31c18c418-0' }"
+        'quay.io/biocontainers/mulled-v2-d3934ca6bb4e61334891ffa2e9a4c87a530e3188:9838874d42d4477d5042782ee019cec9854da7d5-0' }"
 
     input:
     tuple val(meta), path(cram), path(crai)

modules/samtools/ampliconclip/main.nf

@@ -2,10 +2,10 @@ process SAMTOOLS_AMPLICONCLIP {
     tag "$meta.id"
     label 'process_medium'
 
-    conda (params.enable_conda ? "bioconda::samtools=1.14" : null)
+    conda (params.enable_conda ? "bioconda::samtools=1.15" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/samtools:1.14--hb421002_0' :
+        'https://depot.galaxyproject.org/singularity/samtools:1.15--h1170115_1' :
-        'quay.io/biocontainers/samtools:1.14--hb421002_0' }"
+        'quay.io/biocontainers/samtools:1.15--h1170115_1' }"
 
     input:
     tuple val(meta), path(bam)

modules/samtools/bam2fq/main.nf

@@ -2,10 +2,10 @@ process SAMTOOLS_BAM2FQ {
     tag "$meta.id"
     label 'process_low'
 
-    conda (params.enable_conda ? "bioconda::samtools=1.14" : null)
+    conda (params.enable_conda ? "bioconda::samtools=1.15" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/samtools:1.14--hb421002_0' :
+        'https://depot.galaxyproject.org/singularity/samtools:1.15--h1170115_1' :
-        'quay.io/biocontainers/samtools:1.14--hb421002_0' }"
+        'quay.io/biocontainers/samtools:1.15--h1170115_1' }"
 
     input:
     tuple val(meta), path(inputbam)

modules/samtools/depth/main.nf

@@ -2,10 +2,10 @@ process SAMTOOLS_DEPTH {
     tag "$meta.id"
     label 'process_low'
 
-    conda (params.enable_conda ? "bioconda::samtools=1.14" : null)
+    conda (params.enable_conda ? "bioconda::samtools=1.15" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/samtools:1.14--hb421002_0' :
+        'https://depot.galaxyproject.org/singularity/samtools:1.15--h1170115_1' :
-        'quay.io/biocontainers/samtools:1.14--hb421002_0' }"
+        'quay.io/biocontainers/samtools:1.15--h1170115_1' }"
 
     input:
     tuple val(meta), path(bam)

modules/samtools/faidx/main.nf

@@ -2,10 +2,10 @@ process SAMTOOLS_FAIDX {
     tag "$fasta"
     label 'process_low'
 
-    conda (params.enable_conda ? "bioconda::samtools=1.14" : null)
+    conda (params.enable_conda ? "bioconda::samtools=1.15" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/samtools:1.14--hb421002_0' :
+        'https://depot.galaxyproject.org/singularity/samtools:1.15--h1170115_1' :
-        'quay.io/biocontainers/samtools:1.14--hb421002_0' }"
+        'quay.io/biocontainers/samtools:1.15--h1170115_1' }"
 
     input:
     tuple val(meta), path(fasta)

modules/samtools/fastq/main.nf

@@ -2,10 +2,10 @@ process SAMTOOLS_FASTQ {
     tag "$meta.id"
     label 'process_low'
 
-    conda (params.enable_conda ? "bioconda::samtools=1.14" : null)
+    conda (params.enable_conda ? "bioconda::samtools=1.15" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/samtools:1.14--hb421002_0' :
+        'https://depot.galaxyproject.org/singularity/samtools:1.15--h1170115_1' :
-        'quay.io/biocontainers/samtools:1.14--hb421002_0' }"
+        'quay.io/biocontainers/samtools:1.15--h1170115_1' }"
 
     input:
     tuple val(meta), path(bam)

modules/samtools/fixmate/main.nf

@@ -2,10 +2,10 @@ process SAMTOOLS_FIXMATE {
     tag "$meta.id"
     label 'process_low'
 
-    conda (params.enable_conda ? "bioconda::samtools=1.14" : null)
+    conda (params.enable_conda ? "bioconda::samtools=1.15" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/samtools:1.14--hb421002_0' :
+        'https://depot.galaxyproject.org/singularity/samtools:1.15--h1170115_1' :
-        'quay.io/biocontainers/samtools:1.14--hb421002_0' }"
+        'quay.io/biocontainers/samtools:1.15--h1170115_1' }"
 
     input:
     tuple val(meta), path(bam)

modules/samtools/flagstat/main.nf

@@ -2,10 +2,10 @@ process SAMTOOLS_FLAGSTAT {
     tag "$meta.id"
     label 'process_low'
 
-    conda (params.enable_conda ? "bioconda::samtools=1.14" : null)
+    conda (params.enable_conda ? "bioconda::samtools=1.15" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/samtools:1.14--hb421002_0' :
+        'https://depot.galaxyproject.org/singularity/samtools:1.15--h1170115_1' :
-        'quay.io/biocontainers/samtools:1.14--hb421002_0' }"
+        'quay.io/biocontainers/samtools:1.15--h1170115_1' }"
 
     input:
     tuple val(meta), path(bam), path(bai)

modules/samtools/idxstats/main.nf

@@ -2,10 +2,10 @@ process SAMTOOLS_IDXSTATS {
     tag "$meta.id"
     label 'process_low'
 
-    conda (params.enable_conda ? "bioconda::samtools=1.14" : null)
+    conda (params.enable_conda ? "bioconda::samtools=1.15" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/samtools:1.14--hb421002_0' :
+        'https://depot.galaxyproject.org/singularity/samtools:1.15--h1170115_1' :
-        'quay.io/biocontainers/samtools:1.14--hb421002_0' }"
+        'quay.io/biocontainers/samtools:1.15--h1170115_1' }"
 
     input:
     tuple val(meta), path(bam), path(bai)

modules/samtools/index/main.nf

@@ -2,10 +2,10 @@ process SAMTOOLS_INDEX {
     tag "$meta.id"
     label 'process_low'
 
-    conda (params.enable_conda ? "bioconda::samtools=1.14" : null)
+    conda (params.enable_conda ? "bioconda::samtools=1.15" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/samtools:1.14--hb421002_0' :
+        'https://depot.galaxyproject.org/singularity/samtools:1.15--h1170115_1' :
-        'quay.io/biocontainers/samtools:1.14--hb421002_0' }"
+        'quay.io/biocontainers/samtools:1.15--h1170115_1' }"
 
     input:
     tuple val(meta), path(input)

modules/samtools/merge/main.nf

@@ -2,10 +2,10 @@ process SAMTOOLS_MERGE {
     tag "$meta.id"
     label 'process_low'
 
-    conda (params.enable_conda ? "bioconda::samtools=1.14" : null)
+    conda (params.enable_conda ? "bioconda::samtools=1.15" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/samtools:1.14--hb421002_0' :
+        'https://depot.galaxyproject.org/singularity/samtools:1.15--h1170115_1' :
-        'quay.io/biocontainers/samtools:1.14--hb421002_0' }"
+        'quay.io/biocontainers/samtools:1.15--h1170115_1' }"
 
     input:
     tuple val(meta), path(input_files)

modules/samtools/mpileup/main.nf

@@ -2,10 +2,10 @@ process SAMTOOLS_MPILEUP {
     tag "$meta.id"
     label 'process_medium'
 
-    conda (params.enable_conda ? "bioconda::samtools=1.14" : null)
+    conda (params.enable_conda ? "bioconda::samtools=1.15" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/samtools:1.14--hb421002_0' :
+        'https://depot.galaxyproject.org/singularity/samtools:1.15--h1170115_1' :
-        'quay.io/biocontainers/samtools:1.14--hb421002_0' }"
+        'quay.io/biocontainers/samtools:1.15--h1170115_1' }"
 
     input:
     tuple val(meta), path(bam)

modules/samtools/sort/main.nf

@@ -2,10 +2,10 @@ process SAMTOOLS_SORT {
     tag "$meta.id"
     label 'process_medium'
 
-    conda (params.enable_conda ? "bioconda::samtools=1.14" : null)
+    conda (params.enable_conda ? "bioconda::samtools=1.15" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/samtools:1.14--hb421002_0' :
+        'https://depot.galaxyproject.org/singularity/samtools:1.15--h1170115_1' :
-        'quay.io/biocontainers/samtools:1.14--hb421002_0' }"
+        'quay.io/biocontainers/samtools:1.15--h1170115_1' }"
 
     input:
     tuple val(meta), path(bam)

modules/samtools/stats/main.nf

@@ -2,10 +2,10 @@ process SAMTOOLS_STATS {
     tag "$meta.id"
     label 'process_low'
 
-    conda (params.enable_conda ? "bioconda::samtools=1.14" : null)
+    conda (params.enable_conda ? "bioconda::samtools=1.15" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/samtools:1.14--hb421002_0' :
+        'https://depot.galaxyproject.org/singularity/samtools:1.15--h1170115_1' :
-        'quay.io/biocontainers/samtools:1.14--hb421002_0' }"
+        'quay.io/biocontainers/samtools:1.15--h1170115_1' }"
 
     input:
     tuple val(meta), path(input), path(input_index)

modules/samtools/view/main.nf

@@ -2,10 +2,10 @@ process SAMTOOLS_VIEW {
     tag "$meta.id"
     label 'process_medium'
 
-    conda (params.enable_conda ? "bioconda::samtools=1.14" : null)
+    conda (params.enable_conda ? "bioconda::samtools=1.15" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/samtools:1.14--hb421002_0' :
+        'https://depot.galaxyproject.org/singularity/samtools:1.15--h1170115_1' :
-        'quay.io/biocontainers/samtools:1.14--hb421002_0' }"
+        'quay.io/biocontainers/samtools:1.15--h1170115_1' }"
 
     input:
     tuple val(meta), path(input)

modules/ssuissero/main.nf

@@ -0,0 +1,44 @@
+def VERSION = '1.0.1' // Version information not provided by tool on CLI
+
+process SSUISSERO {
+    tag "$meta.id"
+    label 'process_low'
+
+    conda (params.enable_conda ? "bioconda::ssuissero=1.0.1" : null)
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/ssuissero%3A1.0.1--hdfd78af_0':
+        'quay.io/biocontainers/ssuissero:1.0.1--hdfd78af_0' }"
+
+    input:
+    tuple val(meta), path(fasta)
+
+    output:
+    tuple val(meta), path("*.tsv"), emit: tsv
+    path "versions.yml"           , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    def is_compressed = fasta.getName().endsWith(".gz") ? true : false
+    def fasta_name = fasta.getName().replace(".gz", "")
+    """
+    if [ "$is_compressed" == "true" ]; then
+        gzip -c -d $fasta > $fasta_name
+    fi
+
+    SsuisSero.sh \\
+        -i $fasta_name \\
+        -o ./ \\
+        -s $prefix \\
+        -x fasta \\
+        -t $task.cpus
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        ssuissero: $VERSION
+    END_VERSIONS
+    """
+}

modules/ssuissero/meta.yml

@@ -0,0 +1,43 @@
+name: ssuissero
+description: Serotype prediction of Streptococcus suis assemblies
+keywords:
+  - bacteria
+  - fasta
+  - streptococcus
+tools:
+  - ssuissero:
+      description: Rapid Streptococcus suis serotyping pipeline for Nanopore Data
+      homepage: https://github.com/jimmyliu1326/SsuisSero
+      documentation: https://github.com/jimmyliu1326/SsuisSero
+      tool_dev_url: https://github.com/jimmyliu1326/SsuisSero
+      doi: ""
+      licence: ['MIT']
+
+input:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  - fasta:
+      type: file
+      description: Assembly in FASTA format
+      pattern: "*.{fasta,fasta.gz,fa,fa.gz,fna,fna.gz,faa,faa.gz}"
+
+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"
+  - tsv:
+      type: file
+      description: Tab-delimited serotype prediction
+      pattern: "*.{tsv}"
+
+authors:
+  - "@rpetit3"

modules/stranger/main.nf

@@ -0,0 +1,33 @@
+process STRANGER {
+    tag "$meta.id"
+    label 'process_low'
+
+    conda (params.enable_conda ? "bioconda::stranger=0.8.1" : null)
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/stranger:0.8.1--pyh5e36f6f_0':
+        'quay.io/biocontainers/stranger:0.8.1--pyh5e36f6f_0' }"
+
+    input:
+    tuple val(meta), path(vcf)
+
+    output:
+    tuple val(meta), path("*.gz"), emit: vcf
+    path "versions.yml"          , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    stranger \\
+        $args \\
+        $vcf | gzip --no-name > ${prefix}.vcf.gz
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        stranger: \$( stranger --version )
+    END_VERSIONS
+    """
+}

modules/stranger/meta.yml

@@ -0,0 +1,44 @@
+name: stranger
+description: Annotates output files from ExpansionHunter with the pathologic implications of the repeat sizes.
+keywords:
+  - STR
+  - repeat_expansions
+  - annotate
+  - vcf
+tools:
+  - stranger:
+      description: Annotate VCF files with str variants
+      homepage: https://github.com/moonso/stranger
+      documentation: https://github.com/moonso/stranger
+      tool_dev_url: https://github.com/moonso/stranger
+      doi: "10.5281/zenodo.4548873"
+      licence: ['MIT']
+
+input:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  - vcf:
+      type: file
+      description: VCF with repeat expansions
+      pattern: "*.{vcf.gz,vcf}"
+
+output:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  - versions:
+      type: file
+      description: File containing software versions
+      pattern: "versions.yml"
+  - vcf:
+      type: file
+      description: annotated VCF with keys STR_STATUS, NormalMax and PathologicMin
+      pattern: "*.{vcf.gz}"
+
+authors:
+  - "@ljmesi"

modules/untar/main.nf

@@ -2,7 +2,7 @@ process UNTAR {
     tag "$archive"
     label 'process_low'
 
-    conda (params.enable_conda ? "conda-forge::sed=4.7" : null)
+    conda (params.enable_conda ? "conda-forge::tar=1.32" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://containers.biocontainers.pro/s3/SingImgsRepo/biocontainers/v1.2.0_cv1/biocontainers_v1.2.0_cv1.img' :
         'biocontainers/biocontainers:v1.2.0_cv1' }"

modules/yara/mapper/main.nf

@@ -13,6 +13,7 @@ process YARA_MAPPER {
 
     output:
     tuple val(meta), path("*.mapped.bam"), emit: bam
+    tuple val(meta), path("*.mapped.bam.bai"), emit: bai
     path "versions.yml"                  , emit: versions
 
     when:
@@ -28,7 +29,9 @@ process YARA_MAPPER {
             -t $task.cpus \\
             -f bam \\
             ${index}/yara \\
-            $reads | samtools view -@ $task.cpus -hb -F4 > ${prefix}.mapped.bam
+            $reads | samtools view -@ $task.cpus -hb -F4 | samtools sort -@ $task.cpus > ${prefix}.mapped.bam
+
+        samtools index -@ $task.cpus ${prefix}.mapped.bam
 
         cat <<-END_VERSIONS > versions.yml
         "${task.process}":
@@ -46,8 +49,11 @@ process YARA_MAPPER {
             ${reads[0]} \\
             ${reads[1]} > output.bam
 
-        samtools view -@ $task.cpus -hF 4 -f 0x40 -b output.bam > ${prefix}_1.mapped.bam
+        samtools view -@ $task.cpus -hF 4 -f 0x40 -b output.bam | samtools sort -@ $task.cpus > ${prefix}_1.mapped.bam
-        samtools view -@ $task.cpus -hF 4 -f 0x80 -b output.bam > ${prefix}_2.mapped.bam
+        samtools view -@ $task.cpus -hF 4 -f 0x80 -b output.bam | samtools sort -@ $task.cpus > ${prefix}_2.mapped.bam
+
+        samtools index -@ $task.cpus ${prefix}_1.mapped.bam
+        samtools index -@ $task.cpus ${prefix}_2.mapped.bam
 
         cat <<-END_VERSIONS > versions.yml
         "${task.process}":

modules/yara/mapper/meta.yml

@@ -45,6 +45,10 @@ output:
       type: file
       description: Sorted BAM file
       pattern: "*.{bam}"
+  - bai:
+      type: file
+      description: Sorted BAM file index
+      pattern: "*.{bai}"
 
 authors:
   - "@apeltzer"

tests/config/pytest_modules.yml

@@ -98,6 +98,10 @@ bbmap/index:
   - modules/bbmap/index/**
   - tests/modules/bbmap/index/**
 
+bcftools/annotate:
+  - modules/bcftools/annotate/**
+  - tests/modules/bcftools/annotate/**
+
 bcftools/concat:
   - modules/bcftools/concat/**
   - tests/modules/bcftools/concat/**
@@ -352,6 +356,10 @@ cnvkit/batch:
   - modules/cnvkit/batch/**
   - tests/modules/cnvkit/batch/**
 
+controlfreec:
+  - modules/controlfreec/**
+  - tests/modules/controlfreec/**
+
 cooler/cload:
   - modules/cooler/cload/**
   - tests/modules/cooler/cload/**
@@ -744,6 +752,14 @@ gunzip:
   - modules/gunzip/**
   - tests/modules/gunzip/**
 
+hamronization/deeparg:
+  - modules/hamronization/deeparg/**
+  - tests/modules/hamronization/deeparg/**
+
+hamronization/summarize:
+  - modules/hamronization/summarize/**
+  - tests/modules/hamronization/summarize/**
+
 hicap:
   - modules/hicap/**
   - tests/modules/hicap/**
@@ -807,6 +823,10 @@ homer/makeucscfile:
   - modules/homer/makeucscfile/**
   - tests/modules/homer/makeucscfile/**
 
+hpsuissero:
+  - modules/hpsuissero/**
+  - tests/modules/hpsuissero/**
+
 ichorcna/createpon:
   - modules/ichorcna/createpon/**
   - tests/modules/ichorcna/createpon/**
@@ -960,6 +980,10 @@ macs2/callpeak:
   - modules/macs2/callpeak/**
   - tests/modules/macs2/callpeak/**
 
+mafft:
+  - modules/mafft/**
+  - tests/modules/mafft/**
+
 malt/build:
   - modules/malt/build/**
   - tests/modules/malt/build_test/**
@@ -1225,6 +1249,10 @@ picard/sortsam:
   - modules/picard/sortsam/**
   - tests/modules/picard/sortsam/**
 
+picard/sortvcf:
+  - modules/picard/sortvcf/**
+  - tests/modules/picard/sortvcf/**
+
 pirate:
   - modules/pirate/**
   - tests/modules/pirate/**
@@ -1245,6 +1273,10 @@ plink2/extract:
   - modules/plink2/extract/**
   - tests/modules/plink2/extract/**
 
+plink2/score:
+  - modules/plink2/score/**
+  - tests/modules/plink2/score/**
+
 plink2/vcf:
   - modules/plink2/vcf/**
   - tests/modules/plink2/vcf/**
@@ -1533,6 +1565,10 @@ sratools/prefetch:
   - modules/sratools/prefetch/**
   - tests/modules/sratools/prefetch/**
 
+ssuissero:
+  - modules/ssuissero/**
+  - tests/modules/ssuissero/**
+
 staphopiasccmec:
   - modules/staphopiasccmec/**
   - tests/modules/staphopiasccmec/**
@@ -1545,6 +1581,10 @@ star/genomegenerate:
   - modules/star/genomegenerate/**
   - tests/modules/star/genomegenerate/**
 
+stranger:
+  - modules/stranger/**
+  - tests/modules/stranger/**
+
 strelka/germline:
   - modules/strelka/germline/**
   - tests/modules/strelka/germline/**

tests/config/test_data.config

@@ -67,6 +67,8 @@ params {
 
                 test_computematrix_mat_gz                      = "${test_data_dir}/genomics/sarscov2/illumina/deeptools/test.computeMatrix.mat.gz"
 
+                test_bcf                                       = "${test_data_dir}/genomics/sarscov2/illumina/vcf/test.bcf"
+
                 test_vcf                                       = "${test_data_dir}/genomics/sarscov2/illumina/vcf/test.vcf"
                 test_vcf_gz                                    = "${test_data_dir}/genomics/sarscov2/illumina/vcf/test.vcf.gz"
                 test_vcf_gz_tbi                                = "${test_data_dir}/genomics/sarscov2/illumina/vcf/test.vcf.gz.tbi"
@@ -117,14 +119,16 @@ params {
                 genome_bed_gz_tbi                              = "${test_data_dir}/genomics/homo_sapiens/genome/genome.bed.gz.tbi"
                 transcriptome_fasta                            = "${test_data_dir}/genomics/homo_sapiens/genome/transcriptome.fasta"
                 genome2_fasta                                  = "${test_data_dir}/genomics/homo_sapiens/genome/genome2.fasta"
-		        genome_chain_gz                                = "${test_data_dir}/genomics/homo_sapiens/genome/genome.chain.gz"
+                genome_chain_gz                                = "${test_data_dir}/genomics/homo_sapiens/genome/genome.chain.gz"
                 genome_21_fasta                                = "${test_data_dir}/genomics/homo_sapiens/genome/chr21/sequence/genome.fasta"
                 genome_21_fasta_fai                            = "${test_data_dir}/genomics/homo_sapiens/genome/chr21/sequence/genome.fasta.fai"
                 genome_21_dict                                 = "${test_data_dir}/genomics/homo_sapiens/genome/chr21/sequence/genome.dict"
+                genome_21_sizes                                = "${test_data_dir}/genomics/homo_sapiens/genome/chr21/sequence/genome.sizes"
                 genome_21_interval_list                        = "${test_data_dir}/genomics/homo_sapiens/genome/chr21/sequence/genome.interval_list"
                 genome_21_multi_interval_bed                   = "${test_data_dir}/genomics/homo_sapiens/genome/chr21/sequence/multi_intervals.bed"
                 genome_21_multi_interval_bed_gz                = "${test_data_dir}/genomics/homo_sapiens/genome/chr21/sequence/multi_intervals.bed.gz"
                 genome_21_multi_interval_bed_gz_tbi            = "${test_data_dir}/genomics/homo_sapiens/genome/chr21/sequence/multi_intervals.bed.gz.tbi"
+                genome_21_chromosomes_dir                      = "${test_data_dir}/genomics/homo_sapiens/genome/chr21/sequence/chromosomes.tar.gz"
 
                 dbsnp_146_hg38_vcf_gz                          = "${test_data_dir}/genomics/homo_sapiens/genome/vcf/dbsnp_146.hg38.vcf.gz"
                 dbsnp_146_hg38_vcf_gz_tbi                      = "${test_data_dir}/genomics/homo_sapiens/genome/vcf/dbsnp_146.hg38.vcf.gz.tbi"
@@ -134,6 +138,7 @@ params {
                 mills_and_1000g_indels_vcf_gz_tbi              = "${test_data_dir}/genomics/homo_sapiens/genome/vcf/mills_and_1000G.indels.vcf.gz.tbi"
                 syntheticvcf_short_vcf_gz                      = "${test_data_dir}/genomics/homo_sapiens/genome/vcf/syntheticvcf_short.vcf.gz"
                 syntheticvcf_short_vcf_gz_tbi                  = "${test_data_dir}/genomics/homo_sapiens/genome/vcf/syntheticvcf_short.vcf.gz.tbi"
+                syntheticvcf_short_score                       = "${test_data_dir}/genomics/homo_sapiens/genome/vcf/syntheticvcf_short.score"
                 gnomad_r2_1_1_sv_vcf_gz                        = "${test_data_dir}/genomics/homo_sapiens/genome/vcf/gnomAD.r2.1.1-sv.vcf.gz"
 
                 hapmap_3_3_hg38_21_vcf_gz                      = "${test_data_dir}/genomics/homo_sapiens/genome/chr21/germlineresources/hapmap_3.3.hg38.vcf.gz"
@@ -270,6 +275,9 @@ params {
                 test_genome21_indels_vcf_gz                    = "${test_data_dir}/genomics/homo_sapiens/illumina/vcf/test.genome_21.somatic_sv.vcf.gz"
                 test_genome21_indels_vcf_gz_tbi                = "${test_data_dir}/genomics/homo_sapiens/illumina/vcf/test.genome_21.somatic_sv.vcf.gz.tbi"
 
+                test_mpileup                                   = "${test_data_dir}/genomics/homo_sapiens/illumina/mpileup/test.mpileup.gz"
+                test2_mpileup                                  = "${test_data_dir}/genomics/homo_sapiens/illumina/mpileup/test2.mpileup.gz"
+
                 test_broadpeak                                 = "${test_data_dir}/genomics/homo_sapiens/illumina/broadpeak/test.broadPeak"
                 test2_broadpeak                                = "${test_data_dir}/genomics/homo_sapiens/illumina/broadpeak/test2.broadPeak"
 
@@ -314,6 +322,8 @@ params {
             'genome' {
                 genome_fna_gz                   = "${test_data_dir}/genomics/prokaryotes/bacteroides_fragilis/genome/genome.fna.gz"
                 genome_paf                      = "${test_data_dir}/genomics/prokaryotes/bacteroides_fragilis/genome/genome.paf"
+                genome_mapping_potential_arg    = "${test_data_dir}/genomics/prokaryotes/bacteroides_fragilis/genome/genome.mapping.potential.ARG"
+
             }
             'illumina' {
                 test1_contigs_fa_gz             = "${test_data_dir}/genomics/prokaryotes/bacteroides_fragilis/illumina/fasta/test1.contigs.fa.gz"

tests/modules/adapterremoval/test.yml

@@ -1,31 +1,44 @@
 - name: adapterremoval test_adapterremoval_single_end
-  command: nextflow run ./tests/modules/adapterremoval -entry test_adapterremoval_single_end -c ./tests/config/nextflow.config -c ./tests/modules/adapterremoval/nextflow.config
+  command: nextflow run tests/modules/adapterremoval -entry test_adapterremoval_single_end -c tests/config/nextflow.config
   tags:
     - adapterremoval
   files:
+    - path: output/adapterremoval/test.discarded.gz
     - path: output/adapterremoval/test.log
       md5sum: 2fd3d5d703b63ba33a83021fccf25f77
-    - path: output/adapterremoval/test.trimmed.fastq.gz
+    - path: output/adapterremoval/test.truncated.gz
       md5sum: 62139afee94defad5b83bdd0b8475a1f
+    - path: output/adapterremoval/versions.yml
+      md5sum: ac5b46719719b7ee62739530b80869fc
 
 - name: adapterremoval test_adapterremoval_paired_end
-  command: nextflow run ./tests/modules/adapterremoval -entry test_adapterremoval_paired_end -c ./tests/config/nextflow.config -c ./tests/modules/adapterremoval/nextflow.config
+  command: nextflow run tests/modules/adapterremoval -entry test_adapterremoval_paired_end -c tests/config/nextflow.config
   tags:
     - adapterremoval
   files:
+    - path: output/adapterremoval/test.discarded.gz
     - path: output/adapterremoval/test.log
       md5sum: b8a451d3981b327f3fdb44f40ba2d6d1
-    - path: output/adapterremoval/test.pair1.trimmed.fastq.gz
+    - path: output/adapterremoval/test.pair1.truncated.gz
       md5sum: 294a6277f0139bd597e57c6fa31f39c7
-    - path: output/adapterremoval/test.pair2.trimmed.fastq.gz
+    - path: output/adapterremoval/test.pair2.truncated.gz
       md5sum: de7b38e2c881bced8671acb1ab452d78
+    - path: output/adapterremoval/test.singleton.truncated.gz
+    - path: output/adapterremoval/versions.yml
+      md5sum: fa621c887897da5a379c719399c17db7
 
 - name: adapterremoval test_adapterremoval_paired_end_collapse
-  command: nextflow run ./tests/modules/adapterremoval -entry test_adapterremoval_paired_end_collapse -c ./tests/config/nextflow.config -c ./tests/modules/adapterremoval/nextflow.config
+  command: nextflow run tests/modules/adapterremoval -entry test_adapterremoval_paired_end_collapse -c tests/config/nextflow.config
   tags:
     - adapterremoval
   files:
+    - path: output/adapterremoval/test.discarded.gz
     - path: output/adapterremoval/test.log
-      md5sum: 7f0b2328152226e46101a535cce718b3
+      md5sum: b8a451d3981b327f3fdb44f40ba2d6d1
-    - path: output/adapterremoval/test.merged.fastq.gz
+    - path: output/adapterremoval/test.pair1.truncated.gz
-      md5sum: 07a8f725bfd3ecbeabdc41b32d898dee
+      md5sum: 294a6277f0139bd597e57c6fa31f39c7
+    - path: output/adapterremoval/test.pair2.truncated.gz
+      md5sum: de7b38e2c881bced8671acb1ab452d78
+    - path: output/adapterremoval/test.singleton.truncated.gz
+    - path: output/adapterremoval/versions.yml
+      md5sum: fd428f92a8446e0b34c5ae1c447215b8

tests/modules/bcftools/annotate/main.nf

@@ -0,0 +1,23 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { BCFTOOLS_ANNOTATE } from '../../../../modules/bcftools/annotate/main.nf'
+
+workflow test_bcftools_annotate_out_vcf {
+
+    input = [ 
+    [ id:'test_compressed_vcf', single_end:false ], // meta map
+        file(params.test_data['sarscov2']['illumina']['test_vcf_gz'], checkIfExists: true) ]
+
+    BCFTOOLS_ANNOTATE ( input )
+}
+
+workflow test_bcftools_annotate_out_bcf {
+
+    input = [ 
+    [ id:'test_compressed_bcf', single_end:false ], // meta map
+        file(params.test_data['sarscov2']['illumina']['test_bcf'], checkIfExists: true) ]
+
+    BCFTOOLS_ANNOTATE ( input )
+}

tests/modules/bcftools/annotate/nextflow.config

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

tests/modules/bcftools/annotate/test.yml

@@ -0,0 +1,19 @@
+- name: bcftools annotate test_bcftools_annotate_out_vcf
+  command: nextflow run tests/modules/bcftools/annotate -entry test_bcftools_annotate_out_vcf -c tests/config/nextflow.config
+  tags:
+    - bcftools/annotate
+    - bcftools
+  files:
+    - path: output/bcftools/test_compressed_vcf_annotated.vcf.gz
+    - path: output/bcftools/versions.yml
+      md5sum: de86d4d411baef1aaee0e72f519dbe1f
+
+- name: bcftools annotate test_bcftools_annotate_out_bcf
+  command: nextflow run tests/modules/bcftools/annotate -entry test_bcftools_annotate_out_bcf -c tests/config/nextflow.config
+  tags:
+    - bcftools/annotate
+    - bcftools
+  files:
+    - path: output/bcftools/test_compressed_bcf_annotated.bcf
+    - path: output/bcftools/versions.yml
+      md5sum: a57e62a5a189fe85aabd52c010d88ca6

tests/modules/bwa/sampe/test.yml

@@ -5,4 +5,4 @@
     - bwa/sampe
   files:
     - path: output/bwa/test.bam
-      md5sum: f6ad85d66d44c5d26e692109d2e34100
+      md5sum: 01d1d71c88b6de07ed51d1d06e9e970b

tests/modules/bwa/samse/test.yml

@@ -5,4 +5,4 @@
     - bwa/samse
   files:
     - path: output/bwa/test.bam
-      md5sum: 27eb91146e45dee65664c18596be4262
+      md5sum: ddfa4a8f6b65d44704a2d9528abc7e79

tests/modules/controlfreec/main.nf

@@ -0,0 +1,37 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { CONTROLFREEC } from '../../../modules/controlfreec/main.nf'
+include { UNTAR }        from '../../../modules/untar/main.nf'
+workflow test_controlfreec {
+
+    input = [
+        [ id:'test', single_end:false, sex:'XX' ], // meta map
+        file(params.test_data['homo_sapiens']['illumina']['test_mpileup'], checkIfExists: true),
+        file(params.test_data['homo_sapiens']['illumina']['test2_mpileup'], checkIfExists: true),
+        [],[],[],[]
+    ]
+
+    fasta = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta'], checkIfExists: true)
+    fai = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta_fai'], checkIfExists: true)
+
+    dbsnp = file(params.test_data['homo_sapiens']['genome']['dbsnp_138_hg38_21_vcf_gz'], checkIfExists: true)
+    dbsnp_tbi = file(params.test_data['homo_sapiens']['genome']['dbsnp_138_hg38_21_vcf_gz_tbi'], checkIfExists: true)
+
+    chrfiles = file(params.test_data['homo_sapiens']['genome']['genome_21_chromosomes_dir'], checkIfExists: true)
+    target_bed = file(params.test_data['homo_sapiens']['genome']['genome_21_multi_interval_bed'], checkIfExists: true)
+
+    UNTAR(chrfiles)
+    CONTROLFREEC (  input,
+                            fasta,
+                            fai,
+                            [],
+                            dbsnp,
+                            dbsnp_tbi,
+                            UNTAR.out.untar,
+                            [],
+                            target_bed,
+                            []
+                        )
+}

tests/modules/controlfreec/nextflow.config

@@ -0,0 +1,26 @@
+process {
+
+    publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+    withName:CONTROLFREEC{
+        ext.args = { [
+                    "sample":[
+                        inputformat: 'pileup',
+                        mateorientation: 'FR'
+                    ],
+                    "general" :[
+                        bedgraphoutput: "TRUE",
+                        noisydata: "TRUE",
+                        minexpectedgc: "0",
+                        readcountthreshold: "1",
+                        sex: meta.sex,
+                        window: "10",
+                        ],
+                    "control":[
+                        inputformat: "pileup",
+                        mateorientation: "FR"
+                    ]
+                    ]
+        }
+    }
+}

tests/modules/controlfreec/test.yml

@@ -0,0 +1,22 @@
+- name: controlfreec test_controlfreec
+  command: nextflow run tests/modules/controlfreec -entry test_controlfreec -c tests/config/nextflow.config
+  tags:
+    - controlfreec
+  files:
+    - path: output/controlfreec/config.txt
+    - path: output/controlfreec/test.mpileup.gz_control.cpn
+      md5sum: 1768b571677c418560e5a8fe203bdc79
+    - path: output/controlfreec/test2.mpileup.gz_BAF.txt
+      md5sum: 3bb7437001cf061a77eaf87b8558c48d
+    - path: output/controlfreec/test2.mpileup.gz_CNVs
+      md5sum: 1f4f5834dbd1490afdb22f6d3091c4c9
+    - path: output/controlfreec/test2.mpileup.gz_info.txt
+      md5sum: 1a3055d35028525ccc9e693cc9f335e0
+    - path: output/controlfreec/test2.mpileup.gz_ratio.BedGraph
+      md5sum: 8ba455b232be20cdcc5bf1e4035e8032
+    - path: output/controlfreec/test2.mpileup.gz_ratio.txt
+      md5sum: b76b2434de710325069e37fb1e132760
+    - path: output/controlfreec/test2.mpileup.gz_sample.cpn
+      md5sum: c80dad58a77b1d7ba6d273999f4b4b4b
+    - path: output/controlfreec/versions.yml
+      md5sum: ff93f6466d4686aab708425782c6c848

tests/modules/faqcs/nextflow.config

@@ -1,5 +1,6 @@
 process {
 
     publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+    ext.args   = {"--debug" }
 
 }

tests/modules/faqcs/test.yml

@@ -3,8 +3,20 @@
   tags:
     - faqcs
   files:
+    - path: output/faqcs/qa.test.base_content.txt
+      md5sum: f992603f01ca430c03c8aae02eba2f5d
+    - path: output/faqcs/qa.test.for_qual_histogram.txt
+      md5sum: a3d462ab84151e982f99f85f52c21de3
+    - path: output/faqcs/qa.test.length_count.txt
+      md5sum: 80915f09fbaf5884c32e95acab2d031c
+    - path: output/faqcs/test.base_content.txt
+      md5sum: f992603f01ca430c03c8aae02eba2f5d
     - path: output/faqcs/test.fastp.log
       md5sum: be79dc893f87de1f82faf749cdfb848c
+    - path: output/faqcs/test.for_qual_histogram.txt
+      md5sum: a3d462ab84151e982f99f85f52c21de3
+    - path: output/faqcs/test.length_count.txt
+      md5sum: 80915f09fbaf5884c32e95acab2d031c
     - path: output/faqcs/test.stats.txt
       md5sum: ea20e93706b2e4c676004253baa3cec6
     - path: output/faqcs/test.trimmed.fastq.gz
@@ -18,8 +30,20 @@
   tags:
     - faqcs
   files:
+    - path: output/faqcs/qa.test.base_content.txt
+      md5sum: 99aa9a775ccd8d6503f0cf80f775203c
+    - path: output/faqcs/qa.test.for_qual_histogram.txt
+      md5sum: 4f4b131be5425bdfa4b3237e44fa7d48
+    - path: output/faqcs/qa.test.length_count.txt
+      md5sum: 420298983c762754d5b0ef32c9d5dad4
+    - path: output/faqcs/test.base_content.txt
+      md5sum: 99aa9a775ccd8d6503f0cf80f775203c
     - path: output/faqcs/test.fastp.log
       md5sum: be79dc893f87de1f82faf749cdfb848c
+    - path: output/faqcs/test.for_qual_histogram.txt
+      md5sum: 4f4b131be5425bdfa4b3237e44fa7d48
+    - path: output/faqcs/test.length_count.txt
+      md5sum: 420298983c762754d5b0ef32c9d5dad4
     - path: output/faqcs/test.stats.txt
       md5sum: 9a693f8af94ab8c485519d9a523aa622
     - path: output/faqcs/test_1.trimmed.fastq.gz

tests/modules/hamronization/deeparg/main.nf

@@ -0,0 +1,15 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { HAMRONIZATION_DEEPARG } from '../../../../modules/hamronization/deeparg/main.nf'
+
+workflow test_hamronization_deeparg {
+
+    input = [
+        [ id:'test', single_end:false ], // meta map
+        file(params.test_data['bacteroides_fragilis']['genome']['genome_mapping_potential_arg'], checkIfExists: true),
+    ]
+
+    HAMRONIZATION_DEEPARG ( input, 'tsv', '1.0.2', '2'  )
+}

tests/modules/hamronization/deeparg/nextflow.config

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

tests/modules/hamronization/deeparg/test.yml

@@ -0,0 +1,8 @@
+- name: hamronization deeparg test_hamronization_deeparg
+  command: nextflow run tests/modules/hamronization/deeparg -entry test_hamronization_deeparg -c tests/config/nextflow.config
+  tags:
+    - hamronization
+    - hamronization/deeparg
+  files:
+    - path: output/hamronization/test.tsv
+      md5sum: 3c315605aca0c5964796bb5fd4cdd522

tests/modules/hamronization/summarize/main.nf

@@ -0,0 +1,36 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { HAMRONIZATION_DEEPARG                                 } from '../../../../modules/hamronization/deeparg/main.nf'
+include { HAMRONIZATION_DEEPARG as HAMRONIZATION_DEEPARG_SECOND } from '../../../../modules/hamronization/deeparg/main.nf'
+include { HAMRONIZATION_SUMMARIZE                               } from '../../../../modules/hamronization/summarize/main.nf'
+
+workflow test_hamronization_summarize {
+
+    input = [
+        [ id:'test', single_end:false ], // meta map
+        file(params.test_data['bacteroides_fragilis']['genome']['genome_mapping_potential_arg'], checkIfExists: true),
+    ]
+
+    input2 = [
+        [ id:'test2', single_end:false ], // meta map
+        file(params.test_data['bacteroides_fragilis']['genome']['genome_mapping_potential_arg'], checkIfExists: true),
+    ]
+
+    HAMRONIZATION_DEEPARG ( input, 'tsv', '1.0.2', '2'  )
+    HAMRONIZATION_DEEPARG_SECOND ( input2, 'tsv', '1.0.2', '2' )
+
+    ch_deeparg_run_one = HAMRONIZATION_DEEPARG.out.tsv
+    ch_deeparg_run_two = HAMRONIZATION_DEEPARG_SECOND.out.tsv
+
+    ch_deeparg_run_one
+        .mix( ch_deeparg_run_two )
+        .map{
+            [ it[1] ]
+        }
+        .collect()
+        .set { ch_input_for_summarize }
+
+    HAMRONIZATION_SUMMARIZE ( ch_input_for_summarize , 'json' )
+}

tests/modules/hamronization/summarize/nextflow.config

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

tests/modules/hamronization/summarize/test.yml

@@ -0,0 +1,14 @@
+- name: hamronization summarize test_hamronization_summarize
+  command: nextflow run tests/modules/hamronization/summarize -entry test_hamronization_summarize -c tests/config/nextflow.config
+  tags:
+    - hamronization
+    - hamronization/summarize
+  files:
+    - path: output/hamronization/hamronization_combined_report.json
+      md5sum: 1623b6cc3b213208a425e023edd94691
+    - path: output/hamronization/test.tsv
+      md5sum: 3c315605aca0c5964796bb5fd4cdd522
+    - path: output/hamronization/test2.tsv
+      md5sum: 453f38502e35261a50a0849dca34f05b
+    - path: output/hamronization/versions.yml
+      md5sum: 99b5046fac643e16ca3362d1baf3284b

tests/modules/hpsuissero/main.nf

@@ -0,0 +1,15 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { HPSUISSERO } from '../../../modules/hpsuissero/main.nf'
+
+workflow test_hpsuissero {
+    
+    input = [ 
+        [ id:'test', single_end:false ], // meta map
+        file(params.test_data['haemophilus_influenzae']['genome']['genome_fna_gz'], checkIfExists: true) 
+    ]
+
+    HPSUISSERO ( input )
+}

tests/modules/hpsuissero/nextflow.config

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

tests/modules/hpsuissero/test.yml

@@ -0,0 +1,9 @@
+- name: hpsuissero test_hpsuissero
+  command: nextflow run tests/modules/hpsuissero -entry test_hpsuissero -c tests/config/nextflow.config
+  tags:
+    - hpsuissero
+  files:
+    - path: output/hpsuissero/test_serotyping_res.tsv
+      md5sum: 559dd2ca386eeb58f3975e3204ce9d43
+    - path: output/hpsuissero/versions.yml
+      md5sum: f65438e63a74ac6ee365bfdbbd3f996a

tests/modules/mafft/main.nf

@@ -0,0 +1,15 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { MAFFT } from '../../../modules/mafft/main.nf'
+
+workflow test_mafft {
+
+    input = [
+        [ id:'test', single_end:false ], // meta map
+        file(params.test_data['sarscov2']['illumina']['scaffolds_fasta'], checkIfExists: true)
+    ]
+
+    MAFFT ( input )
+}

tests/modules/mafft/nextflow.config

@@ -0,0 +1,6 @@
+process {
+
+    publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+    ext.args = "--auto"
+
+}

tests/modules/mafft/test.yml

@@ -0,0 +1,9 @@
+- name: mafft test_mafft
+  command: nextflow run tests/modules/mafft -entry test_mafft -c tests/config/nextflow.config
+  tags:
+    - mafft
+  files:
+    - path: output/mafft/test.fas
+      md5sum: 23426611f4a0df532b6708f072bd445b
+    - path: output/mafft/versions.yml
+      md5sum: b1b5ab3728ae17401808335f1c8f8215

tests/modules/malt/run/main.nf

@@ -12,10 +12,14 @@ workflow test_malt_run {
     gff = file(params.test_data['sarscov2']['genome']['genome_gff3'], checkIfExists: true)
     seq_type = "DNA"
     map_db = file("https://software-ab.informatik.uni-tuebingen.de/download/megan6/megan-nucl-Jan2021.db.zip", checkIfExists: true)
-    input = file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true)
+    input = [
+        [ id:'test', single_end:false ], // meta map
+        file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true)
+    ]
     mode = "BlastN"
 
     UNZIP ( map_db )
     MALT_BUILD ( fastas, seq_type, gff, UNZIP.out.unzipped_archive )
     MALT_RUN ( input, mode, MALT_BUILD.out.index )
 }
+

tests/modules/malt/run/test.yml

@@ -5,4 +5,4 @@
     - malt/run
   files:
     - path: output/malt/test_1.rma6
-    - path: output/malt/malt-run.log
+    - path: output/malt/test-malt-run.log

tests/modules/picard/cleansam/test.yml

@@ -4,7 +4,7 @@
     - picard/cleansam
     - picard
   files:
-    - path: output/picard/test.sam
+    - path: output/picard/test.bam
-      md5sum: e314171a6060eb79947c13ad126ddf00
+      md5sum: a48f8e77a1480445efc57570c3a38a68
     - path: output/picard/versions.yml
       md5sum: e6457d7c6de51bf6f4b577eda65e57ac

tests/modules/picard/sortvcf/main.nf

@@ -0,0 +1,18 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { PICARD_SORTVCF } from '../../../../modules/picard/sortvcf/main.nf'
+
+workflow test_picard_sortvcf {
+
+    input = [ [ id:'test' ], // meta map
+                file(params.test_data['sarscov2']['illumina']['test_vcf'], checkIfExists: true)
+            ]
+
+    fasta  = [ file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) ]
+
+    dict  = [ file(params.test_data['sarscov2']['genome']['genome_dict'], checkIfExists: true) ]
+
+    PICARD_SORTVCF ( input, fasta, dict )
+}

tests/modules/picard/sortvcf/nextflow.config

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

tests/modules/picard/sortvcf/test.yml

@@ -0,0 +1,7 @@
+- name: picard sortvcf
+  command: nextflow run ./tests/modules/picard/sortvcf -entry test_picard_sortvcf -c ./tests/config/nextflow.config -c ./tests/modules/picard/sortvcf/nextflow.config
+  tags:
+    - picard
+    - picard/sortvcf
+  files:
+    - path: output/picard/test_sorted.vcf.gz

tests/modules/plink2/score/main.nf

@@ -0,0 +1,24 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { PLINK2_VCF } from '../../../../modules/plink2/vcf/main.nf'
+include { PLINK2_SCORE } from '../../../../modules/plink2/score/main.nf'
+
+workflow test_plink2_score {
+    input = [
+        [ id:'test', single_end:false ], // meta map
+        file(params.test_data['homo_sapiens']['genome']['syntheticvcf_short_vcf_gz'], checkIfExists: true)
+    ]
+    PLINK2_VCF ( input )
+
+    scorefile = file(params.test_data['homo_sapiens']['genome']['syntheticvcf_short_score'], checkIfExists: true)
+
+    PLINK2_VCF.out.pgen
+        .concat(PLINK2_VCF.out.psam, PLINK2_VCF.out.pvar)
+        .groupTuple()
+        .map { it.flatten() }
+        .set { ch_target_genome }
+
+    PLINK2_SCORE ( ch_target_genome, scorefile )
+}

tests/modules/plink2/score/nextflow.config

@@ -0,0 +1,15 @@
+process {
+
+    publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+    // relabel input variants to a common scheme chr:pos:alt:ref
+    withName: PLINK2_VCF {
+        ext.args = '--set-missing-var-ids @:#:\\$1:\\$2'
+    }
+
+    // scoring really needs an adjustment for small test dataset (n > 50
+    // normally)
+    withName: PLINK2_SCORE {
+        ext.args = 'no-mean-imputation'
+    }
+}

tests/modules/plink2/score/test.yml

@@ -0,0 +1,16 @@
+- name: plink2 score test_plink2_score
+  command: nextflow run tests/modules/plink2/score -entry test_plink2_score -c tests/config/nextflow.config
+  tags:
+    - plink2
+    - plink2/score
+  files:
+    - path: output/plink2/test.pgen
+      md5sum: fac12ca9041d6950f6b7d60ac2120721
+    - path: output/plink2/test.psam
+      md5sum: e6c714488754cb8448c3dfda08c4c0ea
+    - path: output/plink2/test.pvar.zst
+      md5sum: 98d59e9779a8b62d5032cd98b642a63b
+    - path: output/plink2/test.sscore
+      md5sum: 97bde840f69febd65f2c00e9243126e9
+    - path: output/plink2/versions.yml
+      md5sum: 71499ab14e1583c88ced3a7a4f05bfa7

tests/modules/plink2/vcf/test.yml

@@ -1,12 +1,14 @@
 - name: plink2 vcf test_plink2_vcf
-  command: nextflow run ./tests/modules/plink2/vcf -entry test_plink2_vcf -c ./tests/config/nextflow.config -c ./tests/modules/plink2/vcf/nextflow.config
+  command: nextflow run tests/modules/plink2/vcf -entry test_plink2_vcf -c tests/config/nextflow.config
   tags:
-    - plink2/vcf
     - plink2
+    - plink2/vcf
   files:
     - path: output/plink2/test.pgen
       md5sum: d66d3cd4a6c9cca1a4073d7f4b277041
     - path: output/plink2/test.psam
       md5sum: dc3b77d7753a7bed41734323e3549b10
-    - path: output/plink2/test.pvar
+    - path: output/plink2/test.pvar.zst
-      md5sum: d61e53f847a6335138b584216b4e45d0
+      md5sum: b53cccb83e024a39789af5eab8de1c28
+    - path: output/plink2/versions.yml
+      md5sum: 82ada74bc81473b7cba377f696acf54c

tests/modules/samtools/ampliconclip/test.yml

@@ -5,7 +5,7 @@
     - samtools/ampliconclip
   files:
     - path: output/samtools/test.bam
-      md5sum: 678f9ab04fbe3206f0f96e170fd833e9
+      md5sum: 5d0e8bc9e6059ef3a63ee6328a3935c7
 
 - name: samtools ampliconclip no stats with rejects
   command: nextflow run ./tests/modules/samtools/ampliconclip -entry test_samtools_ampliconclip_no_stats_with_rejects -c ./tests/config/nextflow.config -c ./tests/modules/samtools/ampliconclip/nextflow.config
@@ -14,9 +14,9 @@
     - samtools/ampliconclip
   files:
     - path: output/samtools/test.bam
-      md5sum: bbf65ea626539d96c8271e17d1fc988b
+      md5sum: 2c998295d624c59620b7ffdb0cc080e2
     - path: output/samtools/test.cliprejects.bam
-      md5sum: a0bee15aead020d16d0c81bd9667df46
+      md5sum: f3ebba8d91ad29cc4d2d00943e6f6bab
 
 - name: samtools ampliconclip with stats with rejects
   command: nextflow run ./tests/modules/samtools/ampliconclip -entry test_samtools_ampliconclip_with_stats_with_rejects -c ./tests/config/nextflow.config -c ./tests/modules/samtools/ampliconclip/nextflow.config
@@ -25,8 +25,8 @@
     - samtools/ampliconclip
   files:
     - path: output/samtools/test.bam
-      md5sum: f5a3611ecad34ba2dde77096e1c7dd93
+      md5sum: 87882973b425ab27aad6ef18faf11f25
     - path: output/samtools/test.cliprejects.bam
-      md5sum: 90ee7ce908b4bdb89ab41e4410de9012
+      md5sum: eb5e186e1a69864dc2e99a290f02ff78
     - path: output/samtools/test.clipstats.txt
       md5sum: fc23355e1743d47f2541f2cb1a7a0cda

tests/modules/samtools/bam2fq/test.yml

@@ -14,9 +14,9 @@
     - samtools
   files:
     - path: output/samtools/test_1.fq.gz
-      md5sum: 4522edbe158ec4804765794569f67493
+      md5sum: 1c84aadcdca10e97be2b5b6ce773f5ed
     - path: output/samtools/test_2.fq.gz
-      md5sum: 7e00ef40d5cfe272b67461381019dcc1
+      md5sum: e679ec035d3208785e704458d6b68c8c
     - path: output/samtools/test_other.fq.gz
       md5sum: 709872fc2910431b1e8b7074bfe38c67
     - path: output/samtools/test_singleton.fq.gz

tests/modules/samtools/faidx/test.yml

@@ -7,4 +7,4 @@
     - path: output/samtools/genome.fasta.fai
       md5sum: 9da2a56e2853dc8c0b86a9e7229c9fe5
     - path: output/samtools/versions.yml
-      md5sum: d56671a7c8f8058944d3d536c3058f7f
+      md5sum: 6a16b2148a0ab43e6d0506056e6a0409

tests/modules/samtools/fastq/test.yml

@@ -5,6 +5,6 @@
     - samtools/fastq
   files:
     - path: output/samtools/test_2.fastq.gz
-      md5sum: 3b1c92f33a44a78d82f8360ab4fdfd61
+      md5sum: 51e7a469b554de694799bec982fd722e
     - path: output/samtools/test_1.fastq.gz
-      md5sum: 5a3f9c69a032c4ffd9071ea31a14e6f9
+      md5sum: 6c2d5b467eb94e058300271a542e34e6

tests/modules/samtools/fixmate/test.yml

@@ -5,4 +5,4 @@
     - samtools/fixmate
   files:
     - path: output/samtools/test.bam
-      md5sum: a4092657a4b17170c7702a76cbf192a1
+      md5sum: c7f574bb0c469e0ccfecb6b7210e03c5

tests/modules/samtools/index/test.yml

@@ -23,4 +23,4 @@
     - samtools/index
   files:
     - path: output/samtools/test.paired_end.sorted.bam.csi
-      md5sum: 3dd9e3ed959fca075b88bb8dc3cf7dbd
+      md5sum: 8d63373007553e74d823fc2b9cbcf84d